Annoying creationists

[kleinman]

The insulin molecule is derived from the A and B chain from the preproinsulin molecule. The A and B chain and the C-peptide may be identical in humans and chimpanzees but the signal sequence differs. The following quote is taken from the Sequences of Primate Insulin Genes Support the Hypothesis of a Slower Rate of Molecular Evolution in Humans and Apes than in Monkeys paper.

The signal and C-peptide are cleaved from the preproinsulin to make the insulin molecule. If the differences in the signal sequence between human and chimpanzee preproinsulin causes differences in the conformation of the molecules of the two preproinsulins, different cleaving enzymes would be needed.I'm sorry, but you have not provided enough information for me to make a desicision. Could you provide a citation?
You can download the above paper at http://mbe.oxfordjournals.org/cgi/reprint/9/2/193.pdf and the information about the basic structure of the preproinsulin and insulin molecules can be obtained from the biochemistry text, Principles of Biochemistry, by Lehninger.
This is dull.
Fortunately we have you and Cyborg around to keep this thread interesting. You haven’t run out of jpegs and gifs already?
Why don’t you give us some examples of rare beneficial mutation which in the real world provides a creature with enormous advantage over its competitors?Sure. A certain portion of the human population has inherited a tolerance to lactose which bears a remarkable relationship to that same population's ability to control the most livable areas of the planet. Human populations without the mutation have largely been relegated to third world status -- with the notable exception of the Chinese, who seem to have spent a great deal of the last 4000 years since the mutation appeared, trying to survive in their preexisting environment, but never venturing very far from it.

The ability to digest milk products gave the Western Europeans a ready source of transportable protein, not available to their competitors, and this huge advantage made them more formidable warriors.
I knew Ben and Jerry’s were up to no good. They are out to take over the world. And now I know what you are up to with your string cheese theory of evolution.
Get the following reference: Sequences of Primate Insulin Genes Support the Hypothesis of a Slower Rate of Molecular Evolution in Humans and Apes than in MonkeysI have this reference.

I also have http://www.pubmedcentral.nih.gov/pag...geindex=3#page

which gives the amino acid sequences of human and chimp insulin.

Care to read it?

Then come back and tell us what the difference in aa sequence between human and chimp preproinsulin is.
The reference I give states the amino acid sequence for humans and chimps is identical, unless your reference says something different, no need to read your reference. With respects to the difference in the aa sequence between human and chimp preproinsulin see post http://forums.randi.org/showpost.php?p=2404486&postcount=2992, the response to Taffer’s inquiry.
I don’t know what the structures are for the enzymes that cleave the preproinsulin for humans and chimps but if there are differences between the two cleaving enzymes, you would have to explain how two different genes transformed simultaneously (the insulin gene and the gene which codes for the cleaving enzyme). Perhaps the same cleaving enzyme works for both human and chimpanzee preproinsulin.I suggest you research matters somewhat more thoroughly before spouting mindless speculation.
You’re the one who has said you have mapped the evolution of insulin from zebra fish to humans. I guess the enzyme which cleaves preproinsulin to insulin is out of your area of expertise. If you have mapped the evolution of insulin from the zebra fish, why are you asking me for the differences in the sequences in human and chimpanzee preproinsulin? Or is preproinsulin out of your area of expertise? Just what is the selection process that has led to these differences in preproinsulins?
Dr Richard why do you ignore my question about the cleaving enzyme for the preproinsulins in humans and chimps?I was trying to avoid you further embarrassment. Deal with the aa difference between human and chimp preproinsulin first.
If you had read the reference I gave earlier, you would have the answer. If you had read the thread, I explicitly posted the difference and you would have the answer. You are lazy and inattentive.
How could I pass up the opportunity to annoy evolutionists? This is going to be fun teaching Dr Richard about Dr Schneider’s mathematics of ev. I wonder how long it will take before he starts chanting “recombination, recombination”. He’s already chanted “insertions, deletions”. Dr Richard, you need to learn how to chant “selection process, selection process” because without a selection process, no mechanism for evolving or transforming a gene or genome can work.Your depth of ignorance when it comes to molecular biology is stunning. Is it really true that you are medicaly qualified?
Your depth of ignorance of the mathematics of mutation and natural selection is stunning. Is it really true that you are an expert in the evolution of insulin from the zebra fish to humans? Of course, the theory of evolution started without a mathematical basis and continues this way. None of your extrapolations hold up to mathematical analysis.
Insertions/deletions are so common that researchers in the field have started refering to "indels" and lumping the two together. The fact that you were unaware of these mechanisms of genetic mutation until they were pointed out to you is stunning for someone attempting to conduct a debate on this matter.
So Dr Expert Richard, why don’t you describe indels and natural selection so that it can be put into the ev model and correct the mathematical deficiency in your theory? I’m particularly interested in hearing your description of the selection process that would evolve your so called ancestral insulin gene from the beginning by indels.
The fact that you still ignore them when attempting to claim that ev disproves evolution is equally stunning.
If you weren’t so lazy and inattentive and had read this thread, you would see that I have not ignored indels or any other mutation mechanism. I’m just waiting for you evolutionists to put these mechanisms in ev and correct the mathematical deficiency in your theory. Once you do, I can co-opt your model and show you how these mechanisms don’t allow your theory to be mathematically possible. Don’t forget to use multiple selection processes in your model (if you can figure out what they are), we want the model to be realistic.
I have this reference.

I also have http://www.pubmedcentral.nih.gov/pag...geindex=3#pageNow, kleinman, I have read this page. Have you? There are two amino acid differences between chimp and human sequences. To claim that a second protease is required for cleavage, you have to demonstrate a number of things:
1) That the 'signal peptide' is, in fact, translated into a protein to begin with. It is quite a common practice to compare protein sequences even if the proteins are never made. It is popular with biochemists because it shortens the sequence you are looking at.
The authors of this paper seem to believe that the signal peptide is translated; my biochemistry text indicates that this signal protein is translated and cleaved as well. Both sources were written by evolutionists, should I not believe them?
2) If the protein is produced, you have to show that the enzyme which cleaves the protein is site-specific, how site-specific it is, and what sequence it is specific to.
Well you raise good points. Our resident expert on the evolution of the insulin molecule, Dr Richard, doesn’t seem to have the answers to these questions either.
3) If the enzyme is site specific, and you have produced its specific sequence, you then have to show that the alternative amino acids disrupt the binding of the enzyme. Remember, some amino acids are similar in form, and are occasionally interchangable with little ill effect to the overall protein.
Again, Dr Richard is the expert on the evolution of the insulin, ask him these questions. I’m sure he will have some type of answer such as chanting “indels, indels”.
If you can show any of these things, with your citations, then we have something to discuss. Until then, you are just making blind assertions.
The only thing that I have claimed on this thread is that the theory of evolution is mathematically impossible according to the results of ev. It is Dr Richard who claims that he proves evolution to be true by mapping out insulin in different creatures. I see peculiarities in his claims and you ask me to explain these peculiarities in his hypothesis. I think it is his responsibility to explain his hypothesis just as it is my responsibility to post the data from ev and explain why that proves the theory of evolution to mathematically impossible.
IIRC the signal peptide is transplated but cleaved almost immediately to make proinsulin from preproinsulin.
Well Taffer, I use Dr Richard as a reference to show that 1) above occurs so I have already shown one of the things you require. Now if our resident expert on the evolution of insulin would answer 2) and 3) we can complete this proof.
I will let him find out for himself how "specific" the endosome mediated cleavage of the insulin peptide is. (Hint: dog microsomes can cleave fish preproinsulin and the aa sequences are more divergent than human/chimp)
Does the dog microsome cleave fish preproinsulin at the same rate as the fish microsome? Why don’t you define the sequences for each? Does the fish endosome cleave the dog preproinsulin? Do dog and fish endosomes cleave human and chimp preproinsulin? What is the selection process that leads to all these different forms of insulin which can be cleaved by any endosomes? What is the selective advantage for all these different molecules? What is the selective pressure that would give rise to the ancestral insulin gene from the beginning? Describe this mechanism and let’s put it into ev so you can mathematically prove your theory.

I came across the following reference [url] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15157231&dopt=Abstract[/url (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15157231&dopt=Abstract%5b/url)], it seems that the mosquito produces an insulin like gene. Do you want to tell us how the insulin gene started? Or is it enough to say that similar insulin genes exist in living things and that is enough to prove your theory even though you can not describe the selection process that leads to these different forms of the gene?
On the other hand, exactly what does ev evolve? What is a perfect creature once it is perfect? What functionality does it display? How does it fit with its environment? Or more to the point, to what environment does the creature fit, since ev models no environment.Well, sure it does. It models an environment that prefers better binding site matching over worse binding site matching. What is the "environment" other than an external mechanism that applies pressures to the organisms?

Evolution is a process of transmuting information in the environment into information in the genome.
Thank you Paul, kjkent1 has trouble understanding this concept. Now if we can get Dr Richard to understand this concept then perhaps he will describe the selection process that leads to all these different forms of insulin.

[Dr Richard]

Oops, my bad. :o

We can live in hope. ;)

I confess I haven't dealt with the insulin proteins before (I'm in Genetics, rather then Biochemistry). You don't have a good source off hand that I could learn a bit more about preproinsulin protein splicing?

Forgiven!

Only what I can get off pubmed, web of science and gogle scholar I'm afraid - exactly the same resources available to Kleinman, but he would appear to refuse to use them.

Incidentally, I was reading the inital "evolution is dead" thread he linked to. He was genuinely ignorant of what transcription factors were. For me, I think this puts him out of the running for sensible scientific debate. I thought he was medically trained from what people had posted on here; either his education is vastly inferior to that of UK medical students or my original inference was wrong. In either case, Kleinman, I apologise for talking to you an equal, but I find it hard to see how we can have a constructive debate until you learn some basic science.

[Taffer]

I have to say, kleinman, all arguments aside, I do appreciate the fact that you at least answer my questions. There are a few posters on this board which could learn from your example. :)


You can download the above paper at http://mbe.oxfordjournals.org/cgi/reprint/9/2/193.pdf and the information about the basic structure of the preproinsulin and insulin molecules can be obtained from the biochemistry text, Principles of Biochemistry, by Lehninger.


Thank you. I shall do so when I have time and go over the paper in more detail. I do not believe I have that textbook, especially considering my field is Genetics not Biochem, but I'll have a look around. I can probably find a summer of the insulin gene through google, as well.

The reference I give states the amino acid sequence for humans and chimps is identical, unless your reference says something different, no need to read your reference. With respects to the difference in the aa sequence between human and chimp preproinsulin see post http://forums.randi.org/showpost.php?p=2404486&postcount=2992, the response to Taffer’s inquiry.


I'm a bit confused here, first you say the sequences are identical, then you point to a previous post where you say they are not? At any rate, the two aa sequences are different by two amino acids, as you are well aware.

You’re the one who has said you have mapped the evolution of insulin from zebra fish to humans. I guess the enzyme which cleaves preproinsulin to insulin is out of your area of expertise. If you have mapped the evolution of insulin from the zebra fish, why are you asking me for the differences in the sequences in human and chimpanzee preproinsulin? Or is preproinsulin out of your area of expertise? Just what is the selection process that has led to these differences in preproinsulins?

This question wasn't directed at me, but I'd like to add my comments to it. There needs not selection pressure for things to arrise. For example, if the two amino acid substitutions between humans and chimps does not have any affect on the functionality of the gene, then there are no selection pressures acting on that allele. This is how there is so much genetic variation within populations. These are sometimes referred to as 'silent mutations'. The difference we are seeing could simply be a case of chance.

None of your extrapolations hold up to mathematical analysis.[/SIZE][/FONT]

As a Geneticist who is interested in phylogenetics and population genetics, I highly dispute this statement. There is a vast knowledge of genetic evolution which is entirely mathematically based.

I’m particularly interested in hearing your description of the selection process that would evolve your so called ancestral insulin gene from the beginning by indels.[/SIZE][/FONT]

Unfortunately, evolution is not as simple as you think. It is highly unlikely that only a single phenomenon (such as indel mutations) were the cause of the 'ancestral insulin gene'.

The authors of this paper seem to believe that the signal peptide is translated; my biochemistry text indicates that this signal protein is translated and cleaved as well. Both sources were written by evolutionists, should I not believe them?

I was not disputing any facts, here. I was simply asking for you to provide evidence for one of the assumptions in your argument. You have done so.

Well you raise good points. Our resident expert on the evolution of the insulin molecule, Dr Richard, doesn’t seem to have the answers to these questions either.

Perhaps he doesn't, but this doesn't affect your argument. Your claim, insofar as I understand it, is that there have to be two different protease enzymes to cleave the chimp and human preproinsulin protein, because of the amino acid difference between the two. For this to hold, you would have to, of course, show that the difference has any effect on the protease binding efficiency.

Again, Dr Richard is the expert on the evolution of the insulin, ask him these questions. I’m sure he will have some type of answer such as chanting “indels, indels”.

And again, he doesn't need to have any answer at all. It is your argument (again, insofar as I understand it) and there are a few things you need to show before your argument is sound.

Also, I'm not quite sure what indel mutations have to do with protease sequence specific binding sites. :confused:

The only thing that I have claimed on this thread is that the theory of evolution is mathematically impossible according to the results of ev. It is Dr Richard who claims that he proves evolution to be true by mapping out insulin in different creatures. I see peculiarities in his claims and you ask me to explain these peculiarities in his hypothesis. I think it is his responsibility to explain his hypothesis just as it is my responsibility to post the data from ev and explain why that proves the theory of evolution to mathematically impossible.


You're right about the burden of proof in both cases, except for one thing. I am analysing your claim that the two amino acid difference in the signal protein sequence of the preproinsulin protein requires a different protease cleaving enzyme to be properly cleaved. Thus, the burden of proof is on you. I'm not analysing any of Dr. R's claims.

Well Taffer, I use Dr Richard as a reference to show that 1) above occurs so I have already shown one of the things you require. Now if our resident expert on the evolution of insulin would answer 2) and 3) we can complete this proof.


Yes, you have shown 1). I suspect the answer to 2) and 3), and Dr. R has given some hint as to it, but I will not make any assumptions until evidence is presented, either by you or Dr. Richard. The burden of proof is on you to show evidence for your proof, but you're right, that doesn't mean you personally have to present evidence. Any evidence will do, as long as it supports your proof.

Thank you Paul, kjkent1 has trouble understanding this concept. Now if we can get Dr Richard to understand this concept then perhaps he will describe the selection process that leads to all these different forms of insulin.

Just a friendly piece of advice, kleinman. The fewer insults you throw around, the more seriously you will be taken.

This goes for everyone, by the way. :)

[Taffer]

Forgiven!

:)

Only what I can get off pubmed, web of science and gogle scholar I'm afraid - exactly the same resources available to Kleinman, but he would appear to refuse to use them.

How I ever lived without these, I will never know.

Well, actually, I never lived without these since I've been at uni, but, y'know, it's a nice saying. :D

[Dr Richard]

You can download the above paper at http://mbe.oxfordjournals.org/cgi/reprint/9/2/193.pdf

The paper you cite gives the amino acid sequences for chimp and african green monkey in figure 1A and 1B.

Where is the human sequence in that paper you muppet?

To compare the two, the ref I cited is appropriate.

It is telling that even now you refuse to look at it.

I thought you were interested in an honest debate, but you have demonstrated such willful ignorance and goalpost shifting that I despair of any constructive discussion with you.

In summary Kleinman, you have proved nothing after 70+ pages of discussion. ev is a good model that was designed to test a hypothesis: it did this. You have inappropriately extrapolated the results of the ev model and claimed this disproves the theory of evolution.

This is so obviously stupid, and you willfully avoid understanding this, si there is no point in my trying to explain it to you.

I will answer your posts when you have addressed this challenge:

perhaps you want to add random transpositions and natural selection to the ev model and show how different preproinsulins cannot evolve in humans and chimpanzees

Until then you have the same, tired, insults and mistaken assertions.

Bye for now

[kleinman]

Only what I can get off pubmed, web of science and gogle scholar I'm afraid - exactly the same resources available to Kleinman, but he would appear to refuse to use them.
You have yet to apply these resources to the mathematics of mutation and selection. But most evolutionists believe they don’t need mathematics to prove their theory. That’s why it’s a mushy soft theory that allows you to extrapolate any observation to mean any thing you want. Well chanting your mantra of “mutation and selection” or “indel, indel” won’t work on this thread. You need to describe the selection processes that would transform insulin genes from one form to another, otherwise your tabulation of similarities of insulin genes is nothing more than tabulation and your extrapolation of this tabulation to the theory evolution is without a mathematical basis. You use slogans to do your accounting.
Incidentally, I was reading the inital "evolution is dead" thread he linked to. He was genuinely ignorant of what transcription factors were. For me, I think this puts him out of the running for sensible scientific debate. I thought he was medically trained from what people had posted on here; either his education is vastly inferior to that of UK medical students or my original inference was wrong. In either case, Kleinman, I apologise for talking to you an equal, but I find it hard to see how we can have a constructive debate until you learn some basic science.
If you think that transcription factors will solve the mathematics of ev and prove that your theory is mathematically possible then present your hypothesis, otherwise you are just chanting another mantra, “transcription factors, transcriptions factors”.

Someone point the way to Dr Richard where the ball park is. This thread is about the mathematics of mutation and selection. Your slogans and sloppy nonmathematical extrapolations don’t meet the precision of the mathematical accounting that Dr Schneider has done with his ev model. If you want to get into the ball game, give us a selection process that would evolve your so called ancestral insulin gene from the beginning. Otherwise, you are just one more evolutionist who chants boring, mathematically deficient mantras and think this constitutes a proof of your theory.

So far the only thing you have demonstrated is that you have tabulated the insulin gene in many creatures and are lazy and inattentive in your study of the ev computer model of random point mutations and natural selection. I’ll be patient with you and bring you up to speed in the mathematics of this model and then you will realize why your theory has no mathematical basis.
The reference I give states the amino acid sequence for humans and chimps is identical, unless your reference says something different, no need to read your reference. With respects to the difference in the aa sequence between human and chimp preproinsulin see post http://forums.randi.org/showpost.php...postcount=2992, the response to Taffer’s inquiry. I'm a bit confused here, first you say the sequences are identical, then you point to a previous post where you say they are not? At any rate, the two aa sequences are different by two amino acids, as you are well aware.
You are sloppy in the reading of my posts. I said the aa sequence for human and chimp insulin are identical but the protein from which the insulin is derived (preproinsulin) are not identical.
You’re the one who has said you have mapped the evolution of insulin from zebra fish to humans. I guess the enzyme which cleaves preproinsulin to insulin is out of your area of expertise. If you have mapped the evolution of insulin from the zebra fish, why are you asking me for the differences in the sequences in human and chimpanzee preproinsulin? Or is preproinsulin out of your area of expertise? Just what is the selection process that has led to these differences in preproinsulins?This question wasn't directed at me, but I'd like to add my comments to it. There needs not selection pressure for things to arrise. For example, if the two amino acid substitutions between humans and chimps does not have any affect on the functionality of the gene, then there are no selection pressures acting on that allele. This is how there is so much genetic variation within populations. These are sometimes referred to as 'silent mutations'. The difference we are seeing could simply be a case of chance.
If you want to argue that the differences in insulin genes are simply an example of genetic drift, you open a can of worms. Why don’t we see a wide variety of insulin genes in humans? How did the original ancestral insulin gene arise? What was the selection process that would lead to the evolution of the original ancestral insulin gene? I will again post my argument why there is no selection process that can evolve an original ancestral insulin gene or any gene from the beginning.

A gene is to evolve. The first base in the sequence for the gene is laid down on the genome. One base codes for nothing so there is nothing for natural selection to act upon. A second base added by random chance is laid down in the sequence. Still nothing to code for, natural selection can not act on this sequence. A third base in the sequence is laid down. You now have enough bases to form a codon for a single amino acid. A single amino acid has no functional use so there is still nothing for natural selection to act upon. So bases must be added randomly until you have a long enough sequence of bases to produce a functional polypeptide and then natural selection can act. Adding bases randomly yield probabilities so infinitesimally small that evolution is mathematically impossible.

The insulin gene is 12,000 bases long. What sequence of mutation and selection could give rise to such a gene from the beginning.
None of your extrapolations hold up to mathematical analysis.As a Geneticist who is interested in phylogenetics and population genetics, I highly dispute this statement. There is a vast knowledge of genetic evolution which is entirely mathematically based.
Population genetics is fine for predicting occurrences of harmful mutations in populations or how often recessive alleles are expressed phenotypically but is nowhere near what Dr Schneider is doing with ev. Dr Schneider has taken the concept of random point mutations and natural selection and is brute force doing the accounting of how rapidly information can be accumulated by this mechanism. It is this type of analysis that shows the deficiency in your theory.
I’m particularly interested in hearing your description of the selection process that would evolve your so called ancestral insulin gene from the beginning by indels.Unfortunately, evolution is not as simple as you think. It is highly unlikely that only a single phenomenon (such as indel mutations) were the cause of the 'ancestral insulin gene'.
Use any mechanism of alteration of a sequence of bases you want. What is the selection process that would evolve any gene from the beginning? Unless you have a polymer that gives benefit to a creature, you have no selection process to evolve the polymer. You have no way of selecting for a molecule until it gives benefit to the creature. You can not select for the ancestral insulin gene until the gene exists. Before it exists, there is nothing to select for. You are left with mutation without selection to evolve the first ancestral insulin gene or any new gene from the beginning.
Well you raise good points. Our resident expert on the evolution of the insulin molecule, Dr Richard, doesn’t seem to have the answers to these questions either.Perhaps he doesn't, but this doesn't affect your argument. Your claim, insofar as I understand it, is that there have to be two different protease enzymes to cleave the chimp and human preproinsulin protein, because of the amino acid difference between the two. For this to hold, you would have to, of course, show that the difference has any effect on the protease binding efficiency.
I consider this discussion about insulin a side bar discussion. I don’t dispute Dr Richard’s tabulation of similarities in insulin genes between different creatures. In fact I came across a reference for an insulin type molecule in the mosquito. What I dispute with Dr Richard is his extrapolation that this tabulation is proof of the theory of evolution. He must show how the insulin gene arose initially and what the selection process is that would transform the gene from one to another form.

My argument about the protease enzyme concerns whether they are identical and have same biochemical activity. If they don’t, then you have to describe the selection process that would lead to these differences. I see this as a requirement if Dr Richard is going to do a thorough proof of his hypothesis.
Again, Dr Richard is the expert on the evolution of the insulin, ask him these questions. I’m sure he will have some type of answer such as chanting “indels, indels”.And again, he doesn't need to have any answer at all. It is your argument (again, insofar as I understand it) and there are a few things you need to show before your argument is sound.

Also, I'm not quite sure what indel mutations have to do with protease sequence specific binding sites.
It is Dr Richard’s contention that the insulin gene maps out evolution. I don’t mind if he answers or not because it has no impact on my contention that the ev computer simulation shows that evolution by random point mutation and natural selection is mathematically impossible.

You need to ask Dr Richard about what indel mutations have to do with protease sequence specific binding sites since he raised this mechanism as an explanation for the evolution of the different preproinsulins in humans and chimps.
The only thing that I have claimed on this thread is that the theory of evolution is mathematically impossible according to the results of ev. It is Dr Richard who claims that he proves evolution to be true by mapping out insulin in different creatures. I see peculiarities in his claims and you ask me to explain these peculiarities in his hypothesis. I think it is his responsibility to explain his hypothesis just as it is my responsibility to post the data from ev and explain why that proves the theory of evolution to mathematically impossible.You're right about the burden of proof in both cases, except for one thing. I am analysing your claim that the two amino acid difference in the signal protein sequence of the preproinsulin protein requires a different protease cleaving enzyme to be properly cleaved. Thus, the burden of proof is on you. I'm not analysing any of Dr. R's claims.
I never said the two different preproinsulins require different cleaving enzymes. I only question whether there were two different cleaving enzymes. If there are, it would complicate Dr Richard’s argument. Since Dr Richard has already indicated that dog microsomes can cleave fish preproinsulin, I take it that the enzymes are very similar. A precise analysis of the problem would look at the reaction rates of the different enzymes, not just that enzymes from different species work on other species preproinsulin.
Well Taffer, I use Dr Richard as a reference to show that 1) above occurs so I have already shown one of the things you require. Now if our resident expert on the evolution of insulin would answer 2) and 3) we can complete this proof.Yes, you have shown 1). I suspect the answer to 2) and 3), and Dr. R has given some hint as to it, but I will not make any assumptions until evidence is presented, either by you or Dr. Richard. The burden of proof is on you to show evidence for your proof, but you're right, that doesn't mean you personally have to present evidence. Any evidence will do, as long as it supports your proof.
I’ve done an initial search for signal peptide cleavage enzymes for insulin and so far have not found a lot of publications. Since this issue has no bearing on the mathematics of ev, I’m not going to spend time on this issue right now. If you or other evolutionists can show why this issue has importance to this debate then I’ll spend some time on this topic. What does have bearing on the mathematics of ev is a selection process to evolve the so called ancestral gene for insulin. This is your challenge in order to overcome the mathematical impossibility that ev reveals for the theory of evolution.
Thank you Paul, kjkent1 has trouble understanding this concept. Now if we can get Dr Richard to understand this concept then perhaps he will describe the selection process that leads to all these different forms of insulin.Just a friendly piece of advice, kleinman. The fewer insults you throw around, the more seriously you will be taken.

This goes for everyone, by the way.
What you don’t understand Taffer is that my challenge to the theory of evolution is taken as an insult by many evolutionists. Evolutionists think they have cornered the market on science and anyone who disagrees with your world view are not scientists. The mathematics of ev is far from trivial and Dr Richard and other evolutionists who give only superficial study of this model are ignoring probably the best mathematical model of random point mutations and natural selection. This model shows that the rate of information gain is profoundly slow when realistic genome lengths and mutation rates are used in the model. Too slow to explain the theory of evolution.
You can download the above paper at http://mbe.oxfordjournals.org/cgi/reprint/9/2/193.pdf The paper you cite gives the amino acid sequences for chimp and african green monkey in figure 1A and 1B.

Where is the human sequence in that paper you muppet?
You are truly slow, inattentive and superficial. I will post for at least the third or fourth time the following quote from this reference:
Chimpanzee preproinsulin (fig. 1A) differs from the human protein at two sites in the signal peptide: amino acids - 13 and -2 are Ala in the human protein.
I guess you are one of the evolutionists who need a picture drawn for him. You know they teach the alphabet on Sesame Street. I guess you haven’t gotten past that course.

[kleinman]

Where is the human sequence in that paper you muppet?
I now understand your problem. Since you are a Sesame Street dropout, not only do you have trouble reading, you can’t count and therefore don’t understand ev. You did manage to get some proof for your theory of evolution before you flunked out of Sesame Street, you realized Big Bird is a transitional life form. You should have become a muppet, and then you would have learned how to read and count.

[Mercutio]

If lunacy you must defend,
The moving goalpost is your friend. (http://forums.randi.org/showthread.php?t=76067)

[kleinman]

No mathematics, no selection for your theory
But claims of moving goal posts, you never get weary.

[kjkent1]

I knew Ben and Jerry’s were up to no good. They are out to take over the world. And now I know what you are up to with your string cheese theory of evolutionAppeals to incredulity may cut it in your Christian prayer meetings, but it won't cut it here. If you can't counter the argument, then you lose -- again.

I'm actually surprised that you would try to discredit my example of lactose intolerance as a joke. It demonstrates to me that you're substantially less reasonable than I previously understood. But, now that I do understand, I think I'll let you continue the argument with others. You remind me of a tax protester who continues to claim that there's no law requiring payment of federal income tax -- while he/she is being dragged off to jail.

Thank you Paul, kjkent1 has trouble understanding this concept. Now if we can get Dr Richard to understand this concept then perhaps he will describe the selection process that leads to all these different forms of insulin.You don't realize it, because you're so busy trying to act superior, but you've just played right into making evolution a whole lot more probable. If all a self-replicating molecule requires to appear is selection based on accuracy in chemical bindings, rather than any external environmental stress, then evolving a gene from the beginning becomes an inevitable chemical process.

As for your claim that evolution is impossible -- well, that's a sublime fantasy for the religious zealot. You're welcome to it, but you don't have any scientific facts to support it. Your entire position is ill conceived because you base it on the raw numbers generated by your ridiculous 1 in 4G probability calculation -- a probability number which you cannot experimentally confirm.

Ev cannot evolve any faster than it does, only because it doesn't model any of the evolutionary processes which would speed it up. And, the one time that someone produced a selection method that did speed up ev, you immediately discredited it as unrealistic. Which is, of course, what you would do no matter what other selection method is introduced, because to do otherwise would be to concede that your conclusion is incorrect.

What's even more humorous is reading your incorrect description of the inner workings of ev. You don't even know how it works by default, so your trying to discredit how some alternative selection method might work, while predictable -- is absurd.

[kjkent1]

Well, sure it does. It models an environment that prefers better binding site matching over worse binding site matching. What is the "environment" other than an external mechanism that applies pressures to the organisms?

Evolution is a process of transmuting information in the environment into information in the genome.

~~ PaulMy point is that ev uses an environmental stress which is so minimal, that it's little wonder that the creatures require an inordinately long period of time to evolve. Real-world environmental stress on an organism is magnitudes more severe than mere accuracy in binding site matches.

It's obvious from anthropological history, that the more severe the environment (short of causing complete extinction of all life), the more profound the effect of any beneficial mutation to an existing life form, and the faster the evolutionary changes.

Agree?

[kleinman]

Well, sure it does. It models an environment that prefers better binding site matching over worse binding site matching. What is the "environment" other than an external mechanism that applies pressures to the organisms?

Evolution is a process of transmuting information in the environment into information in the genome.My point is that ev uses an environmental stress which is so minimal, that it's little wonder that the creatures require an inordinately long period of time to evolve. Real-world environmental stress on an organism is magnitudes more severe than mere accuracy in binding site matches.
That minimal environmental stress kills half the creatures every generation. Now if they had only been eating Ben and Jerry’s, the results would have been entirely different.
It's obvious from anthropological history, that the more severe the environment (short of causing complete extinction of all life), the more profound the effect of any beneficial mutation to an existing life form, and the faster the evolutionary changes.

Agree?
Just what is that beneficial mutation that causes the faster evolutionary changes? Is it a random point mutation, or an indel, or a translocation, or and inversion, or maybe you are thinking of a recombination event?

[kjkent1]

That minimal environmental stress kills half the creatures every generation. Now if they had only been eating Ben and Jerry’s, the results would have been entirely different.Leave comedy to the professionals Alan. You're gonna end up pushing that foot of yours so far down your throat that your toenails will be available for polyp removal.

Duh -- ev is a bacterial model. Evolution of bacteria is slow to begin with, and enormous populations are required to achieve any significant change. Dr. Adequate covered this issue pages ago.

But, ignoring this fact, Unnamed's alternate selection method increased ev's performance to satisfy even without a population increase. You've attempted to discredit this routinely, but your attempts have utterly failed, because you cannot accurately describe how either the default selection algorithm or Unnamed's alternate, works.

Funny, how I can answer your questions, but you can't answer mine.

How about comparing the mathematical improbability of God to the mathematical improbability of evolution, even using your own absurd calculations? All of a sudden, evolution starts looking pretty damn good.

Just what is that beneficial mutation that causes the faster evolutionary changes? Is it a random point mutation, or an indel, or a translocation, or and inversion, or maybe you are thinking of a recombination event?I've already read your various excretory analyses attempting to refute the notion that anything other than point mutation can actually accomplish a genetic change. Get over it.

Many people here have explained, and produced supporting peer-reviewed documents, on how genetic errors other than a point mutation can produce more profound change to a host organism.

Bottom line is that you are trying to use ev to prove evolutionary behaviors that ev doesn't model. So, if that's your goal, then it falls to you to reprogram ev to show that those behaviors that you're trying to model don't work as advertised.

Only you can't, because you don't know how. Not my problem, mang. Hire someone to prove up your theory.

[kleinman]

Duh -- ev is a bacterial model. Evolution of bacteria is slow to begin with, and enormous populations are required to achieve any significant change. Dr. Adequate covered this issue pages ago.
This is old territory but I don’t mind going over this again. Recombination without error can not increase information in the gene pool. Recombination with natural selection can cause the loss of information in the gene pool. So do you want to explain how recombination will increase evolution? If this is the problem with ev, why not fix it?
But, ignoring this fact, Unnamed's alternate selection method increased ev's performance to satisfy even without a population increase. You've attempted to discredit this routinely, but your attempts have utterly failed, because you cannot accurately describe how either the default selection algorithm or Unnamed's alternate, works.
I’ve already given a real example of Dr Schneider’s selection process, why don’t you give a real example of Unnamed’s selection process?
Funny, how I can answer your questions, but you can't answer mine.
I particularly like your string cheese answer. Your lactose intolerance example is priceless.
How about comparing the mathematical improbability of God to the mathematical improbability of evolution, even using your own absurd calculations? All of a sudden, evolution starts looking pretty damn good.
Well, I’ve done my part showing that the theory of evolution is mathematically impossible using evolutionist mathematics. Now it’s your turn to disprove the existence of God using creationist mathematics. But wait, I don’t know of any creationists who have tried to mathematically prove the existence of God. So why don’t you post your own mathematics.
Just what is that beneficial mutation that causes the faster evolutionary changes? Is it a random point mutation, or an indel, or a translocation, or and inversion, or maybe you are thinking of a recombination event?I've already read your various excretory analyses attempting to refute the notion that anything other than point mutation can actually accomplish a genetic change. Get over it.
Why kjkent1, are you trying to obtain a phyrrhic victory? Why don’t you show if any or all of the various mutation mechanisms can overcome the mathematical impossibility of the theory of evolution? Of course you have no selection process that would evolve a gene from the beginning (including Unnamed’s) regardless of mutation mechanism, so I’m going to enjoy reading your response.
Many people here have explained, and produced supporting peer-reviewed documents, on how genetic errors other than a point mutation can produce more profound change to a host organism.
Well then it’s quite simple, put these mechanisms into ev and make your case, little gator.
Bottom line is that you are trying to use ev to prove evolutionary behaviors that ev doesn't model. So, if that's your goal, then it falls to you to reprogram ev to show that those behaviors that you're trying to model don't work as advertised.
I’ll tell you what. If you describe the selection mechanism that would evolve a gene from the beginning, I’ll program it into ev.
Only you can't, because you don't know how. Not my problem, mang. Hire someone to prove up your theory.
My goodness, you are correct kjkent1. I can’t program ev to model these evolutionary behaviors you are talking about. Why? Because there are no selection processes to evolve genes from the beginning. But I don’t feel bad about this, because nobody can describe these selection processes, because they don’t exist.

You all put on your thinking caps and maybe you can help out kjkent1 with a selection process that would evolve a gene from the beginning. We can all talk about it next week.

[cyborg]

You still want genes to will themselves into existence?

Idiot.

[kjkent1]

Well, I’ve done my part showing that the theory of evolution is mathematically impossible using evolutionist mathematics. Now it’s your turn to disprove the existence of God using creationist mathematics. But wait, I don’t know of any creationists who have tried to mathematically prove the existence of GodIf you can't prove God mathematically, then you can't rule out evolution as impossible. So, you had better get started with your mathematical proof of God. Because without that proof, evolution is the overwhelmingly superior answer.

[Paul C. Anagnostopoulos]

My point is that ev uses an environmental stress which is so minimal, that it's little wonder that the creatures require an inordinately long period of time to evolve. Real-world environmental stress on an organism is magnitudes more severe than mere accuracy in binding site matches.
Certainly the real world environment is stunningly more complex than Ev's two simple pressures, yes.


It's obvious from anthropological history, that the more severe the environment (short of causing complete extinction of all life), the more profound the effect of any beneficial mutation to an existing life form, and the faster the evolutionary changes.

Agree?
Probably so, but I'm not convinced that Ev is slow compared to the real world. I really don't have much understanding of how environmental pressure relates to evolutionary time.


Bottom line is that you [Kleinman] are trying to use ev to prove evolutionary behaviors that ev doesn't model. So, if that's your goal, then it falls to you to reprogram ev to show that those behaviors that you're trying to model don't work as advertised.
There you have it, my friends.

~~ Paul

[Paul C. Anagnostopoulos]

Well, I’ve done my part showing that the theory of evolution is mathematically impossible using evolutionist mathematics. Now it’s your turn to disprove the existence of God using creationist mathematics. But wait, I don’t know of any creationists who have tried to mathematically prove the existence of God. So why don’t you post your own mathematics.
If you will be so kind as to present a coherent definition of God, I'll give it my best shot.

~~ Paul

[Taffer]

You are sloppy in the reading of my posts. I said the aa sequence for human and chimp insulin are identical but the protein from which the insulin is derived (preproinsulin) are not identical.

Firstly, I have yet to insult you, kleinman. I have tried to keep this debate solely about the science. That is what you want, isn't it?

Secondly, there are only two amino acid differences between the human and chimp preproinsulin proteins. That is not a considerable difference. Also, you might want to look at exactly which amino acids have been changed. The transformation is from ala to ser and val. Ala is a non-polar hydrophobic amino acid. Ser is a polar, very weakly hydrophillic amino acid, and is the most likely change to make any structural difference to the protein. Val is a non-polar, strongly hydrophobic amino acid, and is less likely to cause any major structural difference to the protein. You really need to show that there is any structural difference between the two proteins which makes the protease unable to function.

If you want to argue that the differences in insulin genes are simply an example of genetic drift, you open a can of worms. Why don’t we see a wide variety of insulin genes in humans? How did the original ancestral insulin gene arise? What was the selection process that would lead to the evolution of the original ancestral insulin gene? I will again post my argument why there is no selection process that can evolve an original ancestral insulin gene or any gene from the beginning.

I am not claiming the variation arose from 'genetic drift' (which is not what I'm talking about, but I don't expect everyone to understand jargon). I am simply pointing out that it could have, and you have to show that it hasn't by showing any functional difference between the two proteins.

A gene is to evolve. The first base in the sequence for the gene is laid down on the genome. One base codes for nothing so there is nothing for natural selection to act upon. A second base added by random chance is laid down in the sequence. Still nothing to code for, natural selection can not act on this sequence. A third base in the sequence is laid down. You now have enough bases to form a codon for a single amino acid. A single amino acid has no functional use so there is still nothing for natural selection to act upon. So bases must be added randomly until you have a long enough sequence of bases to produce a functional polypeptide and then natural selection can act. Adding bases randomly yield probabilities so infinitesimally small that evolution is mathematically impossible.

This is a complete misunderstanding of the genetics of evolution. There is no 'laying down' of basepairs on a genome, becuase the basepairs are already there. All that needs to happen is the sequence to be of a useful protein. Given the length of the human genome, this is not surprising at all.

The insulin gene is 12,000 bases long. What sequence of mutation and selection could give rise to such a gene from the beginning.

The same mutation 'sequences' which lead to variation in the population. As for selection models, it is true that an uncoding gene is not selected upon based on the protein it produces, but there are many other mechanisms by which a sequence of basepairs can lead to an overall fitness increase in a genome, even if they are non-coding[/i].

Population genetics is fine for predicting occurrences of harmful mutations in populations or how often recessive alleles are expressed phenotypically but is nowhere near what Dr Schneider is doing with ev. Dr Schneider has taken the concept of random point mutations and natural selection and is brute force doing the accounting of how rapidly information can be accumulated by this mechanism. It is this type of analysis that shows the deficiency in your theory.


Er, no keinman. As someone who has actually studied population genetics, I can tell you that it predicts a hell of a lot more then that. It also predicts the effects of novel muations in a population, the rate of mutation, the overall fitness of an individual and the population as a whole, the change in allele ratios over time per generation, the overall equilibrium level of an allele, and much more. These things have all be tested and varified with evidence.

Use any mechanism of alteration of a sequence of bases you want. What is the selection process that would evolve any gene from the beginning? Unless you have a polymer that gives benefit to a creature, you have no selection process to evolve the polymer. You have no way of selecting for a molecule until it gives benefit to the creature. You can not select for the ancestral insulin gene until the gene exists. Before it exists, there is nothing to select for. You are left with mutation without selection to evolve the first ancestral insulin gene or any new gene from the beginning.

And as I have said many times, producing a protein is not the only benificial mechanism which a sequence of basepairs can produce. Also, what if the ancestral insulin gene produced a protein which had a completely different function, and [b]only through mutation and natural selection has the current function been obtained.

I consider this discussion about insulin a side bar discussion. I don’t dispute Dr Richard’s tabulation of similarities in insulin genes between different creatures. In fact I came across a reference for an insulin type molecule in the mosquito. What I dispute with Dr Richard is his extrapolation that this tabulation is proof of the theory of evolution. He must show how the insulin gene arose initially and what the selection process is that would transform the gene from one to another form.

And you, equally, have to back up any claim you make. You claim it is impossible. You should produce proof.

But, again, I am only really discussing the one claim you have made, namely that the difference in amino acid sequences between the two proteins requires another protease enzyme.


My argument about the protease enzyme concerns whether they are identical and have same biochemical activity. If they don’t, then you have to describe the selection process that would lead to these differences. I see this as a requirement if Dr Richard is going to do a thorough proof of his hypothesis.

But you have claimed that they don't, and have not provided evidence that this is, in fact, the case.

It is Dr Richard’s contention that the insulin gene maps out evolution. I don’t mind if he answers or not because it has no impact on my contention that the ev computer simulation shows that evolution by random point mutation and natural selection is mathematically impossible.

I believe your proof of 'mathematical impossibilty' has been refuted many times on this thread, and that you haven't really answered any of the refutations of it.

You need to ask Dr Richard about what indel mutations have to do with protease sequence specific binding sites since he raised this mechanism as an explanation for the evolution of the different preproinsulins in humans and chimps.


I belive he raised this mechanism as an example of another mutation mechanism other then point mutations. And I really don't have any idea what it has to do with your claim.

I never said the two different preproinsulins require different cleaving enzymes. I only question whether there were two different cleaving enzymes. If there are, it would complicate Dr Richard’s argument. Since Dr Richard has already indicated that dog microsomes can cleave fish preproinsulin, I take it that the enzymes are very similar. A precise analysis of the problem would look at the reaction rates of the different enzymes, not just that enzymes from different species work on other species preproinsulin.

If you have not claimed that they are different, I apologize. I seem to recall you doing so, however.

I’ve done an initial search for signal peptide cleavage enzymes for insulin and so far have not found a lot of publications. Since this issue has no bearing on the mathematics of ev, I’m not going to spend time on this issue right now. If you or other evolutionists can show why this issue has importance to this debate then I’ll spend some time on this topic. What does have bearing on the mathematics of ev is a selection process to evolve the so called ancestral gene for insulin. This is your challenge in order to overcome the mathematical impossibility that ev reveals for the theory of evolution.

I have no idea what importance it has, I'm pretty sure you brought it up first.

Question: do you believe ev to perfectly model the natural system?

What you don’t understand Taffer is that my challenge to the theory of evolution is taken as an insult by many evolutionists. Evolutionists think they have cornered the market on science and anyone who disagrees with your world view are not scientists.[/quote]

Not true at all. What is taken as an insult by 'evolutionists' is when people who do not understand evolution, genetics, or the subject material being discussed claim that it is the 'evolutionists' who do not understand, or are not honest in the discussion because they do not want to subject evolutionary theory to any tests of validity.

A friendly point, kleinman. So called 'evolutionists' have often devoted many, many, years to study and research into evolution and evolutionary theory. They often know the subject material very well indeed, and have personally tested the theory of evolution many times before. They also often have heard most of the arguments made against evolution before, are tired of misunderstandings and intellectually dishonest practices. If you wish an honest debate, then you need to listen to the points raised by the 'other side'.

The mathematics of ev is far from trivial and Dr Richard and other evolutionists who give only superficial study of this model are ignoring probably the best mathematical model of random point mutations and natural selection. This model shows that the rate of information gain is profoundly slow when realistic genome lengths and mutation rates are used in the model. Too slow to explain the theory of evolution.

Firstly, it has been explained many times why your values are inaccurate. I believe Dr. Adequate has answered this point many times.

Secondly, who do you think developted the model? 'Evolutionists'. So to say they have not studied the subject material is a gross misstatement.

Thirdly, it was never claimed that point mutations are the only method of variation arrising in a population. I suggest you study the genetics of mutations.

You are truly slow, inattentive and superficial. I will post for at least the third or fourth time the following quote from this reference:

I guess you are one of the evolutionists who need a picture drawn for him. You know they teach the alphabet on Sesame Street. I guess you haven’t gotten past that course.

This kind of thing doesn't make your argument any better, kleinman. Why don't you stop the insults and borderline ad hominem attacks?

[articulett]

Hey, I resemble that remark! The basis of this entire thread is that creationists are annoying. That's still true, isn't it?

~~ Paul

Q.E.D.

and relentlessly unteachable.

[Foster Zygote]

This kind of thing doesn't make your argument any better, kleinman. Why don't you stop the insults and borderline ad hominem attacks?

Well, if it's all he's got...

[Kotatsu]

Hello again! My workload increased enormously for a while there, but now it's almost down to normal again. Has anything interesting happened while I was gone? Has Kleinman, for instance, had a valid point?

I knew Ben and Jerry’s were up to no good. They are out to take over the world. And now I know what you are up to with your string cheese theory of evolution.

Since you are unable to come up with a coherent response to that example, how about this one, then (1):

In weavers and widowbirds (as well as many other organisms), carotenoids are used for signalling in the males. Carotenoids cannot be synthesised by the birds, but have to be ingested and then modified. There is a trend for females to select males who have a deeper (redder) colouration before those which have a lighter (more yellow) one, as the carotenoids signal that the male has a large enough supply of carotenoids to be able to allocate a large portion to display (other parts are used for the immune system and other things). However, either carotenoids or some product of them is mildly toxic to the bird, adding another layer of signalling: healthier and more toxin-tolerant birds will be able to cope with higher concentrations of the chemical in the blood.

So on one hand, we have the fact that more carotenoids will result in a deeper colouration which will attract females, and on the other hand, the same high concentrations will also be mildly --- and eventually highly --- toxic. There is also the matter of having to eat enough to get all the carotenoids, which will leave little time for other matters. Thus, we may conclude that if an individual was born with a mutation that somehow altered the shape of the carotenoid used for plumage signalling in a way that resulted in a deeper hue at lower concentrations, that bird would have a higher mating success; it would get all the chicks, if you will.

The main point of that presentation/defence was that exactly this had happened. A small mutation in the sequence coding for the carotenoid converting protein has caused some modification to one of the carotenoids, which resulted in them having much redder shoulder patches and necks than their competitors, and at a much lower concentration.

Over time, of course, this difference has been amplified by further mutations, and the protein converting the ingested carotenoid into the form used in display has been changed. However, there are still several species which do not have it, and which thus have to rely on the old-fashioned high-concentration gambit.

---
(1) You will note that I have not referred here to a specific article. I heard about this a while ago in an oral defence/presentation of a master thesis or doctorate thesis, but I cannot remember the name of the person who held the lecture, and I cannot seem to find the article it was based on; possibly it is not actually published yet. Also: as this example is based mainly on memory and a few notes I made, I may be wrong in some details, but the gist is a truthful representation of that presentation. If anyone here knows these things better than I do (which may not be hard), please direct me to where I can read more about this.

[kjkent1]

A gene is to evolve. The first base in the sequence for the gene is laid down on the genome. One base codes for nothing so there is nothing for natural selection to act upon. A second base added by random chance is laid down in the sequence. Still nothing to code for, natural selection can not act on this sequence. A third base in the sequence is laid down. You now have enough bases to form a codon for a single amino acid. A single amino acid has no functional use so there is still nothing for natural selection to act upon. So bases must be added randomly until you have a long enough sequence of bases to produce a functional polypeptide and then natural selection can act. Adding bases randomly yield probabilities so infinitesimally small that evolution is mathematically impossible.Okay, at this point, you've provided enough contradictory points in other posts to make your argument here pretty weak.

You have recently stated in arguing with me (and concurred with Paul A.), that ev's model is an accurate representation, even though it selects for nothing more than accuracy in chemical bindings. Since your entire argument is based on ev's mathematics, then your argument immediately above is falsified, because ev demonstrates that it is not necessary that we must wait for the binding-site region to obtain some useful function.

Instead, a prospective functional gene, will select for accuracy in chemical bindings until such time as the gene begins to exhibit some functionality upon which environmental conditions external to the creature can select for/against.

So, either your gene from the beginning argument is falsified, or ev doesn't model real-world genetic behavior, in which case, your mathematically impossible argument is based on a false premise, and it fails.

Check.

[Paul C. Anagnostopoulos]

Since your entire argument is based on ev's mathematics, then your argument immediately above is falsified, because ev demonstrates that it is not necessary that we must wait for the binding-site region to obtain some useful function.
No, but we do have to wait for the transcription factor gene to perform some useful function, that is, match the binding sites. It is certainly the case in the real world that there could be a gene that produces a transcription factor that matches some loci on the genome that do not control any genes. Then those loci could evolve to produce useful promoters/genes that would be controlled by the transcription factor.

For example, if you visit this site, you'll find a list of all potential transcription factor binding sites for E. coli. Perhaps some of them will turn out to be unused.

http://bayesweb.wadsworth.org/binding_sites/

~~ Paul

[kjkent1]

No, but we do have to wait for the transcription factor gene to perform some useful function, that is, match the binding sites. It is certainly the case in the real world that there could be a gene that produces a transcription factor that matches some loci on the genome that do not control any genes. Then those loci could evolve to produce useful promoters/genes that would be controlled by the transcription factor.

For example, if you visit this site, you'll find a list of all potential transcription factor binding sites for E. coli. Perhaps some of them will turn out to be unused.

http://bayesweb.wadsworth.org/binding_sites/

~~ PaulSo, does this reasonably suggest that the "randomness" threshold for a gene's selective capacity (i.e., before any selection is possible), is determined by the number of possible transcription factor combinations divided by 4transcription_factor_length -- after which, the gene can select based on chemical accuracy?

[Paul C. Anagnostopoulos]

Sorry, kj, I don't understand your question.

I vaguely recall reading about some binding site widths and being surprised how short they are. It would seem that spurious bindings would occur elsewhere. But, of course, transcription control is often much more complex than one binding site.

~~ Paul

[Dr Adequate]

Hello again! My workload increased enormously for a while there, but now it's almost down to normal again. Has anything interesting happened while I was gone? Has Kleinman, for instance, had a valid point? No; nor a new one.

[Dr Adequate]

This is old territory but I don’t mind going over this again. Recombination without error can not increase information in the gene pool. Recombination with natural selection can cause the loss of information in the gene pool. So do you want to explain how recombination will increase evolution? If this is the problem with ev, why not fix it?

I’ve already given a real example of Dr Schneider’s selection process, why don’t you give a real example of Unnamed’s selection process?

I particularly like your string cheese answer. Your lactose intolerance example is priceless.

Well, I’ve done my part showing that the theory of evolution is mathematically impossible using evolutionist mathematics. Now it’s your turn to disprove the existence of God using creationist mathematics. But wait, I don’t know of any creationists who have tried to mathematically prove the existence of God. So why don’t you post your own mathematics.

Why kjkent1, are you trying to obtain a phyrrhic victory? Why don’t you show if any or all of the various mutation mechanisms can overcome the mathematical impossibility of the theory of evolution? Of course you have no selection process that would evolve a gene from the beginning (including Unnamed’s) regardless of mutation mechanism, so I’m going to enjoy reading your response.

Well then it’s quite simple, put these mechanisms into ev and make your case, little gator.

I’ll tell you what. If you describe the selection mechanism that would evolve a gene from the beginning, I’ll program it into ev.

My goodness, you are correct kjkent1. I can’t program ev to model these evolutionary behaviors you are talking about. Why? Because there are no selection processes to evolve genes from the beginning. But I don’t feel bad about this, because nobody can describe these selection processes, because they don’t exist.

You all put on your thinking caps and maybe you can help out kjkent1 with a selection process that would evolve a gene from the beginning. We can all talk about it next week. So, you don't have any new lies?

No new magic words?

Nothing?

Poor kleinman.

[joobz]

No; nor a new one.
I was going to ask the same question... oh well.

I like Mercutio's Poem though. Seems to be a fair description of The methods presented here.

[kleinman]

You still want genes to will themselves into existence?
We all know your explanation cruftborg.
Well, I’ve done my part showing that the theory of evolution is mathematically impossible using evolutionist mathematics. Now it’s your turn to disprove the existence of God using creationist mathematics. But wait, I don’t know of any creationists who have tried to mathematically prove the existence of God.If you can't prove God mathematically, then you can't rule out evolution as impossible. So, you had better get started with your mathematical proof of God. Because without that proof, evolution is the overwhelmingly superior answer.
Doesn’t seem that ev proves the theory of evolution is the overwhelmingly superior answer. In fact ev shows that without a selection process, nothing can evolve and you don’t have a selection process to evolve a gene from the beginning.
My point is that ev uses an environmental stress which is so minimal, that it's little wonder that the creatures require an inordinately long period of time to evolve. Real-world environmental stress on an organism is magnitudes more severe than mere accuracy in binding site matches.Certainly the real world environment is stunningly more complex than Ev's two simple pressures, yes.
And ev shows that one simple pressure gives convergence much more quickly than two simple pressures.
It's obvious from anthropological history, that the more severe the environment (short of causing complete extinction of all life), the more profound the effect of any beneficial mutation to an existing life form, and the faster the evolutionary changes.

Agree?Probably so, but I'm not convinced that Ev is slow compared to the real world. I really don't have much understanding of how environmental pressure relates to evolutionary time.
Why would ev be slow compared to the real world? I believe that ev is accurately simulating the rate of evolution. I think with the proper selection process, ev can accurately simulate the microevolution of HIV viral drug resistance. As I have asked previously, what is the selection process that would evolve a gene from the beginning, there is none. It is the selection process that is the crucial factor for any evolutionary process to occur. It is this issue which slams the brakes on your theory.
Bottom line is that you [Kleinman] are trying to use ev to prove evolutionary behaviors that ev doesn't model. So, if that's your goal, then it falls to you to reprogram ev to show that those behaviors that you're trying to model don't work as advertised.There you have it, my friends.
So you think that insertion/deletions, transpositions,… will solve your problem that you have no selection mechanism to evolve a gene from the beginning? How do you think these other forms of mutation are going to solve your problem? You evolutionists are on a fantasy trip.
Well, I’ve done my part showing that the theory of evolution is mathematically impossible using evolutionist mathematics. Now it’s your turn to disprove the existence of God using creationist mathematics. But wait, I don’t know of any creationists who have tried to mathematically prove the existence of God. So why don’t you post your own mathematics.If you will be so kind as to present a coherent definition of God, I'll give it my best shot.
That’s easy, let’s start with omnipotent and omnipresent. So all you need is a computer that can handle infinity an infinite number of times.
Secondly, there are only two amino acid differences between the human and chimp preproinsulin proteins. That is not a considerable difference. Also, you might want to look at exactly which amino acids have been changed. The transformation is from ala to ser and val. Ala is a non-polar hydrophobic amino acid. Ser is a polar, very weakly hydrophillic amino acid, and is the most likely change to make any structural difference to the protein. Val is a non-polar, strongly hydrophobic amino acid, and is less likely to cause any major structural difference to the protein. You really need to show that there is any structural difference between the two proteins which makes the protease unable to function.
The change of a single amino acid can make a striking change in a protein. You seem to be supporting my argument by describing the differences in the electrochemical behavior of Ala and Ser, one of the substitutions in the human/chimpanzee preproinsulin.
If you want to argue that the differences in insulin genes are simply an example of genetic drift, you open a can of worms. Why don’t we see a wide variety of insulin genes in humans? How did the original ancestral insulin gene arise? What was the selection process that would lead to the evolution of the original ancestral insulin gene? I will again post my argument why there is no selection process that can evolve an original ancestral insulin gene or any gene from the beginning.I am not claiming the variation arose from 'genetic drift' (which is not what I'm talking about, but I don't expect everyone to understand jargon). I am simply pointing out that it could have, and you have to show that it hasn't by showing any functional difference between the two proteins.
All I’m doing is pointing out peculiarities in Dr Richard’s argument that the similarities of insulin genes in different creatures are evidence for the theory of evolution. It is his responsibility to explain the peculiarities in his argument. My argument is the theory of evolution is mathematically impossible based on the results from ev and that there are no selection processes that can evolve a gene de novo.
A gene is to evolve. The first base in the sequence for the gene is laid down on the genome. One base codes for nothing so there is nothing for natural selection to act upon. A second base added by random chance is laid down in the sequence. Still nothing to code for, natural selection can not act on this sequence. A third base in the sequence is laid down. You now have enough bases to form a codon for a single amino acid. A single amino acid has no functional use so there is still nothing for natural selection to act upon. So bases must be added randomly until you have a long enough sequence of bases to produce a functional polypeptide and then natural selection can act. Adding bases randomly yield probabilities so infinitesimally small that evolution is mathematically impossible.This is a complete misunderstanding of the genetics of evolution. There is no 'laying down' of basepairs on a genome, becuase the basepairs are already there. All that needs to happen is the sequence to be of a useful protein. Given the length of the human genome, this is not surprising at all.
Ok, explain the selection process that gives this original useful protein. Did you read earlier in this thread about Professor Behe’s hypothesis of irreducible complexity? It seems that evolutionists don’t find Professor Behe’s example of the flagellum a plausible example of an irreducibly complex system because the components of the flagellum had other uses before they assembled to form the flagellum. I suggest the example of the DNA replicase system because what were the uses of the components for this system doing before DNA could be replicated? In particular, what were the uses of Helicase and Gyrase before DNA could be replicated? So, how did the sequence of base pairs for the DNA replicase system appear?
The insulin gene is 12,000 bases long. What sequence of mutation and selection could give rise to such a gene from the beginning?The same mutation 'sequences' which lead to variation in the population. As for selection models, it is true that an uncoding gene is not selected upon based on the protein it produces, but there are many other mechanisms by which a sequence of basepairs can lead to an overall fitness increase in a genome, even if they are non-coding[/i].
We are all waiting for you to describe these selection processes so that they can be introduced into the ev model.
Population genetics is fine for predicting occurrences of harmful mutations in populations or how often recessive alleles are expressed phenotypically but is nowhere near what Dr Schneider is doing with ev. Dr Schneider has taken the concept of random point mutations and natural selection and is brute force doing the accounting of how rapidly information can be accumulated by this mechanism. It is this type of analysis that shows the deficiency in your theory.Er, no keinman. As someone who has actually studied population genetics, I can tell you that it predicts a hell of a lot more then that. It also predicts the effects of novel muations in a population, the rate of mutation, the overall fitness of an individual and the population as a whole, the change in allele ratios over time per generation, the overall equilibrium level of an allele, and much more. These things have all be tested and varified with evidence.
Why don’t you describe the selection processes that would take these novel mutations and evolve new genes so that this can be modeled in ev?
Use any mechanism of alteration of a sequence of bases you want. What is the selection process that would evolve any gene from the beginning? Unless you have a polymer that gives benefit to a creature, you have no selection process to evolve the polymer. You have no way of selecting for a molecule until it gives benefit to the creature. You can not select for the ancestral insulin gene until the gene exists. Before it exists, there is nothing to select for. You are left with mutation without selection to evolve the first ancestral insulin gene or any new gene from the beginning.And as I have said many times, producing a protein is not the only benificial mechanism which a sequence of basepairs can produce. Also, what if the ancestral insulin gene produced a protein which had a completely different function, and [B]only through mutation and natural selection has the current function been obtained.
Feel free to describe and use any beneficial effect that a mutation may have in your selection process to evolve a gene from the beginning. This effect does not have to pertain to producing a protein.
I consider this discussion about insulin a side bar discussion. I don’t dispute Dr Richard’s tabulation of similarities in insulin genes between different creatures. In fact I came across a reference for an insulin type molecule in the mosquito. What I dispute with Dr Richard is his extrapolation that this tabulation is proof of the theory of evolution. He must show how the insulin gene arose initially and what the selection process is that would transform the gene from one to another form.And you, equally, have to back up any claim you make. You claim it is impossible. You should produce proof.
I have produced proof that the theory of evolution is mathematically impossible. I have produced this proof using an evolutionist written, peer reviewed and published mathematical model of random point mutations and natural selection. In addition, ev shows that the selection process is crucial to modeling any evolutionary process. You don’t have a selection process that can evolve a gene from the beginning.
My argument about the protease enzyme concerns whether they are identical and have same biochemical activity. If they don’t, then you have to describe the selection process that would lead to these differences. I see this as a requirement if Dr Richard is going to do a thorough proof of his hypothesis.But you have claimed that they don't, and have not provided evidence that this is, in fact, the case.
Have I made this claim?
It is Dr Richard’s contention that the insulin gene maps out evolution. I don’t mind if he answers or not because it has no impact on my contention that the ev computer simulation shows that evolution by random point mutation and natural selection is mathematically impossible.I believe your proof of 'mathematical impossibilty' has been refuted many times on this thread, and that you haven't really answered any of the refutations of it.
Which gif or jpeg which Adequate has posted are you talking about?
I never said the two different preproinsulins require different cleaving enzymes. I only question whether there were two different cleaving enzymes. If there are, it would complicate Dr Richard’s argument. Since Dr Richard has already indicated that dog microsomes can cleave fish preproinsulin, I take it that the enzymes are very similar. A precise analysis of the problem would look at the reaction rates of the different enzymes, not just that enzymes from different species work on other species preproinsulin.If you have not claimed that they are different, I apologize. I seem to recall you doing so, however.
What I said was that if the differences in human and chimpanzee preproinsulin require different cleaving enzymes for these metabolic systems to function properly, that Dr Richard would look like a pretzel trying to explain these differences, especially since he claims that humans and chimps share a common ancestor who must already have produced insulin.
I’ve done an initial search for signal peptide cleavage enzymes for insulin and so far have not found a lot of publications. Since this issue has no bearing on the mathematics of ev, I’m not going to spend time on this issue right now. If you or other evolutionists can show why this issue has importance to this debate then I’ll spend some time on this topic. What does have bearing on the mathematics of ev is a selection process to evolve the so called ancestral gene for insulin. This is your challenge in order to overcome the mathematical impossibility that ev reveals for the theory of evolution.I have no idea what importance it has, I'm pretty sure you brought it up first.
What I brought up was the evolution of a gene from the beginning and mention examples such as the hemoglobin, insulin and the DNA replicase system. Dr Richard picked up on insulin and said he could show the evolution of the insulin gene from Zebra fish to humans. He then asked whether the evolution of humans and chimpanzees from a common ancestor represents a macroevolutionary event. I said yes and decided to look at the differences between the human and chimpanzee insulin genes and came across some differences which I thought peculiar for Dr Richard’s argument.
Question: do you believe ev to perfectly model the natural system?
Of course not and I have never said such a thing. I have never seen a computer simulation that perfectly models any natural system. What I have said is that ev is a plausible model of random point mutation and natural selection. What ev does is capture the mathematics of random point mutations and natural selection closely enough to give a good picture of the mathematical behavior of this mechanism. This model shows how important the selection mechanism is for evolution to proceed. Without a selection mechanism, there is no evolution. You might as well get used to hearing this question from me, what is the selection mechanism that would evolve a gene de novo.
What you don’t understand Taffer is that my challenge to the theory of evolution is taken as an insult by many evolutionists. Evolutionists think they have cornered the market on science and anyone who disagrees with your world view are not scientists Not true at all. What is taken as an insult by 'evolutionists' is when people who do not understand evolution, genetics, or the subject material being discussed claim that it is the 'evolutionists' who do not understand, or are not honest in the discussion because they do not want to subject evolutionary theory to any tests of validity.
If you read this thread, you will find that evolutionists claim that the mathematics I am using to make my claims is my own. It is not, it is your own mathematics published in a peer reviewed journal. The only thing that evolutionists have done is diminish and discredit your own model once it was shown what this model reveals.
A friendly point, kleinman. So called 'evolutionists' have often devoted many, many, years to study and research into evolution and evolutionary theory. They often know the subject material very well indeed, and have personally tested the theory of evolution many times before. They also often have heard most of the arguments made against evolution before, are tired of misunderstandings and intellectually dishonest practices. If you wish an honest debate, then you need to listen to the points raised by the 'other side'.
Honest debate? I post the results from an evolutionist written, peer reviewed and published mathematical model of random point mutation and natural selection, results obtained at the suggestion of the author of this model and it shows the theory of evolution to be mathematically impossible. You crybaby evolutionists accuse me of co-opting and abusing your mathematical model.

So, what is the selection process that would evolve a gene from the beginning? Care to have an honest debate on this topic?
The mathematics of ev is far from trivial and Dr Richard and other evolutionists who give only superficial study of this model are ignoring probably the best mathematical model of random point mutations and natural selection. This model shows that the rate of information gain is profoundly slow when realistic genome lengths and mutation rates are used in the model. Too slow to explain the theory of evolution.Firstly, it has been explained many times why your values are inaccurate. I believe Dr. Adequate has answered this point many times.
Are you talking about the same Adequate who has done zero cases with ev which qualifies him as an expert on ev since he has only done one less case than Dr Schneider’s publication on ev? Which of his gifs or jpegs refutes the results we have obtained from ev?
Secondly, who do you think developted the model? 'Evolutionists'. So to say they have not studied the subject material is a gross misstatement.
Really? What evolutionist did a parametric study of the ev model?
Thirdly, it was never claimed that point mutations are the only method of variation arrising in a population. I suggest you study the genetics of mutations.
What method of variation arising in a population is going to overcome the lack of a selection process to evolve a gene from the beginning?
Hey, I resemble that remark! The basis of this entire thread is that creationists are annoying. That's still true, isn't it? Q.E.D.

and relentlessly unteachable.
Oh, I think I have learned your evolutionist mathematics. You know that mathematics, don’t you? It shows your theory to be mathematically impossible.
This kind of thing doesn't make your argument any better, kleinman. Why don't you stop the insults and borderline ad hominem attacks?Well, if it's all he's got...
Foster Zygote, you haven’t been paying attention, I have ev as well.
Hello again! My workload increased enormously for a while there, but now it's almost down to normal again. Has anything interesting happened while I was gone? Has Kleinman, for instance, had a valid point?
How about a valid question? What is the selection process that would evolve a gene from the beginning?
No; nor a new one.I was going to ask the same question... oh well.

I like Mercutio's Poem though. Seems to be a fair description of The methods presented here.
Hey joobz, my favorite alchemical engineer on this thread. Your goal post is to describe how ribose could have formed nonezymatically in the primordial soup, but feel free to describe the selection process that would evolve a gene from the beginning.

[cyborg]

We all know your explanation cruftborg.

Yes but you are too stupid to see why it destroys your argument.

[kleinman]

You still want genes to will themselves into existence?We all know your explanation cruftborg.Yes but you are too stupid to see why it destroys your argument.
Why call me stupid? I think your cruft theory for the appearance of genes de novo is the best explanation for the theory of evolution offered so far. Well, second best, next to kjkent1’s string cheese theory. What devastating evolutionary logic you offer.

[Paul C. Anagnostopoulos]

That’s easy, let’s start with omnipotent and omnipresent. So all you need is a computer that can handle infinity an infinite number of times.
Can God create an object that he cannot move? Can God destroy himself? What does it mean to be omnipotent yet create creatures with free will? Does God have free will? Does a human definition of omnipotent even mean anything in the context of God?

I don't know what "omnipresent" means. It must mean that God is present in the natural world: could you point him out?

~~ Paul

[kjkent1]

Can God create an object that he cannot move? Can God destroy himself? What does it mean to be omnipotent yet create creatures with free will? Does God have free will? Does a human definition of omnipotent even mean anything in the context of God?

I don't know what "omnipresent" means. It must mean that God is present in the natural world: could you point him out?

~~ PaulWell, I don't know about omnipotent or omnipresent, but Abraham's God is definitely sadistic. What other description is there for a deity who would announce its intention to systematically torture all women, during childbirth, for the sole reason that they were born subsequent to Eve, and so women should suffer punishment for Eve's original failure to obey her creator?

This is no God whom I would worship -- by any reasonable human standard, God's actions are malum in se.

Back on point, how many bases long is the average transcription factor?

[Paul C. Anagnostopoulos]

Back on point, how many bases long is the average transcription factor?
I think you mean binding site. As I recall, there are binding site motifs of between 6 and 12 base pairs. Here's an interesting article:

http://www.bioinfo.de/isb/2004/04/0045/main.html

~~ Paul

[kleinman]

That’s easy, let’s start with omnipotent and omnipresent. So all you need is a computer that can handle infinity an infinite number of times.Can God create an object that he cannot move? Can God destroy himself? What does it mean to be omnipotent yet create creatures with free will? Does God have free will? Does a human definition of omnipotent even mean anything in the context of God?
God never does anything inconsistent with Himself or anything foolish. What it means to be omnipotent yet create creatures with free will is that God puts limits on this free will. God ultimately judges sin. Does God have free will? For example can God lie? Or can God sin? God is holy righteous and does nothing outside this holiness and righteousness. Our human definition of omnipotence probably infinitely underestimates the power of God.
I don't know what "omnipresent" means. It must mean that God is present in the natural world: could you point him out?
What the omnipresence of God means is there is nowhere you can go and escape the presence of God. Look anywhere you want Paul, God is there.

I can understand that you want to change the subject off of ev since you are now starting to understand the implications of this model beyond what Dr Schneider has said and written. How long will you hold to the theory of evolution by mutation and selection when there are no selection processes that can evolve a gene from the beginning?

Since natural selection can only select for something which exists, evolutionist must describe how the first genes came into existence without natural selection. There are no selection processes that can do this. The theory of evolution is based on non-existent selection processes. The theory of evolution is without a scientific or mathematical basis.
This is no God whom I would worship -- by any reasonable human standard, God's actions are malum in se.
God will not force you to worship Him, but you will be judged by this God. You better have a good lawyer for this case. If I were you, better for you to cry out for mercy than justice from this Judge.

[Mercutio]

Hmmm...would you agree, Kleinman, that your (and my, and any of our) sensory and perceptual apparatus are inadequate to distinguish between the god you describe and some entity merely much much more powerful and vast than ourselves, yet not omnipotent nor omnipresent?

Your description is far beyond what is needed as an explanation; have you been holding Occam's razor by the wrong end?

[Paul C. Anagnostopoulos]

Our human definition of omnipotence probably infinitely underestimates the power of God.
Well, it does something for sure, because it is illogical.


What the omnipresence of God means is there is nowhere you can go and escape the presence of God. Look anywhere you want Paul, God is there.
Where in hell is He?
:bunpan

[kjkent1]

God will not force you to worship Him, but you will be judged by this God. You better have a good lawyer for this case. If I were you, better for you to cry out for mercy than justice from this Judge.I'll take my chances. God's words in the Bible re women, and slavery, for examples, demonstrate an entity equally capable of good or evil.

So, the odds are really 50/50, despite your anticipated protestations.

[kjkent1]

I think you mean binding site. As I recall, there are binding site motifs of between 6 and 12 base pairs. Here's an interesting article:

http://www.bioinfo.de/isb/2004/04/0045/main.html

~~ PaulSo, does this mean that there is between an ~46 and a ~412 raw probability of a transcription factor arising by chance -- assuming that there is only one viable sequence (which we know from the evidence that there are many more than one)?

Or do we not know enough about the process to begin to make probability estimates?

[kleinman]

Hmmm...would you agree, Kleinman, that your (and my, and any of our) sensory and perceptual apparatus are inadequate to distinguish between the god you describe and some entity merely much much more powerful and vast than ourselves, yet not omnipotent nor omnipresent?
Mercutio, you see moving goal posts where there are none. You are unable to see the results from ev. You choose what you want to see and close your eyes to what you don’t want to see.
Your description is far beyond what is needed as an explanation; have you been holding Occam's razor by the wrong end?
If the only requirement is that something must be more powerful than us in order to be a god, you must have many gods.
Our human definition of omnipotence probably infinitely underestimates the power of God. Well, it does something for sure, because it is illogical.
It doesn’t surprise me that you don’t understand this logic, after all, you have trouble understand the logic of your own mathematical model. The more you understand the logic of the model, the more you deny the validity of the model.
What the omnipresence of God means is there is nowhere you can go and escape the presence of God. Look anywhere you want Paul, God is there.http://forums.randi.org/qb.php?T=Where in hell is He?
Keep looking Paul, you will find Him.
God will not force you to worship Him, but you will be judged by this God. You better have a good lawyer for this case. If I were you, better for you to cry out for mercy than justice from this Judge.I'll take my chances. God's words in the Bible re women, and slavery, for examples, demonstrate an entity equally capable of good or evil.

So, the odds are really 50/50, despite your anticipated protestations.
Kjkent1, how well do you know yourself? Do you need justice or mercy?

[kjkent1]

Kent, how well do you know yourself? Do you need justice or mercy?You're wasting my time, Alan. If you have a logical argument for why God is more likely good than evil, feel free to state it. However, for the purposes of this thread, the only thing that matters is that God is scientifically unprovable, and therefore is non-existent.

This fact creates a serious problem for you as a scientist. Because if you were correct about evolution being impossible, then some other natural explanation must be true -- and suddenly, string cheese and anthropic principle becomes the next best bet.

While God still trails the pack by an infinite expanse.

[kleinman]

Kjkent1, how well do you know yourself? Do you need justice or mercy?You're wasting my time, Alan. If you have a logical argument for why God is more likely good than evil, feel free to state it. However, for the purposes of this thread, the only thing that matters is that God is scientifically unprovable, and therefore is non-existent.
In case you missed it, it is the theory of evolution that is mathematically impossible. What makes you think that the existence of God is scientifically unprovable? I have only said that I am not here to prove the existence of God scientifically. I am here to prove the theory of evolution is mathematically impossible. Thanks to Dr Schneider’s and Paul’s work on ev, I have been able to do this. There are many scientists who are better versed in intelligent design and creationism that can present the data and science that proves the existence of God scientifically.
This fact creates a serious problem for you as a scientist. Because if you were correct about evolution being impossible, then some other natural explanation must be true -- and suddenly, string cheese and anthropic principle becomes the next best bet.
What makes you think that some other natural explanation is true?
While God still trails the pack by an infinite expanse.
Kjkent1, didn’t you know, God created the infinite expanse.

[cyborg]

I am here to prove the theory of evolution is mathematically impossible. Thanks to Dr Schneider’s and Paul’s work on ev, I have been able to do this.

No.

This is why I call you stupid. You are stupid. You have proved no such thing. I'm sorry your god is not real - but don't feel bad, you're in good company with billions of other people whose gods aren't real either. You will have to find another reason to believe in god.

[Mercutio]

Mercutio, you see moving goal posts where there are none. You are unable to see the results from ev. You choose what you want to see and close your eyes to what you don’t want to see.
What an appropriate response--I asked a very simple question, which you do not answer here. Do you have an answer?

If the only requirement is that something must be more powerful than us in order to be a god, you must have many gods.Thank you for illustrating my point. I see no reason to assume that any such entity is a god, and yet here you are saying that I "must have many gods".

My only question was about the limits of our perceptual abilities. Do you, unlike the rest of us, have a way of distinguishing "really really powerful" from "omnipotent"? If you give an entity a hundred tests and it passes, do you then say it is "omnipotent"? How about a thousand tests? A million? I am just curious where you set the bar. Do you fudge the statistics here like you do with ev? I know you don't like to think about population size, so maybe the number of tests your entity passes is likewise irrelevant to you.

[kleinman]

I am here to prove the theory of evolution is mathematically impossible. Thanks to Dr Schneider’s and Paul’s work on ev, I have been able to do this.No.

This is why I call you stupid. You are stupid. You have proved no such thing. I'm sorry your god is not real - but don't feel bad, you're in good company with billions of other people whose gods aren't real either. You will have to find another reason to believe in god.
Oh, that’s right, you have shown that you don’t need a selection process to evolve a gene from the beginning, all you need is cruft. Tell me, is cruft that stuff that floats to the top of your imaginary nonexistent primordial soup?

I’m also here to annoy evolutionists. I also have accomplished this task as well.

[kjkent1]

In case you missed it, it is the theory of evolution that is mathematically impossible.In your unsupported opinion.What makes you think that the existence of God is scientifically unprovable?Because if you were able to prove up God scientifically, you would qualify for Randi's million dollar prize. It's right here for the taking, so please hurry, because I'm really tired of reading about Sylvia Browne's latest week of not responding.I have only said that I am not here to prove the existence of God scientificallyActually, you conceded in this thread that you couldn't prove God scientifically -- if your position has changed, then feel free to state your proof. I am here to prove the theory of evolution is mathematically impossible. Thanks to Dr Schneider’s and Paul’s work on ev, I have been able to do this.In my opinion, the only things you've proved is (1) your ability to claim that you've proved evolution mathematically impossible, and (2) your disingenuous.There are many scientists who are better versed in intelligent design and creationism that can present the data and science that proves the existence of God scientifically.Well I invite them to present their proof to randi.org and then "Count de Money."What makes you think that some other natural explanation is true?Because supernatural events are definitionally unmeasurable, therefore even if God were responsible for creation/evolution, the scientist would measure only a random accidental cause.kjkent1, didn't you know God created the infinite expanse.Even if true, science would only measure a random accident. "Acts of God" are named thus, because they are unpredictable. God and random chance are synonymous in this universe. I'm surprised you haven't figured that out, yet.

[kleinman]

Mercutio, you see moving goal posts where there are none. You are unable to see the results from ev. You choose what you want to see and close your eyes to what you don’t want to see.What an appropriate response--I asked a very simple question, which you do not answer here. Do you have an answer?
And the simple answer is that you and I can look at the same thing and draw entirely different conclusions. You can look at genetic code and see random mutations and natural selection forming this code; I look at the same code and see the intelligence of a creator. The problem with your interpretation of what you are seeing is that it is mathematically impossible.
If the only requirement is that something must be more powerful than us in order to be a god, you must have many gods.Thank you for illustrating my point. I see no reason to assume that any such entity is a god, and yet here you are saying that I "must have many gods".
You do have a god, perhaps many gods.
My only question was about the limits of our perceptual abilities. Do you, unlike the rest of us, have a way of distinguishing "really really powerful" from "omnipotent"? If you give an entity a hundred tests and it passes, do you then say it is "omnipotent"? How about a thousand tests? A million? I am just curious where you set the bar. Do you fudge the statistics here like you do with ev? I know you don't like to think about population size, so maybe the number of tests your entity passes is likewise irrelevant to you.
Really, I have fudged the statistics with ev? You think I haven’t thought about population sizes? Perhaps if you read the thread carefully, you will find I am the one who has run the cases with the largest population sizes. Feel free to run larger population cases that I have run. I would do it except larger cases exceed the memory limits of my computer. Do you think that larger populations will correct the lack of a selection process to evolve a gene from the beginning? Huge populations will not rescue your theory.

Stick with your moving goal posts poems, mathematics is a losing topic for the theory of evolution. Better yet, embrace Cyborg’s cruft theory or kjkent1’s string cheese theory of evolution; at least we can have a laugh.
In case you missed it, it is the theory of evolution that is mathematically impossible.In your unsupported opinion.
I know you are having a hard time understanding ev but keep asking Paul questions, he’ll explain the mathematics to you.
What makes you think that the existence of God is scientifically unprovable?Because if you were able to prove up God scientifically, you would qualify for Randi's million dollar prize. It's right here for the taking, so please hurry, because I'm really tired of reading about Sylvia Browne's latest week of not responding.
You just can’t contain that greedy streak you have. You can’t see doing something just because it is the right thing to do.
I have only said that I am not here to prove the existence of God scientificallyActually, you conceded in this thread that you couldn't prove God scientifically -- if your position has changed, then feel free to state your proof.
If you read carefully what I have said you will see that I have said that you can’t put God in the laboratory but you can put God’s creation in the laboratory and find proof of God’s existence.
I am here to prove the theory of evolution is mathematically impossible. Thanks to Dr Schneider’s and Paul’s work on ev, I have been able to do this.In my opinion, the only things you've proved is (1) your ability to claim that you've proved evolution mathematically impossible, and (2) your disingenuous.
And the only thing you have proved is that (1) you don’t understand the mathematics of ev and (2) that you are too lazy to learn the mathematics.
There are many scientists who are better versed in intelligent design and creationism that can present the data and science that proves the existence of God scientifically.Well I invite them to present their proof to randi.org and then "Count de Money."
Your life does revolve around money doesn’t it? If you are really interested in the topic, there are plenty of web sites that discuss intelligent design but I think you are disingenuous with your claim of interest.
What makes you think that some other natural explanation is true?Because supernatural events are definitionally unmeasurable, therefore even if God were responsible for creation/evolution, the scientist would measure only a random accidental cause.
I think your definition for supernatural events is flawed. A supernatural event is an event that can not be explained by natural laws. You can measure the event but the event does not obey known natural laws.
kjkent1, didn't you know God created the infinite expanse.Even if true, science would only measure a random accident. "Acts of God" are named thus, because they are unpredictable. God and random chance are synonymous in this universe. I'm surprised you haven't figured that out, yet.
Random chance and probability theory is simply a way of mathematically addressing physical situations where the number of events is so large, there is no other way of addressing the situation. You superimpose our finite human nature and capabilities on an infinite God.

[Paul C. Anagnostopoulos]

Really, I have fudged the statistics with ev? You think I haven’t thought about population sizes? Perhaps if you read the thread carefully, you will find I am the one who has run the cases with the largest population sizes. Feel free to run larger population cases that I have run. I would do it except larger cases exceed the memory limits of my computer.
So I will extrapolate from thousands to septillions, while at the same time admonishing everyone else not to extrapolate. I will use the lack of computer power as proof.

~~ Paul

[Mercutio]

And the simple answer is that you and I can look at the same thing and draw entirely different conclusions. You can look at genetic code and see random mutations and natural selection forming this code; I look at the same code and see the intelligence of a creator. The problem with your interpretation of what you are seeing is that it is mathematically impossible.You still have not answered my question. How, please, do you distinguish, in your evidence of "the intelligence of a creator", the omnipotent god you claim and not merely a very powerful non-omnipotent entity? Your last sentence is, of course, wrong, but it is irrelevant to the question I am asking you. Let's say that my view is mathematically impossible. Now will you answer my question?
You do have a god, perhaps many gods.Unless you are looser with definitions than you are with numbers, you are much mistaken. What definition of "god" allows you to make this claim? What is your evidence?
Really, I have fudged the statistics with ev? You think I haven’t thought about population sizes? Perhaps if you read the thread carefully, you will find I am the one who has run the cases with the largest population sizes. Feel free to run larger population cases that I have run. I would do it except larger cases exceed the memory limits of my computer. Do you think that larger populations will correct the lack of a selection process to evolve a gene from the beginning? Huge populations will not rescue your theory. I know, I know... "a gene is to evolve". A goalpost is to shift. A simulation of natural selection is to explain abiogenesis. I forget--your largest population size--what fraction of the population of bacteria in your gut would that have been?
Stick with your moving goal posts poems, mathematics is a losing topic for the theory of evolution. Better yet, embrace Cyborg’s cruft theory or kjkent1’s string cheese theory of evolution; at least we can have a laugh.The poem already won. Thank you for that. Now, since there is very little chance of you understanding evolution, I am trying to understand this God hypothesis of yours. Would you please answer my simple little question?

[Paul C. Anagnostopoulos]

I think your definition for supernatural events is flawed. A supernatural event is an event that can not be explained by natural laws. You can measure the event but the event does not obey known natural laws.
You don't say. How can we tell a supernatural event from a natural event whose laws we do not understand? If it does not follow naturals laws, what sort of laws does it follow? How do those laws interact with the natural laws, which they must do in order to have an effect in the natural world? How can the supernatural laws be any different from the natural laws and still allow us to measure the event?

It's a loser concept, this one.

~~ Paul

[kjkent1]

You just can’t contain that greedy streak you have. You can’t see doing something just because it is the right thing to do.No more than you can contain that brown streak in your underwear after so many years of ____ (fill in the blank).If you read carefully what I have said you will see that I have said that you can’t put God in the laboratory but you can put God’s creation in the laboratory and find proof of God’s existence.You better check your past posts -- I won't bother embarssing you by showing that you expressly stated that you couldn't prove God mathematically.And the only thing you have proved is that (1) you don’t understand the mathematics of ev and (2) that you are too lazy to learn the mathematics.Actually, I'm pretty certain that I understand the mathematics of ev better than you do. After all, you can't even correctly explain how the algorithms work.Your life does revolve around money doesn’t it? If you are really interested in the topic, there are plenty of web sites that discuss intelligent design but I think you are disingenuous with your claim of interest.My life revolves around the Earth at about 1250 km/hr. Everything else is literally relative. As for intelligent design, the human female reproductive system demonstrates conclusively that if the designer is intelligent, he's only barely so.I think your definition for supernatural events is flawed. A supernatural event is an event that can not be explained by natural laws. You can measure the event but the event does not obey known natural laws.A scientific measurment requires reliability. No measurement of God could ever be reliable, because God can change the results of the experiment before, during and after it occurs. My definition is flawless.Random chance and probability theory is simply a way of mathematically addressing physical situations where the number of events is so large, there is no other way of addressing the situation. You superimpose our finite human nature and capabilities on an infinite God.Not me, but you, and obviously so. I'm not claiming to be able to scientifically prove God -- you are.

Here's a simple challenge. Imagine a ruler of unmeasureable length. Now, measure it. If you can't, then you can't measure God, either. And, if you can't measure God, then He is beyond any scientific proof. Period.

PS. You will never beat me in an argument. You proceed from the impossible disadvantage of a definitionally uprovable position.

The fact that you continue to try is a remarkable display of evolution in action. Without your genetic predisposition to compete for intellectual territiory, you would just shrug it all off and move on. But, you can't, because your instincts will not permit you to accept the loss.

You are living proof of evolution.

PPS. Give up on the trading insults with me. If you want to keep it civil, then I will, but if you won't, then I'm gonna start crushing you.

[kleinman]

Really, I have fudged the statistics with ev? You think I haven’t thought about population sizes? Perhaps if you read the thread carefully, you will find I am the one who has run the cases with the largest population sizes. Feel free to run larger population cases that I have run. I would do it except larger cases exceed the memory limits of my computer.So I will extrapolate from thousands to septillions, while at the same time admonishing everyone else not to extrapolate. I will use the lack of computer power as proof.
Paul, are you sure you want to discuss your extrapolations again? You extrapolated from short genomes to longer genomes when the generations for convergence were increasing at an increasing rate using simple curve fits. Go back to my earliest posts and compare my generations for convergence with the values that we are using now. If you want to extrapolate populations, feel free to do this and let’s see how accurate you are when the cases are run with ev.
I think your definition for supernatural events is flawed. A supernatural event is an event that can not be explained by natural laws. You can measure the event but the event does not obey known natural laws.You don't say. How can we tell a supernatural event from a natural event whose laws we do not understand? If it does not follow naturals laws, what sort of laws does it follow? How do those laws interact with the natural laws, which they must do in order to have an effect in the natural world? How can the supernatural laws be any different from the natural laws and still allow us to measure the event?
We have been talking about a supernatural event for months. The creation of life is a supernatural event. Why do you think you are having so much trouble describing this with natural laws? You can still measure the consequences of a supernatural event. This is done all the time with the sequencing of genomes and genes but your hypothesis of mutation and natural selection does not explain how the genome formed. You have two possibilities here, either life is the result of a supernatural event or you don’t know all the natural laws.
It's a loser concept, this one.
Why is that? You understand all the natural laws and are able to explain everything in terms of these laws? If that be the case, you have done a lousy job with ev.
And the simple answer is that you and I can look at the same thing and draw entirely different conclusions. You can look at genetic code and see random mutations and natural selection forming this code; I look at the same code and see the intelligence of a creator. The problem with your interpretation of what you are seeing is that it is mathematically impossible.You still have not answered my question. How, please, do you distinguish, in your evidence of "the intelligence of a creator", the omnipotent god you claim and not merely a very powerful non-omnipotent entity? Your last sentence is, of course, wrong, but it is irrelevant to the question I am asking you. Let's say that my view is mathematically impossible. Now will you answer my question?
Your view is mathematically impossible but you refuse to see it. If you can’t understand that there is no selection process that would evolve a gene from the beginning, how can you see anything else in this discussion?
You do have a god, perhaps many gods.Unless you are looser with definitions than you are with numbers, you are much mistaken. What definition of "god" allows you to make this claim? What is your evidence?
What has happened, are you finally seeing the goal posts?
Really, I have fudged the statistics with ev? You think I haven’t thought about population sizes? Perhaps if you read the thread carefully, you will find I am the one who has run the cases with the largest population sizes. Feel free to run larger population cases that I have run. I would do it except larger cases exceed the memory limits of my computer. Do you think that larger populations will correct the lack of a selection process to evolve a gene from the beginning? Huge populations will not rescue your theory.I know, I know... "a gene is to evolve". A goalpost is to shift. A simulation of natural selection is to explain abiogenesis. I forget--your largest population size--what fraction of the population of bacteria in your gut would that have been?
I like this discussion. Do you think that huge populations will overcome the lack of a selection process to evolve a gene from the beginning? Let’s say that you come up with a selection process to evolve a gene from the beginning. Do you think there was only one selection process acting at a time on your huge bacterial population?
Stick with your moving goal posts poems, mathematics is a losing topic for the theory of evolution. Better yet, embrace Cyborg’s cruft theory or kjkent1’s string cheese theory of evolution; at least we can have a laugh.The poem already won. Thank you for that. Now, since there is very little chance of you understanding evolution, I am trying to understand this God hypothesis of yours. Would you please answer my simple little question?
I must have missed your description of the selection process that would evolve a gene from the beginning in your poems. Do you mind posting those verses again?

[cyborg]

Oh, that’s right, you have shown that you don’t need a selection process to evolve a gene from the beginning, all you need is cruft.

Yes. But you are too stupid to understand this basic fact as you continually show.

[Mercutio]

Your view is mathematically impossible but you refuse to see it. If you can’t understand that there is no selection process that would evolve a gene from the beginning, how can you see anything else in this discussion?Please. Ev models natural selection; your question is one of abiogenesis. Your big argument misses the point entirely.

More to the point, you are continuing to evade. I asked a very simple question. It has been several posts now, and you have not answered it.
What has happened, are you finally seeing the goal posts? I cannot see how this sentence comments on what I said there. Do you have an answer to my question?
I like this discussion. Do you think that huge populations will overcome the lack of a selection process to evolve a gene from the beginning? You are conflating two questions here.
Let’s say that you come up with a selection process to evolve a gene from the beginning. Do you think there was only one selection process acting at a time on your huge bacterial population?No, not at all.
I must have missed your description of the selection process that would evolve a gene from the beginning in your poems. Do you mind posting those verses again?"From the beginning" is your strawman conflation of natural selection and abiogenesis. That is clearly in the poem.

I have answered your questions. Will you answer mine?

[kleinman]

Your view is mathematically impossible but you refuse to see it. If you can’t understand that there is no selection process that would evolve a gene from the beginning, how can you see anything else in this discussion?Please. Ev models natural selection; your question is one of abiogenesis. Your big argument misses the point entirely.
So let’s see if we can understand what you are saying. All genes initially formed during abiogenesis without the benefit of any selection process, then once these randomly formed genes assembled to form the first life forms, mutation and natural selection started to function. Joobz won’t even tell us how ribose forms in the primordial soup and you already have genes forming. Any of those genes include the DNA replicase system?
More to the point, you are continuing to evade. I asked a very simple question. It has been several posts now, and you have not answered it.
You have trouble understanding the obvious results from your own mathematics and you want me to explain to you how to differentiate between events caused by God and events caused by some lesser power than God but greater than our power. Well, let’s see if I can answer your question by example. The creation of the universe, that takes the power of God, the creation of life, that takes the power of God. All other power ultimately stems from God. So any power you have is something from God and you should consider carefully how you use it.
What has happened, are you finally seeing the goal posts?I cannot see how this sentence comments on what I said there. Do you have an answer to my question?
Can you describe the selection process that would evolve a gene de novo?
I like this discussion. Do you think that huge populations will overcome the lack of a selection process to evolve a gene from the beginning?You are conflating two questions here.
Do you think that all genes formed in the primordial soup?
Let’s say that you come up with a selection process to evolve a gene from the beginning. Do you think there was only one selection process acting at a time on your huge bacterial population?No, not at all.
What do you think of the failure of ev to evolve binding sites when you have only two conflicting selection processes?
I must have missed your description of the selection process that would evolve a gene from the beginning in your poems. Do you mind posting those verses again?"From the beginning" is your strawman conflation of natural selection and abiogenesis. That is clearly in the poem.
You evolutionist really need a new playbook, moving goalposts and strawmen. Why don’t you come up with some real arguments like a selection process that would evolve a gene from the beginning, or are you going to adopt cruftborg’s argument that genes just appear without selection. All you need is cruft.
I have answered your questions. Will you answer mine?
Which question? Are you talking about what is the function of a perfect creature in ev? It is to annoy evolutionists.

[Mercutio]

So let’s see if we can understand what you are saying.Oh, perhaps we had better not let you try this.
All genes initially formed during abiogenesis without the benefit of any selection process, then once these randomly formed genes assembled to form the first life forms, mutation and natural selection started to function. Joobz won’t even tell us how ribose forms in the primordial soup and you already have genes forming. Any of those genes include the DNA replicase system?Ok, so far I have not said any of this. I don't know who you are confusing me with, or if you just really have a tough time with this.
You have trouble understanding the obvious results from your own mathematics and you want me to explain to you how to differentiate between events caused by God and events caused by some lesser power than God but greater than our power.The blue "and" serves to separate your misunderstanding of what I have and have not said. After the blue "and", you finally mention my question. Let's see how you do with it.
Well, let’s see if I can answer your question by example. The creation of the universe, that takes the power of God, the creation of life, that takes the power of God. All other power ultimately stems from God. So any power you have is something from God and you should consider carefully how you use it.Well, you don't answer it, but we can see from what you do say that "omnipotence" is not a requirement for your answer. So unless you correct me later, I will assume that your answer is "no, you cannot tell the difference between your god and a powerful enough non-god." I will wait here for a bit before continuing, to see if you do agree with that.
Can you describe the selection process that would evolve a gene de novo?Not to your satisfaction. If you would like to provide adequate definitions of "gene" and "beginning", I could try.
Do you think that all genes formed in the primordial soup? No. Do you?
What do you think of the failure of ev to evolve binding sites when you have only two conflicting selection processes?I think that this is an oversimplification. What would you predict if two or more selection processes were involved that were not "conflicting"? Do you suggest that all selection pressures are mutually incompatible?
You evolutionist really need a new playbook, moving goalposts and strawmen. Why don’t you come up with some real arguments like a selection process that would evolve a gene from the beginning, or are you going to adopt cruftborg’s argument that genes just appear without selection. All you need is cruft.Or you need to understand more about selection by consequences.
Which question? Are you talking about what is the function of a perfect creature in ev? It is to annoy evolutionists.
No, you answered the question above (have you forgotten already?) Well, technically you did not answer it, but the answer you did give did not require your god to be omnipotent. Remember, I paraphrased your position as "no, you cannot tell the difference between your god and a powerful enough non-god." Rather than do as poor a job representing your position as you have mine, I await your confimation or denial that this is your position before pursuing that line any further.

[Mr. Scott]

...the theory of evolution ... is mathematically impossible.

I don't think you've presented a proof that the theory of evolution is mathematically impossible.

The Ev program was designed to simulate only a subset of known features of evolution, so it can't be of any use to prove evolution is impossible. It can be used to prove that evolution is impossible if evolution only uses the principles that Ev simulates. Ev does not simulate all the processes known to be involved in evolution, so it is not useful as a proof that evolution is impossible. It was designed to answer some questions about how life evolved, but it was never designed to answer all questions about how life evolved.

Please, Dr. Kleinman, present your mathematical proof that evolution is impossible.

[Kotatsu]

How about a valid question? What is the selection process that would evolve a gene from the beginning?

The process would likely involve any or all of several mechanisms which have been described to you previously (multiple times, even), as well as several as yet undiscovered mechanisms, and which we can sum up with the phrase "modifications of the genome".

I see you decided to ingore the rest of my post entirely. Was this because it was an "[example] of [a] rare beneficial mutation which in the real world provide[d] a creature with enormous advantage over its competitors?", or because you didn't understand it?

[cyborg]

a selection process that would evolve a gene from the beginning,

Already explained that the definition you provide precludes selection without foreknowledge of future mutations.

genes just appear without selection.

But you are too stupid to understand why this is necessarily so.

You are also too stupid to realise you are only annoying in a village idiot capacity at best.

[Paul C. Anagnostopoulos]

We have been talking about a supernatural event for months. The creation of life is a supernatural event. Why do you think you are having so much trouble describing this with natural laws? You can still measure the consequences of a supernatural event. This is done all the time with the sequencing of genomes and genes but your hypothesis of mutation and natural selection does not explain how the genome formed. You have two possibilities here, either life is the result of a supernatural event or you don’t know all the natural laws.
Complete evasion of my questions about supernatural laws duly noted. Also noted is your bizarre claim that sequencing genomes is measuring supernatural events.

By the way, both of the possibilities you list here are equivalent to "we don't know." However, the "supernatural event" excuse is a permanent abdication of scientific pursuit.


Why is that? You understand all the natural laws and are able to explain everything in terms of these laws? If that be the case, you have done a lousy job with ev.
Of course we don't understand all the natural laws, but what does that have to do with the logical problems associated with the concept of supernatural laws?

~~ Paul

[kleinman]

So let’s see if we can understand what you are saying.Oh, perhaps we had better not let you try this.
Why not?
All genes initially formed during abiogenesis without the benefit of any selection process, then once these randomly formed genes assembled to form the first life forms, mutation and natural selection started to function. Joobz won’t even tell us how ribose forms in the primordial soup and you already have genes forming. Any of those genes include the DNA replicase system? Ok, so far I have not said any of this. I don't know who you are confusing me with, or if you just really have a tough time with this.
When I asked you to describe the selection process that would evolve a gene from the beginning you said the following:
"From the beginning" is your strawman conflation of natural selection and abiogenesis. That is clearly in the poem.
So when did/do genes form?
You have trouble understanding the obvious results from your own mathematics and you want me to explain to you how to differentiate between events caused by God and events caused by some lesser power than God but greater than our power.The blue "and" serves to separate your misunderstanding of what I have and have not said. After the blue "and", you finally mention my question. Let's see how you do with it.
Well, let’s see if I can answer your question by example. The creation of the universe, that takes the power of God, the creation of life, that takes the power of God. All other power ultimately stems from God. So any power you have is something from God and you should consider carefully how you use it.Well, you don't answer it, but we can see from what you do say that "omnipotence" is not a requirement for your answer. So unless you correct me later, I will assume that your answer is "no, you cannot tell the difference between your god and a powerful enough non-god." I will wait here for a bit before continuing, to see if you do agree with that.
It is you who thinks that some non-god created life and the universe. The problem is your view is not supported by your own mathematics. Ev shows this.
Can you describe the selection process that would evolve a gene de novo?Not to your satisfaction. If you would like to provide adequate definitions of "gene" and "beginning", I could try.
Why don’t you try to describe selection so it would work in ev? This is an evolutionist model of random point mutation and natural selection. I’ll help you with the definitions for gene-the functional unit of heredity and beginning-the point of time or space at which anything starts.
Do you think that all genes formed in the primordial soup?No. Do you?
I don’t believe genes formed in the primordial soup, I don’t believe a primordial soup ever existed. The primordial soup is a concocted fantasy that evolutionists have come up with to fill a huge gap in your unscientific theory.

So if genes form on living things, do you want to describe the selection process that would evolve a gene from the beginning?
What do you think of the failure of ev to evolve binding sites when you have only two conflicting selection processes?I think that this is an oversimplification. What would you predict if two or more selection processes were involved that were not "conflicting"? Do you suggest that all selection pressures are mutually incompatible?
Certainly two conflicting selection processes is an oversimplification, in reality as Paul said previously there would be millions of selection processes in action. The only way you can get two or more selection processes not to conflict is that all mutations for a given creature would have to be beneficial, otherwise any good mutations a creature might have would be interfered with by harmful mutations. Selection processes by their very nature conflict. This is demonstrated mathematically in ev when selection to reduce errors in the non-binding site region dominates and prevents binding sites from evolving in the binding site region. This effect is also demonstrated in the real world when double or triple antimicrobials are used to treat infectious diseases and prevent the emergence of resistant microbes.
You evolutionist really need a new playbook, moving goalposts and strawmen. Why don’t you come up with some real arguments like a selection process that would evolve a gene from the beginning, or are you going to adopt cruftborg’s argument that genes just appear without selection. All you need is cruft.Or you need to understand more about selection by consequences.
Oh, I think I understand selection by consequences, ev is a very good model to learn from and I also have used multiple antimicrobials to treat infections.
Which question? Are you talking about what is the function of a perfect creature in ev? It is to annoy evolutionists.No, you answered the question above (have you forgotten already?) Well, technically you did not answer it, but the answer you did give did not require your god to be omnipotent. Remember, I paraphrased your position as "no, you cannot tell the difference between your god and a powerful enough non-god." Rather than do as poor a job representing your position as you have mine, I await your confimation or denial that this is your position before pursuing that line any further.
I understand your desire to abandon this discussion about the mathematics of ev. It is such a wonderful tool to reveal the irrationality of your theory of evolution. You have no selection process to evolve a gene from the beginning and multiple selection process conflict to prevent evolution. So complain about imagined moving goalposts and cry strawman because you have no science or mathematics to support your fundamental slogan for your theory.
...the theory of evolution ... is mathematically impossible.I don't think you've presented a proof that the theory of evolution is mathematically impossible.

The Ev program was designed to simulate only a subset of known features of evolution, so it can't be of any use to prove evolution is impossible. It can be used to prove that evolution is impossible if evolution only uses the principles that Ev simulates. Ev does not simulate all the processes known to be involved in evolution, so it is not useful as a proof that evolution is impossible. It was designed to answer some questions about how life evolved, but it was never designed to answer all questions about how life evolved.

Please, Dr. Kleinman, present your mathematical proof that evolution is impossible.
You are correct that ev only simulates a subset of the known forms of mutations (random point mutations), but ev does includes the concept of natural selection. Dr Schneider’s version of a selection process using a weight matrix to determine if mutations are beneficial or not is contrived. However, even with this contrived selection process, random point mutations and this contrived selection process is profoundly slow. In fact, under certain circumstances, the selection process actually prevents evolution of the binding sites. What makes the theory of evolution mathematically impossible despite the form of mutation mechanism is the lack of a selection process that can evolve a gene from the beginning. In addition, ev shows that selection processes can and do conflict preventing evolution. This effect is seen in the real world and is used to prevent the evolution of drug resistant organisms. Without a selection process that can evolve a gene from the beginning, you are left with random mutations (of any form) in order to generate the initial genes that living things require. The probabilities of doing this are infinitesimally small.
How about a valid question? What is the selection process that would evolve a gene from the beginning?The process would likely involve any or all of several mechanisms which have been described to you previously (multiple times, even), as well as several as yet undiscovered mechanisms, and which we can sum up with the phrase "modifications of the genome".
Kotatsu, what this thread is about is the mathematics of mutation and natural selection. “modifications of the genome” does not qualify as a mathematical description of the selection process that would evolve a gene from the beginning.
I see you decided to ingore the rest of my post entirely. Was this because it was an "[example] of [a] rare beneficial mutation which in the real world provide[d] a creature with enormous advantage over its competitors?", or because you didn't understand it?
Unless you can explain how carotene relates to the mathematics of mutation and natural selection, I have decided to ignore this portion of your post. Of course I know there are rare beneficial mutations that confer an enormous advantage for a creature over its competitors. I have given examples of this in my posts as well. What you can’t do is extrapolate these rare beneficial mutations to the transformation of reptiles to birds or humans and chimpanzees from a common ancestor. You have no way to account for the huge number of genetic changes required and more importantly, you have no selection process that can accomplish the task.
a selection process that would evolve a gene from the beginning,Already explained that the definition you provide precludes selection without foreknowledge of future mutations.
Cyborg, we are not talking about future mutations. We are talking about mutations that have already occurred and evolutionists contend have given rise to the life as we see today.
genes just appear without selection.But you are too stupid to understand why this is necessarily so.
I understand your hypothesis cruftborg.
We have been talking about a supernatural event for months. The creation of life is a supernatural event. Why do you think you are having so much trouble describing this with natural laws? You can still measure the consequences of a supernatural event. This is done all the time with the sequencing of genomes and genes but your hypothesis of mutation and natural selection does not explain how the genome formed. You have two possibilities here, either life is the result of a supernatural event or you don’t know all the natural laws. Complete evasion of my questions about supernatural laws duly noted. Also noted is your bizarre claim that sequencing genomes is measuring supernatural events.
Sequencing genomes is not measuring a supernatural event; it is measuring the consequence of a supernatural event. What I find strange is that you can look at all these complicated genes and think that they arose from random events. Oh yes, let’s not forget natural selection, you know that mechanism, the one which you can’t describe for evolving a gene from the beginning.
By the way, both of the possibilities you list here are equivalent to "we don't know." However, the "supernatural event" excuse is a permanent abdication of scientific pursuit.
What we do know is that your theory of evolution is mathematically impossible; your own computer model shows this. But don’t let that get in the way of your belief system. Just make sure you teach this to every naïve child you can and tell them that the theory of evolution is scientifically true.
Why is that? You understand all the natural laws and are able to explain everything in terms of these laws? If that be the case, you have done a lousy job with ev.Of course we don't understand all the natural laws, but what does that have to do with the logical problems associated with the concept of supernatural laws?
Your own mathematical model shows that the theory of evolution violates what is known about natural law. Natural selection can not and does not do what you propose. You don’t get the accumulation of microevolutionary steps to achieve a macroevolutionary change; your mathematical model shows this. Natural selection does not allow for this.

For someone who puts so much faith in science and mathematics, you abandon these things when they reveal something you don’t believe in.

[cyborg]

Cyborg, we are not talking about future mutations. We are talking about mutations that have already occurred and evolutionists contend have given rise to the life as we see today.

You do not even understand your own contentions.

You defined 'de novo' gene creation as a macroevolutionary event. However your contention is that microevolution cannot lead to this event. You contend this is the case because the macroevolutionary event has no selection mechanism. It has no selection mechanism because selecting for such NOW requires future knowledge. It however doesn't need a selection mechanism because microevolutionary events are sufficient to lead to the occurence of the event. Your problem is that you cannot demonstrate otherwise. You certainly cannot show it is impossible - because it is not. ev absolutely demonstrates that this is so. Your entire reasoning to the contrary is based on many flawed assumptions. You have been told these many times yet refuse to acknowledge them.

You cannot understand that evolution is not goal based - I posit this is due to stupidity. It cannot be ignorance because you have been told this enough times.

You want us to start from time t1, trace back the mutation events to t0 and then provide the selection mechanism that was aiming for the state at time t1 starting from t0 for all the states inbetween.

That you are asking for this shows the depth of how much you do not get what you are arguing against.

Since you have been told this enough times it cannot be ignorance. I posit stupidity.

I understand your hypothesis cruftborg.

If you understood it you wouldn't keep repeating the same incorrect nonsense repeatidly.

[Kotatsu]

Kotatsu, what this thread is about is the mathematics of mutation and natural selection. “modifications of the genome” does not qualify as a mathematical description of the selection process that would evolve a gene from the beginning.

But you didn't ask for a mathematical description of the selection process. You asked for a selection process, and I quickly summed up the process in a short phrase.

Unless you can explain how carotene relates to the mathematics of mutation and natural selection, I have decided to ignore this portion of your post. Of course I know there are rare beneficial mutations that confer an enormous advantage for a creature over its competitors. I have given examples of this in my posts as well.

Then why did you ask for them?

What you can’t do is extrapolate these rare beneficial mutations to the transformation of reptiles to birds or humans and chimpanzees from a common ancestor. You have no way to account for the huge number of genetic changes required and more importantly, you have no selection process that can accomplish the task.

How huge are actually the number of genetic changes needed to go to either a human or a chimp/bonobo from the last common ancestor?

[kleinman]

Cyborg, we are not talking about future mutations. We are talking about mutations that have already occurred and evolutionists contend have given rise to the life as we see today.You do not even understand your own contentions.
Cyborg, certainly I understand my contentions. This is an accounting problem. If the theory of evolution is true by mutation and natural selection, can you account for all the genetic information that we have today by this mechanism. Ev shows that you can’t when you take into account random point mutations alone. In addition, without a selection process to evolve genes from the beginning, no mutation mechanism will accomplish the task you propose. The theory of evolution has failed its audit.
You defined 'de novo' gene creation as a macroevolutionary event. However your contention is that microevolution cannot lead to this event. You contend this is the case because the macroevolutionary event has no selection mechanism. It has no selection mechanism because selecting for such NOW requires future knowledge. It however doesn't need a selection mechanism because microevolutionary events are sufficient to lead to the occurence of the event. Your problem is that you cannot demonstrate otherwise. You certainly cannot show it is impossible - because it is not. ev absolutely demonstrates that this is so. Your entire reasoning to the contrary is based on many flawed assumptions. You have been told these many times yet refuse to acknowledge them.
Cyborg, life exists, living things have genes, your theory of evolution fails to explain how these things came about. In fact, the mathematics of your theory says it is impossible.
You cannot understand that evolution is not goal based - I posit this is due to stupidity. It cannot be ignorance because you have been told this enough times.
Cyborg, your evolutionary mathematics when applied retrospectively to observations made today shows that theory of evolution by random mutations and natural selection is impossible.
You want us to start from time t1, trace back the mutation events to t0 and then provide the selection mechanism that was aiming for the state at time t1 starting from t0 for all the states inbetween.
Now you are getting it. There is no selection process to explain how you get from state 0 at t0 to state 1 at t1.
That you are asking for this shows the depth of how much you do not get what you are arguing against.
I know exactly what I am arguing against. I am arguing against a theory whose proponents can not explain the basic cause and effect mechanism yet think that their theory is scientific. People who believe this way are irrational.
Kotatsu, what this thread is about is the mathematics of mutation and natural selection. “modifications of the genome” does not qualify as a mathematical description of the selection process that would evolve a gene from the beginning.But you didn't ask for a mathematical description of the selection process. You asked for a selection process, and I quickly summed up the process in a short phrase.
The reason I like the ev computer model is that it removes the vague and ambiguous statements the evolutionists are required to make to argue for your theory. How do you use the phrase “modifications of the genome” in ev. What type of conditional statements to you use to determine what a beneficial or detrimental mutation is? Your summation is at best vague and ambiguous, it describes nothing.
Unless you can explain how carotene relates to the mathematics of mutation and natural selection, I have decided to ignore this portion of your post. Of course I know there are rare beneficial mutations that confer an enormous advantage for a creature over its competitors. I have given examples of this in my posts as well.Then why did you ask for them?
There are many examples of beneficial mutations which can be selected for and give advantage to a creature. Do you want to explain how microevolutionary processes like these can accumulate to transform reptiles to birds? What is the selection process that can do this.
What you can’t do is extrapolate these rare beneficial mutations to the transformation of reptiles to birds or humans and chimpanzees from a common ancestor. You have no way to account for the huge number of genetic changes required and more importantly, you have no selection process that can accomplish the task.How huge are actually the number of genetic changes needed to go to either a human or a chimp/bonobo from the last common ancestor?
There are at least 35,000,000 base differences between humans and chimps and that just in the portion of the genomes that are homologous. You have 500,000 generations to accomplish all these changes and remember multiple selection process compete against each other. If you read this thread carefully, you would see that this is not the first time this issue has been raised.

[cyborg]

This is an accounting problem.

No it is not.

If the theory of evolution is true by mutation and natural selection, can you account for all the genetic information that we have today by this mechanism. Ev shows that you can’t when you take into account random point mutations alone.

No it does not. You have told many times why ev shows no such thing.

In addition, without a selection process to evolve genes from the beginning, no mutation mechanism will accomplish the task you propose.

Wrong. You have been shown why repeatedly.

The theory of evolution has failed its audit.

No. You haved failed.

Cyborg, life exists, living things have genes, your theory of evolution fails to explain how these things came about.

Yes. That is a different theory.

This is what it means to move the goal-posts.

In fact, the mathematics of your theory says it is impossible.

There is no mathematics for abiogenetic events here. You are wrong again.

Cyborg, your evolutionary mathematics when applied retrospectively to observations made today shows that theory of evolution by random mutations and natural selection is impossible.

No it does not. Improbable is not, and never will be, impossible. Mathematics can actually show impossibilities. Since you have been told this repeatidly you are not ignorant of this. I posit stupidity.

Because you insist on viewing evolution as goal based you also fail to take into account all the other possible valid iterations. As such you are insisting the cards be dealt one way when many hands are valid.

You are far, far too stupid to possible comprehend this though. I expect you will simply say something witty like 'cardborg'. Oh how I will laugh at the village idiot.

Now you are getting it. There is no selection process to explain how you get from state 0 at t0 to state 1 at t1.

I understood this approximately a million years ago when this thread started.

You have still failed to explain how you are going to stop G increasing.

I know exactly what I am arguing against.

It is evident you have no clue.

I am arguing against a theory whose proponents can not explain the basic cause and effect mechanism yet think that their theory is scientific.

It is not our problem that you lack the ability to understand when people explain it to you.

People who believe this way are irrational.

No, people who believe people rise from the dead are irrational.

[kleinman]

This is an accounting problem.No it is not.
Now it become obvious why you don’t understand this discussion. Hard mathematical science consists of applying mathematical accounting principles to physical cause and effect natural laws. Ev is an example of this type of hard mathematical science and it is this hard mathematical science that reveals why the theory of evolution is mathematically impossible. If you think that the accounting rules are being applied improperly, show how the rules should be modified in ev and then you can make your case.
If the theory of evolution is true by mutation and natural selection, can you account for all the genetic information that we have today by this mechanism. Ev shows that you can’t when you take into account random point mutations alone.No it does not. You have told many times why ev shows no such thing.
You are correct here that there are no such selection mechanisms that can evolve genes from the beginning. So how do you account for the appearance of the hundreds of genes that are required for the simplest living things?
In addition, without a selection process to evolve genes from the beginning, no mutation mechanism will accomplish the task you propose.Wrong. You have been shown why repeatedly.
If the original genes did not come about by mutation and selection, how did they come about?
The theory of evolution has failed its audit.No. You haved failed.
I have the results form ev to support my case, what results do you have?
Cyborg, life exists, living things have genes, your theory of evolution fails to explain how these things came about.Yes. That is a different theory.

This is what it means to move the goal-posts.
Explain how the original genes came about whether they occur by abiogenesis or mutation and natural selection. How do you account for the origin of the original genes?
In fact, the mathematics of your theory says it is impossible.There is no mathematics for abiogenetic events here. You are wrong again.
How did the original genes arise in abiogenesis?
Cyborg, your evolutionary mathematics when applied retrospectively to observations made today shows that theory of evolution by random mutations and natural selection is impossible.No it does not. Improbable is not, and never will be, impossible. Mathematics can actually show impossibilities. Since you have been told this repeatidly you are not ignorant of this. I posit stupidity.
There is no selective process that can accomplish a macroevolutionary process. Without a selection process, your theory is mathematically impossible.
Because you insist on viewing evolution as goal based you also fail to take into account all the other possible valid iterations. As such you are insisting the cards be dealt one way when many hands are valid.
You see this as goal based, I see this as a matter of the accounting of the cause and effect principle of random mutations and natural selection. You can not accomplish what living things require by this mechanism. Mutations occur but there is no selection mechanism that can bring about macroevolution.
Now you are getting it. There is no selection process to explain how you get from state 0 at t0 to state 1 at t1.I understood this approximately a million years ago when this thread started.
Yet you still hold to the unscientific view that genes still arise without any selection process. What is the cause and effect mechanism that leads to the formation of genes?
You have still failed to explain how you are going to stop G increasing.
Would you explain how increasing G creates new genes?
I know exactly what I am arguing against.It is evident you have no clue.
Ask Paul and Dr Schneider if what I am saying about ev is accurate or not. I am going to keep this discussion in front of your face long enough so that you will understand it.
I am arguing against a theory whose proponents can not explain the basic cause and effect mechanism yet think that their theory is scientific.It is not our problem that you lack the ability to understand when people explain it to you.
Understand this Cyborg, if evolutionists had an explanation for the selection process that would evolve a gene from the beginning, this would have been coded into ev and this discussion put to rest. So, if I can’t understand your evolutionist explanation, neither does Paul or Dr Schneider.
People who believe this way are irrational.No, people who believe people rise from the dead are irrational.
I am not the one claiming this as a scientific proof; it is you evolutionists who claim your theory is scientific fact when your own mathematics refutes your theory.

[kjkent1]

No, people who believe people rise from the dead are irrational.This really does sum it up, very well.

The evolution argument depends on the observed proof of random mutations, single-point, gene shift, fusion, deletion, ERVs etc., and the mathematically demonstrable capability of information gain starting with a random system and using nothing but a mechanism which creates single point mutations and a selection mechanism which prefers nothing more than an accurate and complete set of chemical bindings over an inaccurate and incomplete set.

The theological argument depends on all of the observed and mathematical proofs of evolution being unable to overcome the very low mathematical probability of accomplishing the present observed state of evolutionary development of life within the available generational span -- and instead, prefers the mathematically IMPOSSIBLE probability of the existence of God as the obvious answer.

In sum, the theist's position is:

1. Evolution is observed, but mathematically unlikely, therefore "Evolution did it" is false.

2. God is unobserved, and mathematically impossible, therefore "God did it" is true.

The frivolity of the above argument is self-evident.

[Paul C. Anagnostopoulos]

Sequencing genomes is not measuring a supernatural event; it is measuring the consequence of a supernatural event. What I find strange is that you can look at all these complicated genes and think that they arose from random events. Oh yes, let’s not forget natural selection, you know that mechanism, the one which you can’t describe for evolving a gene from the beginning.
False dichotomy.

~~ Paul

[Paul C. Anagnostopoulos]

In sum, the theist's position is:

1. Evolution is observed, but mathematically unlikely, therefore "Evolution did it" is false.

2. God is unobserved, and mathematically impossible, therefore "God did it" is true.
Brilliant!

It's so much easier to attribute something to an unobservable, illogical, magical, no-holds-barred agent than it is to attribute it to a really, really complex natural process.

Science: hard. Magic conquers all.

~~ Paul

[cyborg]

Now it become obvious why you don’t understand this discussion. Hard mathematical science consists of applying mathematical accounting principles

No, a million times no. You are talking nonsense.

Maths is maths. Maths is the model. Maths is not the reality of the situtation. We use maths to understand and predict. Doing maths is not doing science.

'Accouting principles' is just meaningless jingoism. Say 'statistical analysis' if that is what you mean. This ain't business hour.

to physical cause and effect natural laws.

You want to talk physics, talk physics.

Ev is an example of this type of hard mathematical science and it is this hard mathematical science that reveals why the theory of evolution is mathematically impossible.

Except it does not - quite the opposite infact. It shows it is entirely mathematically possible.

What you are actually claiming is that ev demonstrates evolution did not happen in this reality because when, to paraphrase yourself, 'realistic' parameters are used things don't converge to a perfect creature.

You do not even understand your own contentions.

If you think that the accounting rules are being applied improperly, show how the rules should be modified in ev and then you can make your case.

My case is made. I need to modify nothing. Your analysis is simply wrong.

You are correct here that there are no such selection mechanisms that can evolve genes from the beginning.

Yes I am. But you still don't get the point.

So how do you account for the appearance of the hundreds of genes that are required for the simplest living things?

I do not. You are asking about abiogenesis.

You have moved the goalposts. The question is whether or not the macroevolutionary events you describes can occur from microevolution. As such we start from a working system, not an uninitialised one.

If the original genes did not come about by mutation and selection, how did they come about?

The tears of Odin.

Keep the goal posts where they were. You cannot make abiogenetic claims with ev.

I have the results form ev to support my case, what results do you have?

The fact that ev demonstrates evolution is possible.

That it also demonstrates that the system breaks down under certain parameters is irrelevant - you claim impossibility. Impossible means impossible, not "does not happen under these circumstances".

As I said, you do not even understand what you are contending. I suggest you look up the meaning of the word 'impossible'.

How do you account for the origin of the original genes?

I don't.

Keep those goal posts where they were.

How did the original genes arise in abiogenesis?

The tears of Odin.

Keep the goal posts where they were.

There is no selective process that can accomplish a macroevolutionary process.

Yes there is. There is no selection mechanism, but there is a selective process. That selective process is the same one that causes microevolution - you know, that bit that you accept but want to insist cannot lead to macroevolution.

Without a selection process, your theory is mathematically impossible.

No. The claim is that microevolutionary events preclude macroevolution. I have trivially demonstrated that this is mathematically possible.

Buy a dictionary.

You see this as goal based,

YOU see this as goal based.

I see this as a matter of the accounting

This is not a business forum.

You can not accomplish what living things require by this mechanism.

What do living things require?

Mutations occur but there is no selection mechanism that can bring about macroevolution.

Yes there is. It is the selection mechanism that allows microevolution. There is no selection mechanism that can aim for macroevolution.

Of course you do not understand what this means. This is because you are stupid.

Yet you still hold to the unscientific view that genes still arise without any selection process.

No. You hold the unmathematical view that genes won't arise without any selection process.

What is the cause and effect mechanism that leads to the formation of genes?

Mutation + time -> increasing genetic sequences.

Would you explain how increasing G creates new genes?

Again? Would there be any point in doing so? You don't seem to understand the simplest of concepts.

Ask Paul and Dr Schneider if what I am saying about ev is accurate or not.

Paul and Dr Schneider is what he is saying about ev is accurate or not?

I am going to keep this discussion in front of your face long enough so that you will understand it.

Wow. The irony.

Understand this Cyborg, if evolutionists had an explanation for the selection process that would evolve a gene from the beginning, this would have been coded into ev and this discussion put to rest.

Understand this kleinman, genes are going to happen whether or not they are wanted. What is it about the basic premise that benefits to organisms are happy accidents don't you get? New genes are accidents of mutation.

So, if I can’t understand your evolutionist explanation, neither does Paul or Dr Schneider.

If he can't understand my reality-based explanation, do you Paul or Dr Scheider?

I am not the one claiming this as a scientific proof;

Yet you have already told me to fnid another reason not to believe in Jesus boy.

it is you evolutionists who claim your theory is scientific fact when your own mathematics refutes your theory.

No it doesn't.

[Mercutio]

When I asked you to describe the selection process that would evolve a gene from the beginning you said the following:Which I stand by. "Evolve a gene from the beginning" is your conflation of natural selection and abiogenesis.
So when did/do genes form?Then and now, of course; life is a continuous process. Incremental changes happen constantly, at a low level. "A gene" is our artificial category which encompasses quite a huge fuzzy set of things. When a particular gene "begins" is thus not a clear case (as the case of ring species makes abundantly clear). This is why you have been asked for your definition of both "gene" and "beginning". By reasonable definitions, you have been shown the evolution of "the gene for insulin" from something which did not produce insulin. If you have some other definition of "beginning", or of "gene", please provide and defend them.
It is you who thinks that some non-god created life and the universe. The problem is your view is not supported by your own mathematics. Ev shows this. Ev does not model abiogenesis; it is not supposed to. As you say below, ev does what it is supposed to do very well; that it does not model every aspect of natural selection is a function of its being...wait for it...a model.

More to the point, I understand that you think that a god created the universe and life. I am simply trying to understand why you believe this is so. Your own evidence thus far does not support the notion that you can even tell that your god-candidate is omnipotent. You chose that word, so I think it must be important. Suppose you have a being powerful enough to create life, but which cannot make a decent cup of espresso. Such an entity would fit your "evidence", but not be omnipotent. I see nothing in your answer that leads me to believe you are qualified to tell omnipotence from simple power. Given that, I am trying my best to see why you go all the way to "omnipotence", when all the evidence you have implies "powerful".

The gap between the power that you are able to witness (with your human sensory and perceptual systems) and "omnipotence" is far, far greater than the huge gap between your "large" population size and the population of bacteria in your gut. I understand that you are willing to believe in your omnipotent god; I just find it odd that you reject a much much smaller gap as being so improbable that you are willing to call it "impossible".
Why don’t you try to describe selection so it would work in ev? This is an evolutionist model of random point mutation and natural selection. I’ll help you with the definitions for gene-the functional unit of heredity and beginning-the point of time or space at which anything starts.So the first change in function is enough? Just wanting to be sure here.
I don’t believe genes formed in the primordial soup, I don’t believe a primordial soup ever existed. The primordial soup is a concocted fantasy that evolutionists have come up with to fill a huge gap in your unscientific theory.And god is...?
So if genes form on living things, do you want to describe the selection process that would evolve a gene from the beginning?"On"? By your definition, any change in function is the "beginning" of a new gene, yes? By that definition, your question has been answered several times over in this thread.
Certainly two conflicting selection processes is an oversimplification, in reality as Paul said previously there would be millions of selection processes in action. The only way you can get two or more selection processes not to conflict is that all mutations for a given creature would have to be beneficial, otherwise any good mutations a creature might have would be interfered with by harmful mutations. Selection processes by their very nature conflict. This is demonstrated mathematically in ev when selection to reduce errors in the non-binding site region dominates and prevents binding sites from evolving in the binding site region. This effect is also demonstrated in the real world when double or triple antimicrobials are used to treat infectious diseases and prevent the emergence of resistant microbes."Beneficial" should be "beneficial, neutral, or simply better than the competition". And yes, combinations that are harmful, even if one mutation is good, will end up in the scrapheap. That is why it is called "selection" rather than "design". And in the real world, we are very worried because we are down to our last few antibiotics. Microbes have died off in unfathomable numbers, and yet there is concern about overuse of antibiotics in cattle because we want to reserve the remaining effective antibiotics for humans. Why? Because even with the selection pressure of triple antibiotics, with a large enough population (and the cattle industry provides this) there will be resistant strains. Or do you have no fear of this?
Oh, I think I understand selection by consequences, ev is a very good model to learn from and I also have used multiple antimicrobials to treat infections.First, I note again that you admit that ev is a very good model at what it is intended to model. Secondly, have you heard of the new resistant strains of MRSA?
I understand your desire to abandon this discussion about the mathematics of ev. It is such a wonderful tool to reveal the irrationality of your theory of evolution. You have no selection process to evolve a gene from the beginning and multiple selection process conflict to prevent evolution. So complain about imagined moving goalposts and cry strawman because you have no science or mathematics to support your fundamental slogan for your theory.If the worst you can complain about ev is that it does not work for what it is not designed for, keep pounding that drum. Meanwhile, I note you do not deny that you cannot perceive omnipotence, nor do you provide any evidence of special abilities or evidence that would allow for same. The gap in your explanation is substantial; I can see why you are running from it rather than defending it.

[lupus_in_fabula]

In sum, the theist's position is:

1. Evolution is observed, but mathematically unlikely, therefore "Evolution did it" is false.

2. God is unobserved, and mathematically impossible, therefore "God did it" is true.

The frivolity of the above argument is self-evident.


Oooh nice… Pavlov’s dog had its response; mine was as follows (howl, howl):


The only possibility for an agnostic to acknowledge the existence of a traditional god-like force in the universe is when the universe becomes a closed system where everything is known; i.e. it is fully deterministic and all the determinants are known and understood. Only then, when everything is known in the scientific sense, and something would happen that defies every possible law in the universe, would/should the traditional “God” be a serious contender for the explanation.

Of course, we do not know or understand everything so we have to put “God-did-it” on hold during our journey towards knowing and understanding. Moreover, we would probability never even realize that we know everything if we in fact knew everything. Nevertheless, the deeper we go via scientific understanding the more clutter can be removed from current religious belief systems that seem to have hijacked the prerogative of explaining “God”. “God” might eventually show up, but probably not in the form any current religious dogma now proclaims. It might be as simple as: “God really is everything”, which would mean almost ‘nothing’ in a religious-systemic context, but ironically, ‘everything’ in a scientific context (albeit “God” then being redundant as a term).

Now, I know many religions already proclaim “God” to be everything, yet they seem to be preoccupied with infantile worship of that everything by a specific method… almost as if the method of worship is more important that “God” itself. Why proclaim that “God” is everything and then throw away the notion straight away; almost forbidding further examination of that everything? It just happens that science appears to be more reliable that bronze age scriptures when it comes to the particular.

Science or evolution theory is no threat to “God” (whatever that is); it’s a threat to infantile methodological dogma.

[kleinman]

Sequencing genomes is not measuring a supernatural event; it is measuring the consequence of a supernatural event. What I find strange is that you can look at all these complicated genes and think that they arose from random events. Oh yes, let’s not forget natural selection, you know that mechanism, the one which you can’t describe for evolving a gene from the beginning. False dichotomy.
You only have two possibilities, either the creation of life was a supernatural event or it can be explained by natural laws and you don’t know what these natural laws are. You have chosen the later alternative but the application of natural laws shows it could not have happened this way. I happen to believe that Dr Schneider basically has applied the natural laws appropriately. The results of Dr Schneider’s computer model show that the theory of evolution is impossible mathematically. No selection process, no theory of evolution.
In sum, the theist's position is:

1. Evolution is observed, but mathematically unlikely, therefore "Evolution did it" is false.

2. God is unobserved, and mathematically impossible, therefore "God did it" is true.Brilliant!

It's so much easier to attribute something to an unobservable, illogical, magical, no-holds-barred agent than it is to attribute it to a really, really complex natural process.

Science: hard. Magic conquers all.
Paul, in case the results of your own computer model slipped past you unnoticed, your own computer model shows that your theory of evolution is illogical and mathematically impossible. Regardless of my personal view of how life came to be, this has no bearing on the impossibility of your theory. Where is Myriad and Dr Schneider, the only other evolutionists who have run cases with ev, to refute the results of what ev has shown. Hard mathematical science shows that your theory of evolution is mathematically impossible.
Now it become obvious why you don’t understand this discussion. Hard mathematical science consists of applying mathematical accounting principlesNo, a million times no. You are talking nonsense.
You are talking like someone who has no experience in modern science.
Maths is maths. Maths is the model. Maths is not the reality of the situtation. We use maths to understand and predict. Doing maths is not doing science.
Of course we use math to understand and predict. This is what Dr Schneider has done with ev. What ev predicts is that the theory of evolution by random point mutation and natural selection is far too slow to explain the theory. The lack of a selection process explains that the theory is mathematically impossible.
'Accouting principles' is just meaningless jingoism. Say 'statistical analysis' if that is what you mean. This ain't business hour.
This is not statistical analysis. Ev is the accounting of random point mutations and natural selection. Ev models the rate at which information can be accumulated in a genome by this mechanism. This is not a statistical analysis, this is a bookkeeping problem. If you studied the model a bit, you would understand this.
to physical cause and effect natural laws.You want to talk physics, talk physics.
This is a discussion of the accounting of the physical laws of mutation and natural selection. What this mathematical accounting shows is that evolutionists have extrapolated this principle far beyond what actually happens.
Ev is an example of this type of hard mathematical science and it is this hard mathematical science that reveals why the theory of evolution is mathematically impossible.Except it does not - quite the opposite infact. It shows it is entirely mathematically possible.
I must have missed your post of the data from ev that supports your contention. Do you want to repost that data?
What you are actually claiming is that ev demonstrates evolution did not happen in this reality because when, to paraphrase yourself, 'realistic' parameters are used things don't converge to a perfect creature.
That’s a fairly accurate paraphrase but don’t stop there, include the fact that there are no selection processes that can evolve a gene from the beginning. The later point is the death blow to the theory of evolution. And if that was not enough, ev shows that conflicting selection processes interfere with evolution. This effect is observed in reality and is used in the practice of clinical medicine.
You do not even understand your own contentions.
Cyborg, you do not understand my contentions but I will be patient with you and until you do.
If you think that the accounting rules are being applied improperly, show how the rules should be modified in ev and then you can make your case.My case is made. I need to modify nothing. Your analysis is simply wrong.
I have the results from ev to support my case. This is a peer reviewed and published model of random point mutations and natural selection written by the head of computational molecular biology at the National Cancer Institute. What mathematical data have you presented that supports your case?
You are correct here that there are no such selection mechanisms that can evolve genes from the beginning.Yes I am. But you still don't get the point.
I get your point, genes came about without a selection process.
So how do you account for the appearance of the hundreds of genes that are required for the simplest living things?I do not. You are asking about abiogenesis.
Are you talking about the abiogenesis that evolutionists say occurred in the nonexistent primordial soup?
You have moved the goalposts. The question is whether or not the macroevolutionary events you describes can occur from microevolution. As such we start from a working system, not an uninitialised one.
Cyborg, you are still looking for the ballpark, how would you know if the goalposts have been moved.
If the original genes did not come about by mutation and selection, how did they come about?The tears of Odin.
I think Odin has some cruft on his eyelids. I think he needs some eye drops.
Keep the goal posts where they were. You cannot make abiogenetic claims with ev.
Did all genes arise by abiogenesis?
I have the results form ev to support my case, what results do you have?The fact that ev demonstrates evolution is possible.
Did you post that data from ev that shows this?
That it also demonstrates that the system breaks down under certain parameters is irrelevant - you claim impossibility. Impossible means impossible, not "does not happen under these circumstances".
Just because those parameters are the realistic ones that show that the system breaks down, don’t let that interfere with your belief system.
As I said, you do not even understand what you are contending. I suggest you look up the meaning of the word 'impossible'.
Without a selection process to evolve a gene from the beginning, abiogenesis and the theory of evolution is impossible.
How do you account for the origin of the original genes?I don't.

Keep those goal posts where they were.
That’s smart; avoid the question that gives the death blow to the theory of evolution. Since neither you nor any other evolutionist has the answer to this question, it doesn’t matter where the goalposts are.
There is no selective process that can accomplish a macroevolutionary process.Yes there is. There is no selection mechanism, but there is a selective process. That selective process is the same one that causes microevolution - you know, that bit that you accept but want to insist cannot lead to macroevolution.
Fair enough, describe the process and put it into ev and show us how it happens.
Without a selection process, your theory is mathematically impossible.No. The claim is that microevolutionary events preclude macroevolution. I have trivially demonstrated that this is mathematically possible.
Slogans don’t cut it on this thread, you have to produce the data.
I see this as a matter of the accountingThis is not a business forum.
Sure it is, just don’t buy any stock in the theory of evolution.
You can not accomplish what living things require by this mechanism.What do living things require?
At a minimum, living things require hundreds of genes to carry on the chemistry of metabolism and reproduction. Among those genes are the genes for the DNA replicase system. Sound irreducibly complex, doesn’t it.
Mutations occur but there is no selection mechanism that can bring about macroevolution.Yes there is. It is the selection mechanism that allows microevolution. There is no selection mechanism that can aim for macroevolution.
Cyborg, I believe you are correct here. So do you want to show us how a series of microevolutionary events can lead to a macroevolutionary change?
Yet you still hold to the unscientific view that genes still arise without any selection process.No. You hold the unmathematical view that genes won't arise without any selection process.
Oh no! There is a mathematical view why genes won’t arise without a selection process.
What is the cause and effect mechanism that leads to the formation of genes?Mutation + time -> increasing genetic sequences.
Paul, Dr Schneider, look! Cyborg has solved your problem.
Would you explain how increasing G creates new genes?Again? Would there be any point in doing so? You don't seem to understand the simplest of concepts.
Come on. I’ll try my hardest. G wiz.
Ask Paul and Dr Schneider if what I am saying about ev is accurate or not.Paul and Dr Schneider is what he is saying about ev is accurate or not?
Well Paul, there’s your question. Maybe Dr Schneider is willing to answer as well. Oh, I forgot, Dr Schneider has moved on after more than 20 years work on this model.
I am going to keep this discussion in front of your face long enough so that you will understand it.Wow. The irony.
Well, maybe I’m wrong about this, you may be so mathematically challenged that you never understand ev.
Understand this Cyborg, if evolutionists had an explanation for the selection process that would evolve a gene from the beginning, this would have been coded into ev and this discussion put to rest.Understand this kleinman, genes are going to happen whether or not they are wanted. What is it about the basic premise that benefits to organisms are happy accidents don't you get? New genes are accidents of mutation.
What you still don’t understand is that ev shows that the accidents of mutation are far too slow to explain the theory of evolution.
So, if I can’t understand your evolutionist explanation, neither does Paul or Dr Schneider.If he can't understand my reality-based explanation, do you Paul or Dr Scheider?
There you go Paul, are you going to answer Cyborg’s question? Why don’t you put Cyborg’s suggestion into ev and show how the theory of evolution works.
it is you evolutionists who claim your theory is scientific fact when your own mathematics refutes your theory.No it doesn't.
I’ve posted the data from ev that supports my contention, what data have you posted to support your contention.
When I asked you to describe the selection process that would evolve a gene from the beginning you said the following:Which I stand by. "Evolve a gene from the beginning" is your conflation of natural selection and abiogenesis.
Quit hiding from this question. Genes had to arise somehow. How did the first genes arise?
So when did/do genes form? Then and now, of course; life is a continuous process. Incremental changes happen constantly, at a low level. "A gene" is our artificial category which encompasses quite a huge fuzzy set of things. When a particular gene "begins" is thus not a clear case (as the case of ring species makes abundantly clear). This is why you have been asked for your definition of both "gene" and "beginning". By reasonable definitions, you have been shown the evolution of "the gene for insulin" from something which did not produce insulin. If you have some other definition of "beginning", or of "gene", please provide and defend them.
Why Mercutio, you are moving the goalposts for the definition of a gene. You think this amorphous, vague evolutionist jargon you are giving here is convincing? What is the selection process that takes the incremental changes from a gene that does not produce insulin to a gene that produces insulin?
It is you who thinks that some non-god created life and the universe. The problem is your view is not supported by your own mathematics. Ev shows this.Ev does not model abiogenesis; it is not supposed to. As you say below, ev does what it is supposed to do very well; that it does not model every aspect of natural selection is a function of its being...wait for it...a model.
What ev models is random point mutation and natural selection. Are you going to join Cyborg and say that the original genes arose in the nonexistent primordial soup without selection?
Why don’t you try to describe selection so it would work in ev? This is an evolutionist model of random point mutation and natural selection. I’ll help you with the definitions for gene-the functional unit of heredity and beginning-the point of time or space at which anything starts.So the first change in function is enough? Just wanting to be sure here.
Why Mercutio, I gave you the definitions you requested then you don’t answer the question. Tsk, tsk, how unfair. Let me speculate a bit here, you don’t have the answer. Let me speculate a bit more here, no evolutionist has the answer.
So if genes form on living things, do you want to describe the selection process that would evolve a gene from the beginning?"On"? By your definition, any change in function is the "beginning" of a new gene, yes? By that definition, your question has been answered several times over in this thread.
Really? Why don’t you repost those answers? Let’s clarify something, there is no selection until a sequence of bases has function. I repost the argument why there is no selection process that evolves a gene from the beginning.

A gene is to evolve. The first base in the sequence for the gene is laid down on the genome. One base codes for nothing so there is nothing for natural selection to act upon. A second base added by random chance is laid down in the sequence. Still nothing to code for, natural selection can not act on this sequence. A third base in the sequence is laid down. You now have enough bases to form a codon for a single amino acid. A single amino acid has no functional use so there is still nothing for natural selection to act upon. So bases must be added randomly until you have a long enough sequence of bases to produce a functional polypeptide and then natural selection can act. Adding bases randomly yield probabilities so infinitesimally small that evolution is mathematically impossible.
Certainly two conflicting selection processes is an oversimplification, in reality as Paul said previously there would be millions of selection processes in action. The only way you can get two or more selection processes not to conflict is that all mutations for a given creature would have to be beneficial, otherwise any good mutations a creature might have would be interfered with by harmful mutations. Selection processes by their very nature conflict. This is demonstrated mathematically in ev when selection to reduce errors in the non-binding site region dominates and prevents binding sites from evolving in the binding site region. This effect is also demonstrated in the real world when double or triple antimicrobials are used to treat infectious diseases and prevent the emergence of resistant microbes. "Beneficial" should be "beneficial, neutral, or simply better than the competition". And yes, combinations that are harmful, even if one mutation is good, will end up in the scrapheap. That is why it is called "selection" rather than "design". And in the real world, we are very worried because we are down to our last few antibiotics. Microbes have died off in unfathomable numbers, and yet there is concern about overuse of antibiotics in cattle because we want to reserve the remaining effective antibiotics for humans. Why? Because even with the selection pressure of triple antibiotics, with a large enough population (and the cattle industry provides this) there will be resistant strains. Or do you have no fear of this?
What still hasn’t registered with you is that ev shows that competing selection processes stop evolution. I have already suggested to Paul that in order to make ev more realistic, evolve two sets of binding sites simultaneously and see what happens to the generations for convergence. Paul already has a sense of what would happen and I doubt he would add this feature to ev. It would only make the theory of evolution appear more ridiculous.
Oh, I think I understand selection by consequences, ev is a very good model to learn from and I also have used multiple antimicrobials to treat infections.First, I note again that you admit that ev is a very good model at what it is intended to model. Secondly, have you heard of the new resistant strains of MRSA?
I think that ev is as Paul’s latest evaluation of ev is a stylized model of random point mutations and natural selection. Resistant strains of MRSA have been around for more than 20 years. Many of these strains are sensitive to sulfa drugs and tetracycline class drugs as well as Vancomycin and gentamicin. Use of multiple drug regimes can reduce the emergence of multiple drug resistant strains. Applying multiple selective pressures to infectious agents reduces the likelihood of evolving drug resistant strains. Using single agents greatly increases the likelihood of evolving drug resistant strains. This same strategy is used with treatment of HIV where triple drug therapy is now standard of care.
I understand your desire to abandon this discussion about the mathematics of ev. It is such a wonderful tool to reveal the irrationality of your theory of evolution. You have no selection process to evolve a gene from the beginning and multiple selection process conflict to prevent evolution. So complain about imagined moving goalposts and cry strawman because you have no science or mathematics to support your fundamental slogan for your theory. If the worst you can complain about ev is that it does not work for what it is not designed for, keep pounding that drum. Meanwhile, I note you do not deny that you cannot perceive omnipotence, nor do you provide any evidence of special abilities or evidence that would allow for same. The gap in your explanation is substantial; I can see why you are running from it rather than defending it.
I did exactly what ev was designed for. So don’t complain about the results. Here is what Dr Schneider intended for ev:
Variations of the program could be used to investigate how population size, genome length, number of sites, size of recognition regions, mutation rate, selective pressure, overlapping sites and other factors affect the evolution.
In the process of doing the parametric study that Dr Schneider suggested, two things became apparent about the selection process he used. The first is that his selection process is contrived and the second is that his competing selection process can prevent evolution of binding sites when errors in the non-binding site region dominate the selection process. The first problem with Dr Schneider’s selection process illustrates the fundamental flaw in the theory of evolution, which is that there is no selection process to evolve a gene from the beginning, the second problem that Dr Schneider’s selection process illustrates is that competing selection process stop the evolutionary process. Dr Schneider’s application of mathematics to the theory of evolution by random point mutations and natural selection shows why the theory is mathematically impossible.

[Mr. Scott]

It is you who thinks that some non-god created life and the universe. The problem is your view is not supported by your own mathematics. Ev shows this.

No, it's been clearly explained that Ev does not show this.

I understand your desire to abandon this discussion about the mathematics of ev. It is such a wonderful tool to reveal the irrationality of your theory of evolution.

There is no desire to abandon the discussion about the mathematics of Ev. You have not proven that Ev proves evolution to be mathematically impossible.

Indeed, by your reasoning, the lack of a computer model for god would prove god mathematically impossible.

What we do know is that your theory of evolution is mathematically impossible; your own computer model shows this.

No, it doesn't, because Ev does not model all characteristics of evolution.

Your own mathematical model shows that the theory of evolution violates what is known about natural law.

Your insistence on repeating this indicates you are woefully ignorant about modeling natural systems in computer programs. Why don't you pick up a few books on it from Amazon?

When "Computer Modeling of Natural Systems For Dummies" comes out I'll buy you a copy.

[cyborg]

Just because those parameters are the realistic ones that show that the system breaks down, don’t let that interfere with your belief system.

Impossible means IMPOSSIBLE ALWAYS.

I am done with you. You are a total moron.

On ignore you go.

[Mr. Scott]

I happen to believe that Dr Schneider basically has applied the natural laws appropriately. The results of Dr Schneider’s computer model show that the theory of evolution is impossible mathematically. No selection process, no theory of evolution.

Well, no one who actually understands computer models happens to agree with you.

Paul, in case the results of your own computer model slipped past you unnoticed, your own computer model shows that your theory of evolution is illogical and mathematically impossible.

No, it actually doesn't show that.

What you still don’t understand is that ev shows that the accidents of mutation are far too slow to explain the theory of evolution.

But this is false, because Ev doesn't model every facet of the evolutionary process.

Dr Schneider’s application of mathematics to the theory of evolution by random point mutations and natural selection shows why the theory is mathematically impossible.

Naw, I think you are mistaken about that. Ev was not designed to be that comprehensive a model of evolution.

[Mr. Scott]

Dr. Kleinman, you evaded my question. Where is your mathematical proof that evolution of species on this planet was impossible?

[kleinman]

It is you who thinks that some non-god created life and the universe. The problem is your view is not supported by your own mathematics. Ev shows this.No, it's been clearly explained that Ev does not show this.
Really? I’ve posted the results from hundreds of cases from ev that shows this. How many cases from ev have you posted?
I understand your desire to abandon this discussion about the mathematics of ev. It is such a wonderful tool to reveal the irrationality of your theory of evolution. There is no desire to abandon the discussion about the mathematics of Ev. You have not proven that Ev proves evolution to be mathematically impossible.
Read the thread Mr Scott. How many cases from ev have you posted?
Indeed, by your reasoning, the lack of a computer model for god would prove god mathematically impossible.
I’ve never reasoned like this. What we do have is a peer reviewed and published model of random point mutations and natural selection that shows that the theory of evolution is impossible by this mechanism. Further more, this model reveals the importance of a selection process in order for evolution to proceed. There is no selection process that can evolve a gene from the beginning. What I find interesting about this debate is that evolutionists would much rather talk about religion than the mathematics of your own theory. I guess you evolutionists don’t have much to say about your theory mathematically.
What we do know is that your theory of evolution is mathematically impossible; your own computer model shows this. No, it doesn't, because Ev does not model all characteristics of evolution.
What ev does not model is a selection process that can evolve a gene from the beginning. The reason is that no such selection process exists. Without such a selection process, your theory is mathematically impossible no matter what mutation mechanism you want to consider.
Your own mathematical model shows that the theory of evolution violates what is known about natural law. Your insistence on repeating this indicates you are woefully ignorant about modeling natural systems in computer programs. Why don't you pick up a few books on it from Amazon?
We have a mathematical model of random point mutations and natural selection that has been made available to us by the good programming skills of Paul. Why don’t you study this model and do some cases with it so you won’t speak out of ignorance of this model.
When "Computer Modeling of Natural Systems For Dummies" comes out I'll buy you a copy.
I don’t need to write this computer model. We already have Dr Schneider’s peer reviewed and published model. You have shown that your mind was already made up before you ever looked at this model. It is enough that other scientists and mathematicians who are not evolutionist dogmatists learn what Dr Schneider’s model really shows about the theory of evolution.
On ignore you go.
Kjkent1 said good bye pages ago. I will miss your cruft.

[kjkent1]

Paul:

I think I have found an interesting artifact contained within ev's published selection mechanism, assuming that your Java version operates using the same algorithms as the original. In the Java version, there are three variables with which to weight the various mutation errors/mistakes that ev makes for the purposes of selection. They are:

1. Missing bindings.
2. Spurious bindings within the binding-site region.
3. Spurious bindings outside the binding-site region.

Although the program allows for a weight between 0 - 100 for each variable, if we assume that the choices for each setting is either on or off (1 or 0), this yields only eight possible (binary) mistake settings.

Using the default settings for all of the other program settings, and then running the program through each one of the eight possible mistake settings, I find that only two settings permit any convergence toward a perfect creature (the other settings just wander around aimlessly forever). The working settings are:

1. Missed binding sites, and spurious bindings outside the binding-site region (1, 0, 1).
2. All three settings turned on (1, 1, 1).

Assuming that the ev selection method is a reasonable model of a possible evolutionary selection process, this proves that the type(s) of mistakes and their locations absolutely effects the speed at which evolution takes place.

This conclusion completely refutes kleinman's position that no possible selection mechanism exists which can possibly cause real-world evolution to occur, because it's clear that even with only the three random point mistakes allowed by ev, that the choice of those mistakes has a profound effect on ev's evolutionary abilities.

kleinman's argument has been that ev's selection mechanism demonstrates that conflicting selective processes will inhibit evolution. Changing these settings demonstrates the contrary, because by enabling only one of the three mistakes and disabling the other two, so that there can be no conflict, there is no convergence at all.

To be fair, however, I must include the other possibility: ev's default selection method is defective, and the defect is causing this observed behavior.

However, if ev's selection method is not defective, then my test demonstrates that if gene shifts, fusions, deletions, additions, were all modeled, one can assume that these different and more complex mistake mechanisms would have very different and perhaps very profound effects on the evolutionary process.

Either way, until the current selection method is confirmed as functioning correctly, results from ev may not be a reasonable measure of the possible outcomes for natural evolution.

[kleinman]

Assuming that the ev selection method is a reasonable model of a possible evolutionary selection process, this proves that the type(s) of mistakes and their locations absolutely effects the speed at which evolution takes place.
There you go, you are actually thinking about the mathematics of ev. I think if you want to challenge this issue of the selection process, you will need to model reality more closely. As I suggested a while back, instead of modeling a random genome and look for the evolution of binding sites as the source of errors, model an evolved genome with a portion set aside for the evolution of binding sites. Mutations to the non-binding site region would have to be evaluated as harmful or neutral and mutations to the binding site region as beneficial, neutral or harmful. Selection then is made based on these results.

Don’t forget, as you attempt to model the real situation more accurately, you will have competing selection processes. This could be simulated by evolving two or more sets of binding sites simultaneously as previously suggested.

Ultimately, you will still encounter the problem of evolving a gene from the beginning. There is no selection process that will select for a sequence that doesn’t exist or produce a functioning molecule.

I commend you for studying the mathematics of ev.
However, if ev's selection method is not defective, then my test demonstrates that if gene shifts, fusions, deletions, additions, were all modeled, one can assume that these different and more complex mistake mechanisms would have very different and perhaps very profound effects on the evolutionary process.
You can’t assume that frame shifts, and other more complex mutation mechanisms will speed up the evolutionary process. In fact it is probably more likely that frame shift mutations will slow the evolutionary process. What do you think happens to a functioning gene when there is a frame shift?
Either way, until the current selection method is confirmed as functioning correctly, results from ev may not be a reasonable measure of the possible outcomes for natural evolution.
As you compare Dr Schneider’s selection mechanism with the real situation, I think you will find that his mechanism gives over optimistic rates of convergence. How would you extend Dr Schneider’s concept to the evolution of a gene. There is no such selection mechanism. The insulin gene is 12,000 bases long. What kind of weight matrix can you use to simulate a partial match in this type of situation? Consider this, when would a gene like the insulin gene evolve? Would it evolve in the primordial soup? Probably not since insulin is a signaling hormone to signal cells to take up glucose and therefore only be useful in multi-cellular organisms.

I encourage you to study this model and the associated concepts in detail.

[Paul C. Anagnostopoulos]

You only have two possibilities, either the creation of life was a supernatural event or it can be explained by natural laws and you don’t know what these natural laws are. You have chosen the later alternative but the application of natural laws shows it could not have happened this way.
Still a false dichotomy. You are assuming life came about either by supernatural events or by evolution as currently explained. There might be another naturalistic explanation.

~~ Paul

[Paul C. Anagnostopoulos]

I think I have found an interesting artifact contained within ev's published selection mechanism, assuming that your Java version operates using the same algorithms as the original. In the Java version, there are three variables with which to weight the various mutation errors/mistakes that ev makes for the purposes of selection. They are:

1. Missing bindings.
2. Spurious bindings within the binding-site region.
3. Spurious bindings outside the binding-site region.
This feature exists only in the Java version. It was added as a result of a conversation with another creationist, who insisted that equal mistake points for all three situations was artificial.


Although the program allows for a weight between 0 - 100 for each variable, if we assume that the choices for each setting is either on or off (1 or 0), this yields only eight possible (binary) mistake settings.
The feature was intended to allow different mistake points for the three situations, not specifically to allow situations to be ignored.

So let's see what happens when evolving a perfect creature. The three parameters assign mistake points for the following situations:

1. Missed binding site
2. Spurious binding within the gene
3. Spurious binding outside the gene

0,0,0: immediate pause; always 0 mistakes
0,0,1: fast pause as soon as no spurious bindings outside gene
0,1,0: fast pause as soon as no spurious bindings within gene
0,1,1: fast pause as soon as no spurious bindings anywhere
1,0,0: almost immediate pause as soon as bindings everywhere
1,0,1: typical run; spurious bindings remain within gene
1,1,0: typical run; spurious bindings remain outside gene
1,1,1: standard run

So I'm not sure what you were seeing.

~~ Paul

[kleinman]

You only have two possibilities, either the creation of life was a supernatural event or it can be explained by natural laws and you don’t know what these natural laws are. You have chosen the later alternative but the application of natural laws shows it could not have happened this way.Still a false dichotomy. You are assuming life came about either by supernatural events or by evolution as currently explained. There might be another naturalistic explanation.
I’m not sure what other naturalistic explanation you are talking about, perhaps its panspermia. If panspermia is what you are talking about, you still had to have life arise in some manner on some other planet. If it was not panspermia that you are talking about, what other naturalistic explanation for the occurrence of life are you talking about since your own computer model makes the theory of evolution kaput?

[Paul C. Anagnostopoulos]

I’m not sure what other naturalistic explanation you are talking about, perhaps its panspermia. If panspermia is what you are talking about, you still had to have life arise in some manner on some other planet. If it was not panspermia that you are talking about, what other naturalistic explanation for the occurrence of life are you talking about since your own computer model makes the theory of evolution kaput?
I do not have another explanation in mind, but that does not alter the fact that you have a false dichotomy. You don't get to leap to God just because you don't like evolution.

~~ Paul

[kleinman]

I’m not sure what other naturalistic explanation you are talking about, perhaps its panspermia. If panspermia is what you are talking about, you still had to have life arise in some manner on some other planet. If it was not panspermia that you are talking about, what other naturalistic explanation for the occurrence of life are you talking about since your own computer model makes the theory of evolution kaput?I do not have another explanation in mind, but that does not alter the fact that you have a false dichotomy. You don't get to leap to God just because you don't like evolution.
It is not whether I like evolution or not, it is that evolution does not have a sound mathematical scientific basis. Your own computer model shows this. I don’t know how many times I have been required to offer an alternative explanation for life since I have shown using your computer model that the theory of evolution is mathematically impossible. Now that you understand the mathematical problems that your theory has, what other naturalistic explanation is available? Like the lack of a selection process to evolve a gene from the beginning, there is no other naturalistic explanation for the occurrence of life. The occurrence of life is a supernatural event and this is why you can’t give a mathematical scientific naturalistic explanation, but that doesn’t stop evolutionists from trying to impose your belief system on everyone.

[Mercutio]

I do not have another explanation in mind, but that does not alter the fact that you have a false dichotomy. You don't get to leap to God just because you don't like evolution.

~~ Paul

This is why I was trying to explore his evidence *for* a god; so far he cannot support the descriptor "omnipotent"; I doubt he will find any for omniscience, either.

[kleinman]

I do not have another explanation in mind, but that does not alter the fact that you have a false dichotomy. You don't get to leap to God just because you don't like evolution.This is why I was trying to explore his evidence *for* a god; so far he cannot support the descriptor "omnipotent"; I doubt he will find any for omniscience, either.
Descriptor for Mercutio for omnipotence=all powerful. Example of what someone who is omnipotent can do=create life. Example of failure of naturalistic explanation for life=theory of evolution. Of course God already knew this because He is omniscient.

[Mercutio]

Descriptor for Mercutio for omnipotence=all powerful. Example of what someone who is omnipotent can do=create life. Example of failure of naturalistic explanation for life=theory of evolution. Of course God already knew this because He is omniscient.

Oh, I have no problem with the definition of omnipotent. What I have asked you, though, is whether you (or any person) has the ability to differentiate, based on the evidence you have seen, between an omnipotent being and a very very powerful non-omnipotent one. Again, my trivial example is of an entity that can create life but cannot make a decent cup of espresso. Not omnipotent, yet still fits your example of what an omnipotent entity can do.

It is clear that you cannot differentiate between "sufficiently powerful to fool a human's perceptual systems" from omnipotence. Indeed, it is a trivial matter to demonstrate that there are any number of sufficiently powerful, non-omnipotent theoretical entities that the concept of having evidence for an omnipotent being is beyond human capability.

Simply being able to define omnipotence is not enough, not nearly. You need to be able to demonstrate that you, or any human, can tell omnipotence from non-omnipotence. As long as you have human sensory and perceptual abilities, you simply cannot.

[kleinman]

Descriptor for Mercutio for omnipotence=all powerful. Example of what someone who is omnipotent can do=create life. Example of failure of naturalistic explanation for life=theory of evolution. Of course God already knew this because He is omniscient.Oh, I have no problem with the definition of omnipotent. What I have asked you, though, is whether you (or any person) has the ability to differentiate, based on the evidence you have seen, between an omnipotent being and a very very powerful non-omnipotent one. Again, my trivial example is of an entity that can create life but cannot make a decent cup of espresso. Not omnipotent, yet still fits your example of what an omnipotent entity can do.
Not only have I given you a definition for an omnipotent being, I have given you an example of how to differentiate between that being and a very, very powerful non-omnipotent being.
It is clear that you cannot differentiate between "sufficiently powerful to fool a human's perceptual systems" from omnipotence. Indeed, it is a trivial matter to demonstrate that there are any number of sufficiently powerful, non-omnipotent theoretical entities that the concept of having evidence for an omnipotent being is beyond human capability.
You have been fooled into thinking that life has come to be as we see it now by random mutations and natural selection. You know that natural selection we are talking about. That’s the natural selection that can not evolve a gene from the beginning. So your perceptual systems have failed you with the theory of evolution, this has been shown to you mathematically using the ev computer model.
Simply being able to define omnipotence is not enough, not nearly. You need to be able to demonstrate that you, or any human, can tell omnipotence from non-omnipotence. As long as you have human sensory and perceptual abilities, you simply cannot.
When you get tired of looking at the supernatural event of the creation of life, you can look at the supernatural creation of the universe and wonder where the energy for the big bang came from.

[kjkent1]

This feature exists only in the Java version. It was added as a result of a conversation with another creationist, who insisted that equal mistake points for all three situations was artificial.


The feature was intended to allow different mistake points for the three situations, not specifically to allow situations to be ignored.

So let's see what happens when evolving a perfect creature. The three parameters assign mistake points for the following situations:

1. Missed binding site
2. Spurious binding within the gene
3. Spurious binding outside the gene

0,0,0: immediate pause; always 0 mistakes
0,0,1: fast pause as soon as no spurious bindings outside gene
0,1,0: fast pause as soon as no spurious bindings within gene
0,1,1: fast pause as soon as no spurious bindings anywhere
1,0,0: almost immediate pause as soon as bindings everywhere
1,0,1: typical run; spurious bindings remain within gene
1,1,0: typical run; spurious bindings remain outside gene
1,1,1: standard run

So I'm not sure what you were seeing.

~~ PaulMaybe I'm misunderstanding ev, but it seems to me that the only fair measure of whether any evolution is taking place is the convergence of Rseq to Rfreq. The point of ev is to demonstrate information gain, and that only happens where Rseq converges to Rfreq.

If you pause on a perfect creature, then there is no real qualitative selection occuring, unless the premise is that filling all the binding sites with random bindings or a lack of spurious bindings, by itself, creates a viable life form.

Assuming you agree with my premise, then set the program to only pause on convergence, not on a "perfect" creature, and you should see the same thing that I'm seeing.

If you don't agree, then please explain why, so we're all on the same page.

[Mercutio]

Not only have I given you a definition for an omnipotent being, I have given you an example of how to differentiate between that being and a very, very powerful non-omnipotent being.Gee, I must have missed it. The example you gave could have been performed by a non-omnipotent being. (My trivial counterexample shows that.) You have defined one, but in no way whatsoever have you shown that you have the ability to perceive one. Besides, the example that you gave is clearly not one you have witnessed yourself. "Creating life" happened long before your life got here. If Victor Frankenstein succeeds in doing it again, you may call him a god if you like, but I will wait to see if he can brew espresso.
You have been fooled into thinking that life has come to be as we see it now by random mutations and natural selection. You know that natural selection we are talking about. That’s the natural selection that can not evolve a gene from the beginning. So your perceptual systems have failed you with the theory of evolution, this has been shown to you mathematically using the ev computer model.I can see why you chose not to address what I actually said.

Gee, Kleinie, you have me all wrong! You have convinced me of the error of my ways; never more an evolutionist, I. Why, your devastating attack on ev as being incapable of modeling abiogenesis has proven beyond the shadow of a doubt that I was mistaken! Evolution is for idiots! Dolts! Fools with no understanding of math or logic!

Now, can we get on with the evidence *for* your god? Remember, what I said was "It is clear that you cannot differentiate "sufficiently powerful to fool a human's perceptual systems" from omnipotence. Indeed, it is a trivial matter to demonstrate that there are any number of sufficiently powerful, non-omnipotent theoretical entities that the concept of having evidence for an omnipotent being is beyond human capability."

That statement has absolutely nothing to do with natural selection, so there is no need to try to misdirect. Can you provide me with evidence that you *can* differentiate (in practice, not in definition) between omnipotence and anything less?
When you get tired of looking at the supernatural event of the creation of life, you can look at the supernatural creation of the universe and wonder where the energy for the big bang came from.
And you can tell me how you, a human, can differentiate between an entity powerful enough to create one big bang but not two, from an entity powerful enough to create one or two but not three, from an entity powerful enough to create one, two, or three but not four.... from an omnipotent entity. I am certain you can convince me that the scientists are wrong, but can you convince me that you are right?

[Paul C. Anagnostopoulos]

I doubt he will find any for omniscience, either.
Ooh, let's try! I want to know how something can be omniscient, have free will, and endow its creations with free will.

~~ Paul

[Paul C. Anagnostopoulos]

Maybe I'm misunderstanding ev, but it seems to me that the only fair measure of whether any evolution is taking place is the convergence of Rseq to Rfreq. The point of ev is to demonstrate information gain, and that only happens where Rseq converges to Rfreq.
But there is no selective pressure to reach Rfreq, only to evolve a perfect creature. The convergence of Rseq to Rfreq is simply a measure of the information gain during the evolution.

~~ Paul

[kleinman]

Not only have I given you a definition for an omnipotent being, I have given you an example of how to differentiate between that being and a very, very powerful non-omnipotent being.Gee, I must have missed it. The example you gave could have been performed by a non-omnipotent being. (My trivial counterexample shows that.) You have defined one, but in no way whatsoever have you shown that you have the ability to perceive one. Besides, the example that you gave is clearly not one you have witnessed yourself. "Creating life" happened long before your life got here. If Victor Frankenstein succeeds in doing it again, you may call him a god if you like, but I will wait to see if he can brew espresso.
I guess you did miss the examples I gave. Have your non-omnipotent being create life and the universe.
You have been fooled into thinking that life has come to be as we see it now by random mutations and natural selection. You know that natural selection we are talking about. That’s the natural selection that can not evolve a gene from the beginning. So your perceptual systems have failed you with the theory of evolution, this has been shown to you mathematically using the ev computer model.I can see why you chose not to address what I actually said.
I can see why you choose not to accept my response.
Gee, Kleinie, you have me all wrong! You have convinced me of the error of my ways; never more an evolutionist, I. Why, your devastating attack on ev as being incapable of modeling abiogenesis has proven beyond the shadow of a doubt that I was mistaken! Evolution is for idiots! Dolts! Fools with no understanding of math or logic!
Gee Murky, I mistakenly thought that you were discrediting the results from your own evolutionist written and peer reviewed computer model of random point mutations and natural selection. But now I understand that you would never discredit anything that disagrees with your belief system.
Now, can we get on with the evidence *for* your god? Remember, what I said was "It is clear that you cannot differentiate "sufficiently powerful to fool a human's perceptual systems" from omnipotence. Indeed, it is a trivial matter to demonstrate that there are any number of sufficiently powerful, non-omnipotent theoretical entities that the concept of having evidence for an omnipotent being is beyond human capability."
What is clear is that you cannot differentiate the creation of life and the universe as events that transcend natural scientific laws.
That statement has absolutely nothing to do with natural selection, so there is no need to try to misdirect. Can you provide me with evidence that you *can* differentiate (in practice, not in definition) between omnipotence and anything less?
Life and the universe, Murky.
When you get tired of looking at the supernatural event of the creation of life, you can look at the supernatural creation of the universe and wonder where the energy for the big bang came from. And you can tell me how you, a human, can differentiate between an entity powerful enough to create one big bang but not two, from an entity powerful enough to create one or two but not three, from an entity powerful enough to create one, two, or three but not four.... from an omnipotent entity. I am certain you can convince me that the scientists are wrong, but can you convince me that you are right?
You need to ask God those questions.
I doubt he will find any for omniscience, either.Ooh, let's try! I want to know how something can be omniscient, have free will, and endow its creations with free will.
Paul, you are confused about this. God can not and does not do things that are inconsistent with His nature. God did not create us with completely free wills.

[Pardalis]

I'm sorry to come to this thread so late, I never come to the religion subforum.

But I'd like to ask a few questions for creationists if you don't mind.

Why does humans have four limbs, a complete nervous and sensory system, a digestive track and are standing upwards if they are created in God's image?

Does God have all these things too? If so, why does he need them for?

Thanks.

(sorry if it's been adressed before)

ETA; I've just noticed this is not the religion subforum. Well, I don't post in the science forum either, but for totally different reasons. :D

[Mercutio]

I guess you did miss the examples I gave. Have your non-omnipotent being create life and the universe.

Ok, these posts are getting much too large. Let's stay simple, and come back to the other points if and when needed.

You are still answering a different question than the one I have asked. Let us suppose that you (you, yourself, personally) actually *could* witness an entity creating life and the universe. (Have you? Or have you merely inferred that it *must* have happened?) By what criteria could you be certain that there was not a more powerful entity that created this first one that you witnessed creating the universe? How do you know that this entity is not simply powerful enough to create life and the universe, but not powerful enough to do anything more than that, like the other entities on his block (who tease him mercilessly--sad, but true).

You were the one who specified omnipotence, not I. But now, it seems you are settling for the mere ability to create life and the universe. What is more, you are inferring this "creating entity" from the mere existence of life and the universe itself, which is of course begging the question. You have taught me to challenge these assumptions, and have given the example of how they fail in evolution. You must have something more than circular reasoning to support your god, mustn't you?

In response to your challenge (quoted above), there is every bit as much evidence of my non-omnipotent universe-and-life-creator as there is for your omnipotent one. Life and the universe are here, ergo something had to create them. My theory fits, without the added baggage of being more powerful than the evidence (life and the universe) can support. Occam says my entity is to be preferred over yours, unless you have additional evidence to bring to bear. Which, being human and confined to this life and this universe, you do not.

[kleinman]

Why does humans have four limbs, a complete nervous and sensory system, a digestive track and are standing upwards if they are created in God's image?

Does God have all these things too? If so, why does he need them for?
I think it was a manifestation of God’s goodness that we were created this way. I don’t believe that being created in God’s image means that we are exactly like God any more than a photograph is an exact image of what is photographed.

God does not need any of our physical attributes we have but did take on these things for other reasons.
I guess you did miss the examples I gave. Have your non-omnipotent being create life and the universe.You are still answering a different question than the one I have asked. Let us suppose that you (you, yourself, personally) actually *could* witness an entity creating life and the universe. (Have you? Or have you merely inferred that it *must* have happened?) By what criteria could you be certain that there was not a more powerful entity that created this first one that you witnessed creating the universe? How do you know that this entity is not simply powerful enough to create life and the universe, but not powerful enough to do anything more than that, like the other entities on his block (who tease him mercilessly--sad, but true).
Neither you nor I were there when life and the universe were formed so your supposition that God can’t do more than this has no logical or scientific basis. I don’t know what God’s limits are but I believe they are far greater than anything we can imagine.
In response to your challenge (quoted above), there is every bit as much evidence of my non-omnipotent universe-and-life-creator as there is for your omnipotent one. Life and the universe are here, ergo something had to create them. My theory fits, without the added baggage of being more powerful than the evidence (life and the universe) can support. Occam says my entity is to be preferred over yours, unless you have additional evidence to bring to bear. Which, being human and confined to this life and this universe, you do not.
I take it that your evidence of your non-omnipotent universe no longer includes ev computer model.

[Paul C. Anagnostopoulos]

Paul, you are confused about this. God can not and does not do things that are inconsistent with His nature. God did not create us with completely free wills.
If either God or humans have any free will whatsoever, then God cannot be omniscient. Either that, or, along the lines of Mercutio's point, God is really just kinda quasi-omniscient. How would we know, anyway?

~~ Paul

[kjkent1]

But there is no selective pressure to reach Rfreq, only to evolve a perfect creature. The convergence of Rseq to Rfreq is simply a measure of the information gain during the evolution.

~~ PaulAccording to Schneider's published NAR paper, "The purpose of this paper is to demonstrate that Rsequence can indeed evolve to match Rfrequency.12"

The notion of a "perfect creature" is found nowhere in the article. So, now I'm completely lost.

[Mercutio]

Neither you nor I were there when life and the universe were formed so your supposition that God can’t do more than this has no logical or scientific basis.Neither you nor I were there when life and the universe were formed so your supposition that God *can* do more than this has no logical or scientific basis. (Or even this much, actually. Since we were not there, we have no direct evidence that god was involved at all.)

ETA--I also did not posit that it was god that did the creating; you asked for a non-omnipotent entity in my example, and that was what I provided. It does not have to be god--just indistinguishable to us puny humans.
I don’t know what God’s limits are but I believe they are far greater than anything we can imagine.[/FONT]Thank you for your honesty. I assume, then, that "omnipotence" is no longer a necessary characteristic of your god. Would you agree that the same reasoning holds true for omniscience?

[kleinman]

Neither you nor I were there when life and the universe were formed so your supposition that God can’t do more than this has no logical or scientific basis.Neither you nor I were there when life and the universe were formed so your supposition that God *can* do more than this has no logical or scientific basis. (Or even this much, actually. Since we were not there, we have no direct evidence that god was involved at all.)
However, we do have direct evidence that the theory of evolution is mathematically impossible. That evidence is in the ev computer model. You know that model. It is the evolutionist written, peer reviewed and published computer simulation of random point mutation and natural selection.

[Pardalis]

I think it was a manifestation of God’s goodness that we were created this way. I don’t believe that being created in God’s image means that we are exactly like God any more than a photograph is an exact image of what is photographed.

God does not need any of our physical attributes we have but did take on these things for other reasons.


Why did he decide to create us in this particular format?

Why mammalian? Why not gelly fish, or bird? What is so good about this primate format?

[Mercutio]

However, we do have direct evidence that the theory of evolution is mathematically impossible. That evidence is in the ev computer model. You know that model. It is the evolutionist written, peer reviewed and published computer simulation of random point mutation and natural selection.Well, we have proof that a program not designed to model abiogenesis does not, in fact, model abiogenesis.

But that is not nearly enough--remember, you have already convinced me that evolution is wrong. Now we must prove that god is right. As Paul said, there may be many other possible explanations. Unless you can show that the only two possibilities are evolution and god (and we already know that at least two possibilities remain--some powerful entity and some omnipotent god), then disproving natural selection is only the first step. This is the science forum, after all--logic, mathematics, evidence! I am perfectly comfortable with "I don't know" as an answer until one acquires sufficient evidence.

[kleinman]

I think it was a manifestation of God’s goodness that we were created this way. I don’t believe that being created in God’s image means that we are exactly like God any more than a photograph is an exact image of what is photographed.

God does not need any of our physical attributes we have but did take on these things for other reasons.Why did he decide to create us in this particular format?

Why mammalian? Why not gelly fish, or bird? What is so good about this primate format?
I don’t know. God did not create us in primate format. We may have some superficial similarities to primates but the sequencing of the human and chimpanzee genomes is showing how different we really are from chimpanzees and any other primates for that matter. What I do know is that God does it right.
However, we do have direct evidence that the theory of evolution is mathematically impossible. That evidence is in the ev computer model. You know that model. It is the evolutionist written, peer reviewed and published computer simulation of random point mutation and natural selection.Well, we have proof that a program not designed to model abiogenesis does not, in fact, model abiogenesis.
Unless you take the position that all genes originated during abiogenesis, ev is a fine example of why there is no selection process to evolve a gene from the beginning.

Now I think it’s a good idea for you evolutionists to write a computer simulation of abiogenesis. I would love to see you make a systematic simulation of how life arose in this so-called primordial soup. That would be hilarious.
But that is not nearly enough--remember, you have already convinced me that evolution is wrong. Now we must prove that god is right. As Paul said, there may be many other possible explanations. Unless you can show that the only two possibilities are evolution and god (and we already know that at least two possibilities remain--some powerful entity and some omnipotent god), then disproving natural selection is only the first step. This is the science forum, after all--logic, mathematics, evidence! I am perfectly comfortable with "I don't know" as an answer until one acquires sufficient evidence.
There is more than enough evidence in the creation to prove God is right. But since I doubt your sincerity that you are convinced that evolution is wrong, I must content myself with showing you that your own mathematics proves your theory wrong. Paul can say that there are many other explanations for life and the universe, it just so happens that the explanation you believe in can be proved wrong mathematically.

[Pardalis]

What I do know is that God does it right.


Everytime I hit my ulnar nerve I'm saying: that's not right...

[Mr. Scott]

You know that natural selection we are talking about. That’s the natural selection that can not evolve a gene from the beginning. So your perceptual systems have failed you with the theory of evolution, this has been shown to you mathematically using the ev computer model

There is a great article on flower evolution in the June 2006 Natural History (pp 34 Origins of Floral Diversity) that quite clearly explains how a gene can evolve de novo: something you claim can't happen except by divine intervention.

It happens by duplication of an existing gene and then subsequent mutation until the duplicate endows an advantage to the organism and becomes a new gene.

I'll create an illustrative example:

We begin with a successfully reproducing flower. In a genetic accident, a gene becomes duplicated in the next generation (known to happen). This may be inconsequential at first, but when one of the duplicates mutations (e.g. by point mutation), one of four things can occur:

1) It does something harmful, and that plant fails to reproduce;
2) It makes no difference and the plant reproduces because it still has a good copy of the gene;
3) The modified duplicate causes a neutral change in the plant;
4) The modified duplicate causes an advantageous reproductive change.

#2 can happen repeatedly until #1, #3, or #4 can happen. When #1 happens there is little consequence: one plant, out of perhaps millions like it, just doesn't reproduce.

However, #2 and #3 can occur repeatedly without negative consequence until #4 occurs: an advantageous mutation to what then becomes a unique new gene.

Suppose that new gene causes each of the flower's pedals to split in two right down the middle. Our flower species already has a symbiotic bee which finds these pedals quite attractive. Now the bee suddenly sees a flower with twice the number of pedals, and it is doubly attracted to it over the unmutated flowers. In very little time, the bees vigorously pollinate the mutated flowers, and the flower's unmutated bretheren die off. They may die off so thoroughly that the origin of the new gene may be completely obscured as the new gene is perfected through further mutations.

This scenario could easily be applied to the flower's pigment composition, pattern, pedal shape, size, etc.

The problem with applying Ev to de novo gene creation is one that, I believe, all computer models suffer. We can model something with a number of pre-programmed "knobs" to adjust, say, a flower's pedal count, size, spacing, or intensity of pigmentation. However, a gene evolving de novo may require, in a simulation, the spontaneous creation of a "new knob." The last time I studied computer simulations, we knew of no way to implement a knob that, when turned, makes novel knobs form. It is easily shown that evolution, as in my illustrative example, comes up with new knobs.

This is just one instance, and I think a critical one, of how your use of Ev cannot prove what you think it proves: that evolution is mathematically impossible.

Dr. Kleinman, I await your refutation.

[Paul C. Anagnostopoulos]

According to Schneider's published NAR paper, "The purpose of this paper is to demonstrate that Rsequence can indeed evolve to match Rfrequency."

The notion of a "perfect creature" is found nowhere in the article. So, now I'm completely lost.
Yes, that was the purpose of Ev: To show that evolution results in information gain in the genome, and that the gain is predictable according to information theory. But the model has no selection pressure "make Rseq approach Rfreq." The selective pressure is "reduce the number of mistakes."

Schneider didn't use the term "perfect creature," but the notion is certainly there. From the abstract:

The simulation begins with zero information and, as in naturally occurring genetic systems, the information measured in the fully evolved binding sites is close to that needed to locate the sites in the genome. [emphasis mine]


~~ Paul

[Paul C. Anagnostopoulos]

The problem with applying Ev to de novo gene creation is one that, I believe, all computer models suffer. We can model something with a number of pre-programmed "knobs" to adjust, say, a flower's pedal count, size, spacing, or intensity of pigmentation. However, a gene evolving de novo may require in a simulation the creation of a "new knob." The last time I studied computer simulations, we knew of no way to implement a knob that, when turned, allowed new, novel knobs to form. It is easily shown that evolution, as in my illustrative example, comes up with new knobs.
Some of the simulations that use instruction sets to represent genes can evolve novel functions. What I haven't seen yet is a simulation at the level of chemistry, which could evolve entirely new chemical pathways.

~~ Paul

[kleinman]

What I do know is that God does it right.Everytime I hit my ulnar nerve I'm saying: that's not right...
That’s a very common misconception. What do you think life without pain would be like? Ask a diabetic with neuropathy and a gangrenous foot.
You know that natural selection we are talking about. That’s the natural selection that can not evolve a gene from the beginning. So your perceptual systems have failed you with the theory of evolution, this has been shown to you mathematically using the ev computer model There is a great article on flower evolution in the June 2006 Natural History (pp 34 Origins of Floral Diversity) that quite clearly explains how a gene can evolve de novo: something you claim can't happen except by divine intervention.

It happens by duplication of an existing gene and then subsequent mutation until the duplicate endows an advantage to the organism and becomes a new gene.
This is Delphi_ote’s argument from about a million pages ago in this thread.

My first question for you is how did you get the original gene? My second question is what is the selection process that transforms the copy of the gene to an entirely new function? Each mutation in the transformation must either be beneficial or at least neutral; otherwise that creature will be selected against. My third question is how do you get this transformation to occur when you have many competing selection processes occurring simultaneously?
The problem with applying Ev to de novo gene creation is one that, I believe, all computer models suffer. We can model something with a number of pre-programmed "knobs" to adjust, say, a flower's pedal count, size, spacing, or intensity of pigmentation. However, a gene evolving de novo may require, in a simulation, the spontaneous creation of a "new knob." The last time I studied computer simulations, we knew of no way to implement a knob that, when turned, makes novel knobs form. It is easily shown that evolution, as in my illustrative example, comes up with new knobs.
Your example does not simulate the evolution of a new knob. What your example is of the copying of a knob and then somehow modifying this copy to some new function.
This is just one instance, and I think a critical one, of how your use of Ev cannot prove what you think it proves: that evolution is mathematically impossible.
Your example could be coded into ev. You would still be faced with the same problem as previous. What is the selection process that evolved the original gene and what is the selection process that transforms the gene to a new function. The known examples of modifications of genes have only a very small number of mutations (microbial antibiotic resistance and sickle cell hemoglobin for example). There is no selection process that allows for large numbers of changes in bases to create new genes with new functions.
Dr. Kleinman, I await your refutation.
I hope I didn’t make you wait too long.

[kjkent1]

Yes, that was the purpose of Ev: To show that evolution results in information gain in the genome, and that the gain is predictable according to information theory. But the model has no selection pressure "make Rseq approach Rfreq." The selective pressure is "reduce the number of mistakes."

~~ PaulBut, if the program stumbles on a perfect creature before any information gain, then the creature is the product of a random accident, rather than "evolution" of the genome via RMNS. So, if we turn off a mistake/selective pressure, and the creature fails to generate any information gain, this means that the particular mistake/selective pressure is necessary to evolution. Whereas if we turn off a mistake/selective pressure and it has no effect on the information gain, then that mistake is irrelevant to evolution.

Bringing this back to my results (missed bindings, spurious inside, spurious outside):

0,0,0: no convergence -- some mistakes are required for evolution.
1,0,0: no convergence -- spurious bindings inside and/or outside are necessary to evolution.
0,1,0: no convergence -- missed bindings and/or spurious outside are necessary to evolution.
1,1,0: no convergence -- spurious bindings outside are necessary to evolution.
0,0,1: no convergence -- missed bindings and/or spurious inside are necessary to evolution.
1,0,1: convergence -- spurious bindings inside are unnecessary to evolution.
0,1,1: no convergence -- missed bindings are necessary to evolution.
1,1,1 convergence -- all mistakes are sufficient for evolution.

To summarize:

In order for convergence to occur, both missed binding sites and spurious bindings outside the binding site region must be enabled. If true (and not a program bug), then the questions are:

1. why are both of these mistakes simultaneously necessary to ev's evolutionary process? Why can't they work alone?

2. Why are spurious mistakes inside the binding site region irrelevant to ev's evolutionary process?

3. What other basic chemical mistakes can occur which are not modeled by ev, but which would effect its evolutionary process? If other errors could cause a dramatic performance improvement, then this would simultaneously explain both why ev is slow and how evolution occurs.

[kjkent1]

Dr. Kleinman:

Danial Tammet is a different sort of genius. He was born with congenital epilepsy. However if his "diseased" genes were to be reproduced, his successors would have a HUGE advantage over the rest of homo sapiens. I regard Mr. Tammet as a major evolutionary leap forward, assuming he produces offspring with his rather incredible intellectual powers. Those offspring would skew all standardized test curves right off the page.

Of course, it's possible that Tammet's beneficial genetic change will not be passed on, as Tammet is apparently homosexual. But, assuming that he does eventually have children, how would you evaluate Tammet and his offspring? Just a bunch of incredibly smart kids -- or something more?

See http://en.wikipedia.org/wiki/Daniel_Tammet (http://en.wikipedia.org/wiki/Daniel_Tammet).

[Mercutio]

Unless you take the position that all genes originated during abiogenesis, ev is a fine example of why there is no selection process to evolve a gene from the beginning.Oh, but there is, when "the beginning" is defined as a new function. The trouble is, whenever this happens you move "the beginning" back further, saying "Your example does not simulate the evolution of a new knob. What your example is of the copying of a knob and then somehow modifying this copy to some new function." But when I asked you to define "the beginning" and "gene", the definitions you gave me are answered by Mr. Scott's example. You then move the goalpost to "What is the selection process that evolved the original gene and what is the selection process that transforms the gene to a new function."

If you insist on moving the goalpost whenever a new gene is demonstrated, your end point must be abiogenesis. Using the definitions of "gene" and "beginning" that you gave me earlier, your question is already answered. Using "abiogenesis" as "the beginning" and "the modern version of a specific gene" as "gene", and you may be safe. I see, though, that I was right and that you have laid the groundwork for requiring the Big Bang explained in addition.
There is more than enough evidence in the creation to prove God is right. But since I doubt your sincerity that you are convinced that evolution is wrong, I must content myself with showing you that your own mathematics proves your theory wrong. Paul can say that there are many other explanations for life and the universe, it just so happens that the explanation you believe in can be proved wrong mathematically.I am absolutely serious that evolution by natural selection does not explain abiogenesis. I don't see how it could. Natural selection starts with a replicant, and abiogenesis results in one. It is impossible to have natural selection unless abiogenesis has already happened. Mind you, the instant you have a replicant, natural selection is viable.

I have seen some pretty neat attempts at explaining abiogenesis. One involves an omnipotent entity; others do not. Some are testable; at least one is not. I do not make any claim whatsoever about which is "the explanation [I] believe in"; the question is still out.

So please be assured that I am utterly serious that I do not believe that natural selection explains abiogenesis. Now, what is your evidence that god explains it? The existence of life is evidence of abiogenesis, but not of any particular explanation of it. You, though, claim that "[t]here is more than enough evidence in the creation to prove God is right." Wonderful. I look forward to seeing it.

[kleinman]

Danial Tammet is a different sort of genius. He was born with congenital epilepsy. However if his "diseased" genes were to be reproduced, his successors would have a HUGE advantage over the rest of homo sapiens. I regard Mr. Tammet as a major evolutionary leap forward, assuming he produces offspring with his rather incredible intellectual powers. Those offspring would skew all standardized test curves right off the page.
You evolutionists see everything in the world through your evolutionist lens. If this savant has such a selective advantage, his offspring should rapidly take over the population.
Unless you take the position that all genes originated during abiogenesis, ev is a fine example of why there is no selection process to evolve a gene from the beginning.Oh, but there is, when "the beginning" is defined as a new function. The trouble is, whenever this happens you move "the beginning" back further, saying "Your example does not simulate the evolution of a new knob. What your example is of the copying of a knob and then somehow modifying this copy to some new function." But when I asked you to define "the beginning" and "gene", the definitions you gave me are answered by Mr. Scott's example. You then move the goalpost to "What is the selection process that evolved the original gene and what is the selection process that transforms the gene to a new function."
You evolutionists can’t come up with a coherent argument so you retreat behind your moving goalposts complaint. The theory of evolution and the concept of abiogenesis are tightly intertwined. Without abiogenesis, you have no theory of evolution. You have no way of making the transition from the abiogenesis concept to the theory of evolution but both require selection processes to have any mathematical possibility of occurring. When do genes arise? Does it happen during abiogenesis and only during abiogenesis? Does gene formation happen both in abiogenesis and when life has arisen? Your concepts are so irrational and illogical, it is a wonder that anyone believes them to be true.
If you insist on moving the goalpost whenever a new gene is demonstrated, your end point must be abiogenesis. Using the definitions of "gene" and "beginning" that you gave me earlier, your question is already answered. Using "abiogenesis" as "the beginning" and "the modern version of a specific gene" as "gene", and you may be safe. I see, though, that I was right and that you have laid the groundwork for requiring the Big Bang explained in addition.
Do you think whining about moving goalposts somehow makes your arguments more convincing? Do you want to explain the difference between a gene produced during abiogenesis and a “modern version of a specific gene”. Were genes produced during abiogenesis reproduced using the DNA replicase system?
There is more than enough evidence in the creation to prove God is right. But since I doubt your sincerity that you are convinced that evolution is wrong, I must content myself with showing you that your own mathematics proves your theory wrong. Paul can say that there are many other explanations for life and the universe, it just so happens that the explanation you believe in can be proved wrong mathematically.I am absolutely serious that evolution by natural selection does not explain abiogenesis. I don't see how it could. Natural selection starts with a replicant, and abiogenesis results in one. It is impossible to have natural selection unless abiogenesis has already happened. Mind you, the instant you have a replicant, natural selection is viable.
Oh, I see, we are now back talking about self replicators. Care to describe these self replicators? Care to try to describe the primordial soup? If you are a subscriber to the RNA world hypothesis, care to describe how ribose came into being non-enzymatically? The only thing more unscientific than the theory of evolution is the concept of abiogenesis. The most difficult chemical reactions to be done in a laboratory, evolutionists think occurred in a puddle with sunlight driving the reaction. This is how low the field of biology has sunk. I wonder how long these ridiculous ideas will dominate the field of biology.
I have seen some pretty neat attempts at explaining abiogenesis. One involves an omnipotent entity; others do not. Some are testable; at least one is not. I do not make any claim whatsoever about which is "the explanation [i] believe in"; the question is still out.
The high point for the concept of abiogenesis occurred in the 1950’s with the Miller experiment. At least Miller showed that some amino acids could be formed non-enzymatically. Do you know of any experiment where ribose is formed non-enzymatically and then RNA bases were formed?
So please be assured that I am utterly serious that I do not believe that natural selection explains abiogenesis. Now, what is your evidence that god explains it? The existence of life is evidence of abiogenesis, but not of any particular explanation of it. You, though, claim that "[t]here is more than enough evidence in the creation to prove God is right." Wonderful. I look forward to seeing it.
Hey, I never said that I could prove to you scientifically the existence of God. It is you evolutionists who say you have the scientific explanation for life. Your scientific proof comes down to two slogans, “mutation and natural selection” and “abiogenesis”, two of the most illogical and irrational concepts to hit the field of science in all of history.

[kjkent1]

You evolutionists see everything in the world through your evolutionist lens. If this savant has such a selective advantage, his offspring should rapidly take over the population.So, is this your evaluation, or are you attempting to assert what you think my view is?

I know what my view is -- I was asking for your evaluation.

[kjkent1]

Hey, I never said that I could prove to you scientifically the existence of God. It is you evolutionists who say you have the scientific explanation for life. Your scientific proof comes down to two slogans, “mutation and natural selection” and “abiogenesis”, two of the most illogical and irrational concepts to hit the field of science in all of history.The concept of God is infinitely less rational.

Simultaneous observation of both the speed and location of a quantum particle is mathematically and scientifically impossible. One wonders how God is omniscient in view of this minor obsticle.

[kleinman]

Hey, I never said that I could prove to you scientifically the existence of God. It is you evolutionists who say you have the scientific explanation for life. Your scientific proof comes down to two slogans, “mutation and natural selection” and “abiogenesis”, two of the most illogical and irrational concepts to hit the field of science in all of history.The concept of God is infinitely less rational.

Simultaneous observation of both the speed and location of a quantum particle is mathematically and scientifically impossible. One wonders how God is omniscient in view of this minor obsticle.
Now if only the theory of evolution was mathematically possible, then you would have an argument to work with.

[Paul C. Anagnostopoulos]

But, if the program stumbles on a perfect creature before any information gain, then the creature is the product of a random accident, rather than "evolution" of the genome via RMNS. So, if we turn off a mistake/selective pressure, and the creature fails to generate any information gain, this means that the particular mistake/selective pressure is necessary to evolution. Whereas if we turn off a mistake/selective pressure and it has no effect on the information gain, then that mistake is irrelevant to evolution.
Correct. Just be careful that you don't assume the only choices are full information gain or no information gain.

I have the feeling we're talking past each other.


1,1,0: no convergence -- spurious bindings outside are necessary to evolution.
You ran it with random seed 0, which doesn't converge in 10,000 generations. Try it with seed 1: it converges in 621 generations, before the perfect creature even evolves.

There is great variance in the results depending on the random seed. And perfect binding can occur even before Rseq >= Rfreq.

~~ Paul

[kjkent1]

Now if only the theory of evolution was mathematically possible, then you would have an argument to work with.Oh, but I do. Quantum uncertainty proves the non-involvment of God in our universe, regardless if his existence or non-existence, because for God to allow quantum uncertainty, he must intentionally shield himself from the knowledge of the outcome of all events in our universe. Otherwise, there would be no uncertainty, or conversely, both science and math are fraudulent deceptions of God, because they do not function correctly. And, if the latter is the case, then your attempts to demonstrate that evolution is impossible is built on the foundation of the illusion that your calculations are correct, no matter how accurate they may appear.

Having proven that God is either not involved in the universe, or math/science is a fraud, there remains only two other theories for the existence of life:

(1) evolution
(2) anthropic principle

Either way, God is not the answer, no matter how badly you would like to believe it to be true.

[kleinman]

Now if only the theory of evolution was mathematically possible, then you would have an argument to work with.Oh, but I do. Quantum uncertainty proves the non-involvment of God in our universe, regardless if his existence or non-existence, because for God to allow quantum uncertainty, he must intentionally shield himself from the knowledge of the outcome of all events in our universe. Otherwise, there would be no uncertainty, or conversely, both science and math are fraudulent deceptions of God, because they do not function correctly. And, if the latter is the case, then your attempts to demonstrate that evolution is impossible is built on the foundation of the illusion that your calculations are correct, no matter how accurate they may appear.
Now if you only code this logic into ev.

[kjkent1]

Correct. Just be careful that you don't assume the only choices are full information gain or no information gain.

I have the feeling we're talking past each other.


You ran it with random seed 0, which doesn't converge in 10,000 generations. Try it with seed 1: it converges in 621 generations, before the perfect creature even evolves.

There is great variance in the results depending on the random seed. And perfect binding can occur even before Rseq >= Rfreq.

~~ PaulI'm a little concerned about the pseudo-random number generator. I know that the variance of outcomes for a particular random seed can be considerable, however, I ran the program using 1,1,0, first with a seed of 0, where it never converged after 1,000,000 generations, and then with 3, where it converged after 106,559. Assuming that the random generator is reasonably well-behaved, it doesn't seem possible to me that a variance of 621 to 1,000,000 is likely.

[kleinman]

Correct. Just be careful that you don't assume the only choices are full information gain or no information gain.

I have the feeling we're talking past each other.


You ran it with random seed 0, which doesn't converge in 10,000 generations. Try it with seed 1: it converges in 621 generations, before the perfect creature even evolves.

There is great variance in the results depending on the random seed. And perfect binding can occur even before Rseq >= Rfreq.I'm a little concerned about the pseudo-random number generator. I know that the variance of outcomes for a particular random seed can be considerable, however, I ran the program using 1,1,0, first with a seed of 0, where it never converged after 1,000,000 generations, and then with 3, where it converged after 106,559. Assuming that the random generator is reasonably well-behaved, it doesn't seem possible to me that a variance of 621 to 1,000,000 is likely.
You are not the first to consider this issue.
The following is taken from Dr Schneider’s web page at:
http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html)
2006 Jun 27. Alan Kleinman stated: Some people may start questioning the validity of ev based on the marked variations of the generations for Rs->Rf simply by changing the random seed to start the calculation. (http://www.evolutionisdead.com/forum/viewtopic.php?t=348&postdays=0&postorder=asc&start=60) Given that Evj is a stochastic process, we expect variation in the generation time. To investigate this, I ran Ev (the original Pascal program) 1000 times and got this distribution (http://www.ccrnp.ncifcrf.gov/~toms/papers/ev/generations/ex3/histog). Clearly it is not a Gaussian but it is a defined distribution. (The full analysis (http://www.ccrnp.ncifcrf.gov/~toms/papers/ev/generations/) is available.)

[kjkent1]

You are not the first to consider this issue.
The following is taken from Dr Schneider’s web page at:
http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html)
Schneider's frequency distribution shows a variance of ~29,000. No convergence at 1,000,000 is WAY outside any normalized distribution.

I wish Paul would create an option to use www.random.org, or some other source to create a string of undeniably random numbers, prior to an ev run. Then we would know for certain if results were an artifact of the pseudo-random number generator, or something in ev.

Results could still be repeatable, because once the program pulled a fixed string of random numbers, the program could store it in a file for a subsequent run under identical conditions.

I've seen this sort of pseudo-random number problem appear in certain C and Pascal compliers over the years. Sometimes pseudo-random is just not good enough. And, if this one is not, then it would mean that all results from ev are suspect, including yours, Alan.

[Mercutio]

You evolutionists can’t come up with a coherent argument so you retreat behind your moving goalposts complaint.Um... the goalpost moving happens only after your previous goalposts have been conquered. Don't complain about the "moving goalpost complaint"--specify the correct definitions the first time.
The theory of evolution and the concept of abiogenesis are tightly intertwined. Without abiogenesis, you have no theory of evolution. Um... Duh. True. But evolution by natural selection does not require any particular method of abiogenesis.
You have no way of making the transition from the abiogenesis concept to the theory of evolution but both require selection processes to have any mathematical possibility of occurring.Um...no. Abiogenesis requires (by some theories) polymerization (which does not require selection at all, but simple chemistry), then replicating polymers (not hundreds, but dozens of units long--these are not even close to the simplest bacteria yet), which most would not call "life" but which will compete... eventually you get to the equivalent of the simplest bacteria, but please do not suggest that the pre-replicant processes "require selection processes"; until they replicate, they cannot be subject to selection.
When do genes arise? Does it happen during abiogenesis and only during abiogenesis? No. Well, "no" by the definition of gene you gave a while ago. By the definition where you get to say "de novo" a lot, only one gene has ever arisen, and that defined abiogenesis. If you think that sounds ludicrous, I suggest you rethink your definitions of "gene" and "beginning". (I liked the ones you gave earlier, but it does not appear that you do.)
Does gene formation happen both in abiogenesis and when life has arisen? Your concepts are so irrational and illogical, it is a wonder that anyone believes them to be true.True. If it weren't for the evidence, I doubt anyone would. And as for irrational and illogical, how is that God hypothesis working out?
Do you think whining about moving goalposts somehow makes your arguments more convincing? Do you want to explain the difference between a gene produced during abiogenesis and a “modern version of a specific gene”.Sure. Modern genes have been built upon billions of years of previous genes. To suggest that the simplest current organisms are identical to the earliest replicants is disingenuous at best. There is absolutely no reason to suspect that our current simple life is as simple as it gets. But... if genes are defined functionally, and the function is replication, we can get much much simpler for our early genes.
Were genes produced during abiogenesis reproduced using the DNA replicase system?I doubt it very much, but I am not an expert. There is no requirement that they are.
Oh, I see, we are now back talking about self replicators. Care to describe these self replicators? Care to try to describe the primordial soup? If you are a subscriber to the RNA world hypothesis, care to describe how ribose came into being non-enzymatically? The only thing more unscientific than the theory of evolution is the concept of abiogenesis.I just needed to highlight this sentence, given your alternative theory.
The most difficult chemical reactions to be done in a laboratory, evolutionists think occurred in a puddle with sunlight driving the reaction. This is how low the field of biology has sunk. I wonder how long these ridiculous ideas will dominate the field of biology.The neat thing is, these theories are testable. Lots and lots of flasks. Speaking of which, could you estimate the difference in volume between all the flasks used in this research ... and (just for fun) the volume of tidal pools? (I know, there are many more places than tide pools where such reactions could take place, but I am on your side here...)
The high point for the concept of abiogenesis occurred in the 1950’s with the Miller experiment.Please, could you tell me the historic high point for the God hypothesis? I suggest that an honest accounting would place it considerably earlier than the Miller experiment. (I will take your 1950's estimate at face value, although whenever I look for sources, I have a really tough time finding anything prior to 1990; I admit, perhaps I am at a handicap, looking out of my field. It seems odd, though, that I would find only more recent sources...)
At least Miller showed that some amino acids could be formed non-enzymatically. Do you know of any experiment where ribose is formed non-enzymatically and then RNA bases were formed?I do not. Do you know that this is necessary for replication? Could you cite sources to support that if it is the case?
Hey, I never said that I could prove to you scientifically the existence of God.You did, though, say there was "more than enough evidence in the creation to prove God is right."
It is you evolutionists who say you have the scientific explanation for life. Well, the explanation for variation.
Your scientific proof comes down to two slogans, “mutation and natural selection” and “abiogenesis”, two of the most illogical and irrational concepts to hit the field of science in all of history.And exactly where does "Goddidit" fit in this parade of slogans?

"Mutation and natural selection" is a testable idea, and I am certain you are aware of the literature available to evaluate this hypothesis. "Abiogenesis", of course, includes a number of hypotheses, including your "god" hypothesis. Why you call it irrational is a bit of a puzzle--unless you think life always existed, then abiogenesis must have happened. (Do you think that your god created life at the same time everything else was created? I ask seriously.) It is the particular explanation of abiogenesis that is the bone of contention.

An unrelated question--have you, yourself, personally, subjected your own belief system to the type of scrutiny you are trying to apply to other people's beliefs? Could you describe this process? Feel free to open another thread to do so--I know it is not the main point here.

[kleinman]

You are not the first to consider this issue.
The following is taken from Dr Schneider’s web page at:
http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.htmlSchneider's frequency distribution shows a variance of ~29,000. No convergence at 1,000,000 is WAY outside any normalized distribution.

I wish Paul would create an option to use www.random.org, or some other source to create a string of undeniably random numbers, prior to an ev run. Then we would know for certain if results were an artifact of the pseudo-random number generator, or something in ev.

Results could still be repeatable, because once the program pulled a fixed string of random numbers, the program could store it in a file for a subsequent run under identical conditions.

I've seen this sort of pseudo-random number problem appear in certain C and Pascal compliers over the years. Sometimes pseudo-random is just not good enough. And, if this one is not, then it would mean that all results from ev are suspect, including yours, Alan.
The results from ev already are repeatable but do your analysis because we don’t need another issue for you to whine about. Do you think the random number generator will correct the issue that you don’t have a selection process to evolve a gene from the beginning? Perhaps the random number generator will correct the irrationality of the concept of abiogenesis.
You evolutionists can’t come up with a coherent argument so you retreat behind your moving goalposts complaint. Um... the goalpost moving happens only after your previous goalposts have been conquered. Don't complain about the "moving goalpost complaint"--specify the correct definitions the first time.
Mercutio, all the posts are out there to read, there are no moving goalposts.
The theory of evolution and the concept of abiogenesis are tightly intertwined. Without abiogenesis, you have no theory of evolution.Um... Duh. True. But evolution by natural selection does not require any particular method of abiogenesis.
There is no particular method of abiogenesis. Take a course in organic chemistry and you will understand why there is no abiogenesis. You can’t form ribose inorganically let alone RNA bases. Even if you could form the RNA bases, you can’t get the bases to link without enzymes. Even if you could get RNA bases to link without enzymes, you won’t get the sequences to form functional ribozymes and on and on… People who believe in abiogenesis and the theory of evolution have a form of hysteria.
Does gene formation happen both in abiogenesis and when life has arisen? Your concepts are so irrational and illogical, it is a wonder that anyone believes them to be true. True. If it weren't for the evidence, I doubt anyone would. And as for irrational and illogical, how is that God hypothesis working out?
Oh yes, we all see the evidence, the experiments with genes arising de novo, the test tubes with life arising abiogenically. How could such evidence be refuted?
Do you think whining about moving goalposts somehow makes your arguments more convincing? Do you want to explain the difference between a gene produced during abiogenesis and a “modern version of a specific gene”.Sure. Modern genes have been built upon billions of years of previous genes. To suggest that the simplest current organisms are identical to the earliest replicants is disingenuous at best. There is absolutely no reason to suspect that our current simple life is as simple as it gets. But... if genes are defined functionally, and the function is replication, we can get much much simpler for our early genes.
Really? Modern bacteria have totally different genes than the one celled creatures that arose out of the non-existent primordial soup? Save these stories for devout evolutionists and naïve school children. Your idea of evidence is concocted stories. What ev gives is hard mathematical science, so save your stories to tell around the camp fire at evolutionist summer camp.

[kjkent1]

The results from ev already are repeatable but do your analysis because we don’t need another issue for you to whine about. Do you think the random number generator will correct the issue that you don’t have a selection process to evolve a gene from the beginning? Perhaps the random number generator will correct the irrationality of the concept of abiogenesis.You have provided the answer for the gene from the beginning question. Ev selects for nothing more meaningful than accurate chemical bindings. The only thing required, according to Paul, is a transcription factor, which averages 6 - 12 bases in length. Evolving a transcription factor by random chance is thus a relatively trivial issue as there are a maximum of 16,777,216 combinations, and we know for a certainty that there are many possible transcription factor sequences, so the odds of a randomly produced TF is much lower than 1 in 17 million.

After the TF is produced at random, ev can select for the accurate bindings using its ordinary selection mechanism.

Having dispensed with your first insurmountable problem, we are faced with the second, i.e., your claim that ev is unreasonably slow, generationally speaking. And, here, frankly, I agree with you -- it's too slow. However, where we part is that I'm reasonably certain that the gene shifts and fusions which you claim would not produce faster evolutionary process, will do just that. And, while I admit that I can't prove it without completely reprogramming ev's mutation mechanism, the evidence of such "macro-evolutionary" events creating an enormous change in an organism is observed from examining the genomes of existing organisms.

Your counter, of course, is that most gene shifts and fusions produce "disease." My rebuttal is that no one with a beneficial gene shift or fusion would ever present to a physician for treatment, because there would be nothing to treat.

This leads us to the final question: where do these rare and remarkable positive changes come from -- because they are clearly far less prevalent than than an ordinary point mutation.

And, the answer is random accident, of course. Are these random accidents caused by God, or by quantum uncertainty?

Well, that, my friend, is and always will be determined solely by faith. Faith that the universe is controlled by an omniscient and omnipresent creator, who cares for His creations and helps them toward their ultimate reward -- or, faith that uncertainty is all that is required, and that we humans have a unique opportunity to chart our own future, without suffering eternal bondage to a judgmental master.

Some have chosen the former -- some, the latter. And, that's what makes a horse race.

[Mr. Scott]

My first question for you is how did you get the original gene?

You mean gene #1, the first gene of all of life on Earth? We don't know that yet. The evidence has been obscured by the genes that it evolved into. But we're working on it.

My second question is what is the selection process that transforms the copy of the gene to an entirely new function?

I explained that quite clearly. It mutates until it performs a new function.

Each mutation in the transformation must either be beneficial or at least neutral; otherwise that creature will be selected against.

Exactly what I said. Read my post again.

My third question is how do you get this transformation to occur when you have many competing selection processes occurring simultaneously?

I don't see the problem with this. In fact, many competing mutation/selection processes makes evolution go even faster because parallel changes are happening within individual organisms. Thanks for pointing this out.

Your example does not simulate the evolution of a new knob. What your example is of the copying of a knob and then somehow modifying this copy to some new function.

Well, sure, you duplicate a knob, then modify its function until it performs a function that no previous knob performed. That's the definition of a new knob. Like a "pedal split" function -- a type de novo knob transformation that a program like Ev may not implement.

Your example could be coded into ev.

Well, since it wasn't, and you depend on Ev to show evolution is mathematically impossible, then you've refuted your own conclusion.

What is the selection process that evolved the original gene and what is the selection process that transforms the gene to a new function.

The "original gene" in that context I think you mean the gene that duplicated and then its duplicate mutated. If so, the "original gene" may very well have come about the same way as the new gene. Go backwards gene by gene to the beginning of life and you will find the first gene, perhaps an RNA gene that accidentally doubled-up, that assembled more generations previously out of other pieces of replicating molecules that were mutated and selected for. We don't know how all this started, but that doesn't prove god did it. Not having an answer to any question should never be construed as proof of the intervention of a divine entity.

[Mr. Scott]

...evolution does not have a sound mathematical scientific basis. Your own computer model shows this. I don’t know how many times I have been required to offer an alternative explanation for life since I have shown using your computer model that the theory of evolution is mathematically impossible.

You know, Dr. Kleinman, I don't think you are correct about this. Ev has never shown that evolution is mathematically impossible, because Ev is not a complete simulation of all processes involved.

The theory of evolution does have a mountain of observational data to support it, like the fossil record and the tracing of genetic changes. A huge mountain. An absolutely tremendous, overwhelming mass of consistent evidence. That it has yet to be fully explained to the first or last molecule or simulated in today's computers should not be construed as proof life came about through divine intervention. There is an enormous amount of consistent evidence that evolution is correct -- an absolutely vast amount.

There is no evidence at all for the god hypothesis. None whatsoever.

[Dr Adequate]

So he hasn't thought of any new lies to tell?

Say, kleinman, you could save yourself a lot of time by just numbering them. Then instead of having to type all this halfwitted drivel, you could just type: "Lie #1, Lie #4, Lie #5, and Lie #1 again". You only have about half-a-dozen lies, so it shouldn't take long.

I think this should be Lie #1:

I have shown using your computer model that the theory of evolution is mathematically impossible.

Next time, just type "Lie #1" and we'll know what you mean.

I too could save a little time.

Truth #1: You have "shown" nothing of the sort; your stupid childish mistakes were exposed many pages ago; and drooling out your dull-witted lies will not change reality.

[Paul C. Anagnostopoulos]

I'm a little concerned about the pseudo-random number generator. I know that the variance of outcomes for a particular random seed can be considerable, however, I ran the program using 1,1,0, first with a seed of 0, where it never converged after 1,000,000 generations, and then with 3, where it converged after 106,559. Assuming that the random generator is reasonably well-behaved, it doesn't seem possible to me that a variance of 621 to 1,000,000 is likely.
You're still using convergence to Rfreq rather than perfect creature. There is no selective pressure to converge. Furthermore, because you have eliminated selective pressure for accurate binding (spurious bindings are allowed outside the gene), a perfect creature can evolve with a lower Rseq. This is because the binding site motif only has to be unique enough to eliminate spurious bindings within the gene, rather than throughout the entire genome. You are essentially watching for this convergence:

Rseq-allowing-spurious-bindings ==> Rfreq-assuming-perfect-bindings

So it's unlikely to converge, even while evolving a perfect creature.

~~ Paul

[kleinman]

The results from ev already are repeatable but do your analysis because we don’t need another issue for you to whine about. Do you think the random number generator will correct the issue that you don’t have a selection process to evolve a gene from the beginning? Perhaps the random number generator will correct the irrationality of the concept of abiogenesis. You have provided the answer for the gene from the beginning question. Ev selects for nothing more meaningful than accurate chemical bindings. The only thing required, according to Paul, is a transcription factor, which averages 6 - 12 bases in length. Evolving a transcription factor by random chance is thus a relatively trivial issue as there are a maximum of 16,777,216 combinations, and we know for a certainty that there are many possible transcription factor sequences, so the odds of a randomly produced TF is much lower than 1 in 17 million.
What good is a binding site without an associated gene?
My first question for you is how did you get the original gene? You mean gene #1, the first gene of all of life on Earth? We don't know that yet. The evidence has been obscured by the genes that it evolved into. But we're working on it.
Oh, that’s right, the gap theory.
My second question is what is the selection process that transforms the copy of the gene to an entirely new function? I explained that quite clearly. It mutates until it performs a new function.
Paul, take Mr Scott’s explanation, put it in ev and transform some genes.
Each mutation in the transformation must either be beneficial or at least neutral; otherwise that creature will be selected against. Exactly what I said. Read my post again.
No gaps in that explanation!
My third question is how do you get this transformation to occur when you have many competing selection processes occurring simultaneously? I don't see the problem with this. In fact, many competing mutation/selection processes makes evolution go even faster because parallel changes are happening within individual organisms. Thanks for pointing this out.
Now if ev only showed what you are proposing. In fact, Dr Schneider’s computer simulation shows the exact opposite of what you are saying.
Your example does not simulate the evolution of a new knob. What your example is of the copying of a knob and then somehow modifying this copy to some new function. Well, sure, you duplicate a knob, then modify its function until it performs a function that no previous knob performed. That's the definition of a new knob. Like a "pedal split" function -- a type de novo knob transformation that a program like Ev may not implement.
Could you review the selection process again that would do this so Paul can put this in ev and demonstrate what you propose?
Your example could be coded into ev. Well, since it wasn't, and you depend on Ev to show evolution is mathematically impossible, then you've refuted your own conclusion.
No, you have just demonstrated another example of amathematica sciencea.
What is the selection process that evolved the original gene and what is the selection process that transforms the gene to a new function. The "original gene" in that context I think you mean the gene that duplicated and then its duplicate mutated. If so, the "original gene" may very well have come about the same way as the new gene. Go backwards gene by gene to the beginning of life and you will find the first gene, perhaps an RNA gene that accidentally doubled-up, that assembled more generations previously out of other pieces of replicating molecules that were mutated and selected for. We don't know how all this started, but that doesn't prove god did it. Not having an answer to any question should never be construed as proof of the intervention of a divine entity.
You have now demonstrated speculitis and hyperextraplopia. Your denialophila of the results from ev and your previous demonstration of amathematica sciencea completes the diagnostic criteria for evolutionism.
...evolution does not have a sound mathematical scientific basis. Your own computer model shows this. I don’t know how many times I have been required to offer an alternative explanation for life since I have shown using your computer model that the theory of evolution is mathematically impossible. You know, Dr. Kleinman, I don't think you are correct about this. Ev has never shown that evolution is mathematically impossible, because Ev is not a complete simulation of all processes involved.
Add your gene duplication concept to ev and prove me wrong. Do you see the goalposts?

[Mercutio]

Mercutio, all the posts are out there to read, there are no moving goalposts.The posts are indeed out there. I invite the readers to make their own conclusions about movement.
There is no particular method of abiogenesis. Take a course in organic chemistry and you will understand why there is no abiogenesis. You can’t form ribose inorganically let alone RNA bases. Even if you could form the RNA bases, you can’t get the bases to link without enzymes. Even if you could get RNA bases to link without enzymes, you won’t get the sequences to form functional ribozymes and on and on… People who believe in abiogenesis and the theory of evolution have a form of hysteria.Please, Kleinman; you asked earlier whether the first genes were formed using the modern DNA replicase system, and were told that there is no requirement that this be the case. As long as you are asking for how modern structures arose spontaneously from primordial ooze, you will be frustrated. You are quite simply asking the wrong questions.
Oh yes, we all see the evidence, the experiments with genes arising de novo, the test tubes with life arising abiogenically. How could such evidence be refuted?Despite your claim of the Miller experiments as the zenith of abiogenesis research, there is quite a bit of ongoing research (with competing views and everything--my goodness, it's almost like science!). In truth, I must thank you; this is not my area, so I have had to actually go out and read things I was not familiar with. You have opened my eyes to how much is actually known, how much of the chemistry tested, how rapidly the gaps in which your god lives are closing.
Really? Modern bacteria have totally different genes than the one celled creatures that arose out of the non-existent primordial soup? Save these stories for devout evolutionists and naïve school children. Your idea of evidence is concocted stories. What ev gives is hard mathematical science, so save your stories to tell around the camp fire at evolutionist summer camp.Yes, modern bacteria have totally different genes, and you are assuming quite a bit when you speak of "the one celled creatures that arose..." By the time there was a cell membrane as we currently know it, quite a bit of change had already taken place. A fatty acid globule (one hypothesized cell-precursor--the molecular structure of fatty acids allows them to spontaneously form globules) is quite different from a cell membrane, after all. Since your definition of "gene" is functional, the genes forming cell walls are already different from their ancestors. I suppose you could quibble on "totally" different; since your own cellular mechanisms share quite a bit with...well, with any living cells, you are not "totally" different from amoeba.

So...anyway, since there actually is research ongoing into possible abiogenesis mechanisms, suppose you share with us the ongoing research into the god hypothesis?

[Dr Adequate]

You have now demonstrated speculitis and hyperextraplopia. Your denialophila of the results from ev and your previous demonstration of amathematica sciencea completes the diagnostic criteria for evolutionism.

Oh look, kleinman's invented some new magic words!

I notice that like his old magic words, they are not in fact magical and don't really make the facts disappear in a puff of smoke.

Poor little man.

[Dr Richard]

Mercutio, all the posts are out there to read, there are no moving goalposts.



link to Kleinman's goalposts on the definition of macroevolution (http://forums.randi.org/showthread.php?postid=2392519#post2392519)

[kleinman]

There is no particular method of abiogenesis. Take a course in organic chemistry and you will understand why there is no abiogenesis. You can’t form ribose inorganically let alone RNA bases. Even if you could form the RNA bases, you can’t get the bases to link without enzymes. Even if you could get RNA bases to link without enzymes, you won’t get the sequences to form functional ribozymes and on and on… People who believe in abiogenesis and the theory of evolution have a form of hysteria. Please, Kleinman; you asked earlier whether the first genes were formed using the modern DNA replicase system, and were told that there is no requirement that this be the case. As long as you are asking for how modern structures arose spontaneously from primordial ooze, you will be frustrated. You are quite simply asking the wrong questions.
So the nonsensical response that evolutionists give to how the first genes formed without the DNA replicase system is “billions and billions of years”. You have no science, no mathematics, only slogans to support your theory.
Oh yes, we all see the evidence, the experiments with genes arising de novo, the test tubes with life arising abiogenically. How could such evidence be refuted? Despite your claim of the Miller experiments as the zenith of abiogenesis research, there is quite a bit of ongoing research (with competing views and everything--my goodness, it's almost like science!). In truth, I must thank you; this is not my area, so I have had to actually go out and read things I was not familiar with. You have opened my eyes to how much is actually known, how much of the chemistry tested, how rapidly the gaps in which your god lives are closing.
There are no experiments that demonstrate how the basic components of life formed nonezymatically. Your theory is nothing but gaps.
Really? Modern bacteria have totally different genes than the one celled creatures that arose out of the non-existent primordial soup? Save these stories for devout evolutionists and naïve school children. Your idea of evidence is concocted stories. What ev gives is hard mathematical science, so save your stories to tell around the camp fire at evolutionist summer camp. Yes, modern bacteria have totally different genes, and you are assuming quite a bit when you speak of "the one celled creatures that arose..." By the time there was a cell membrane as we currently know it, quite a bit of change had already taken place. A fatty acid globule (one hypothesized cell-precursor--the molecular structure of fatty acids allows them to spontaneously form globules) is quite different from a cell membrane, after all. Since your definition of "gene" is functional, the genes forming cell walls are already different from their ancestors. I suppose you could quibble on "totally" different; since your own cellular mechanisms share quite a bit with...well, with any living cells, you are not "totally" different from amoeba.
The only thing you evolutionists have proved is that if you trot out one speculation after another, you start to believe these things as true. The theory of evolution and abiogenesis really should be discussed on the paranormal forum, that is if you can raise a sufficient amount of mathematical scientific proof to qualify for that forum.
So...anyway, since there actually is research ongoing into possible abiogenesis mechanisms, suppose you share with us the ongoing research into the god hypothesis?
Too bad you and other evolutionists don’t accept the results of Dr Schneider’s research, then research money could go to something worthwhile, not your silly, irrational concept of abiogenesis.
Mercutio, all the posts are out there to read, there are no moving goalposts. link to Kleinman's goalposts on the definition of macroevolution (http://forums.randi.org/showthread.php?postid=2392519#post2392519)
Why Dr Richard, our own Sesame Street drop-out. Since you dropped out of Sesame Street before you learned how to count, we will review that topic for you. The number you are to learn today is “0”. “0” is the number of selection processes that evolve a gene from the beginning. “0” is the amount of mathematics you have that supports your theory of evolution. And “0” is the possibility that your theory of evolution is true. So remember the number “0” because that is what your theory of evolution is.

Once you learn the number “0”, we will start you on reading since you think that the only information in a publication is in the figures.

[kjkent1]

What good is a binding site without an associated gene?Hey, you're the one relying on ev's model as disproving evolutionary theory. If you're position is that the ev model is impossible from the beginning, then you can't assert that an ev program run proves anything, because you are starting from the premise that the ev model is a fantasy.

So, make up your mind -- either the ev model is viable or it's not. If it is, then my description works and resolves your question re the gene from the beginning. If not, then my description doesn't work -- but neither does yours, and this entire thread has been a gross waste of time for everyone.

[kleinman]

What good is a binding site without an associated gene?Hey, you're the one relying on ev's model as disproving evolutionary theory. If you're position is that the ev model is impossible from the beginning, then you can't assert that an ev program run proves anything, because you are starting from the premise that the ev model is a fantasy.
In case you haven’t noticed, it takes billions of generations to evolve the binding sites in ev on a realistic length genome with realistic mutation rates. Do you think that evolving the gene that goes with the binding site is going to speed up this process, especially when you don’t have a selection process to do this?
So, make up your mind -- either the ev model is viable or it's not. If it is, then my description works and resolves your question re the gene from the beginning. If not, then my description doesn't work -- but neither does yours, and this entire thread has been a gross waste of time for everyone.
Of course ev is a plausible model. This simplified model show how profoundly slow the evolution of binding sites is. You think by making the model more complex, the evolutionary process will speed up. Well, show us.

[Mercutio]

So the nonsensical response that evolutionists give to how the first genes formed without the DNA replicase system is “billions and billions of years”. You have no science, no mathematics, only slogans to support your theory.Oh, you are a hoot! You got that out of what I wrote? (well, no, you didn't--but that didn't stop you.)
There are no experiments that demonstrate how the basic components of life formed nonezymatically. Your theory is nothing but gaps.1) Could you please list what you mean here by "basic components of life"? I am curious as to whether you are simply asking the wrong things again, or whether you are making an actual point. 2) Nothing but gaps? Is this one of those deals where, when a gap is filled in, you get to claim that we have merely created two more gaps? These gaps you speak of are shrinking rapidly; soon there may be nowhere left for your god to hide.
The only thing you evolutionists have proved is that if you trot out one speculation after another, you start to believe these things as true. The theory of evolution and abiogenesis really should be discussed on the paranormal forum, that is if you can raise a sufficient amount of mathematical scientific proof to qualify for that forum.Note once again that you conflate evolution and abiogenesis. Oh, and lest I quote your first sentence here right back at you (with one minor change--let's see if you can guess it!), how's that evidence for your god hypothesis coming along?
Too bad you and other evolutionists don’t accept the results of Dr Schneider’s research, then research money could go to something worthwhile, not your silly, irrational concept of abiogenesis.
Hey, "evolutionists" can work just fine with a god-created abiogenesis (and it is not difficult to find examples of evolutionists admitting this; as an aside, my very first school exposure to natural selection was by a visiting entomologist who said that, in his opinion, "god touched the earth" and created life, which then proceeded via natural selection). When you speak of a "silly, irrational concept of abiogenesis", remember that the term applies to your god hypothesis every bit as much as to the tidal pool hypothesis, the thermal vent hypothesis, the volcanic gas hypothesis, Odin's tears, and the Great Green Arkleseizure.

So please, in your continuing conflation of natural selection and abiogenesis, be careful which targets you think you are aiming at. Sloppy use of vocabulary might lead some to believe that you don't know what you are talking about.

[kjkent1]

You're still using convergence to Rfreq rather than perfect creature. There is no selective pressure to converge. Furthermore, because you have eliminated selective pressure for accurate binding (spurious bindings are allowed outside the gene), a perfect creature can evolve with a lower Rseq. This is because the binding site motif only has to be unique enough to eliminate spurious bindings within the gene, rather than throughout the entire genome. You are essentially watching for this convergence:

Rseq-allowing-spurious-bindings ==> Rfreq-assuming-perfect-bindings

So it's unlikely to converge, even while evolving a perfect creature.

~~ PaulOK, fair enough. So if I understand correctly (and, I probably don't), then with ev's default settings, a perfect creature can arise by chance during nearly any generation, and if it does, that's really the end of the experiment, regardless of the amount of convergence which may have already occured.

[kjkent1]

In case you haven’t noticed, it takes billions of generations to evolve the binding sites in ev on a realistic length genome with realistic mutation rates. Do you think that evolving the gene that goes with the binding site is going to speed up this process, especially when you don’t have a selection process to do this?You're being disingenuous. My description resolves your gene from the beginning is impossible argument. So, all that remains is to speed up the ev selection method.

And, Unnamed produced a different selection method which does speed up ev sufficiently. The fact that you don't like that method is really irrelevant. All that matters is that it has already been demonstrated that other selection methods can speed up ev.

Moreover, your complaint about Unnamed's method was that it largely ignored non-binding site region errors. But, as I've recently shown, ignoring non-binding site errors actually slows down the convergence of Rseq to Rfreq. This suggests that you are misunderstanding how Unnamed's selection process works.

I'm not saying that Unnamed's method is more realistic than the ev default selection method. I'm just saying that until we have a selection method which is realistic, reliance on ev's slowness to demonstrate that evolution is impossible is not reasonable, because you don't know whether the default ev model is a more reasonable model of evolution than is some other version with a different selection method.

So, we're back to the selection method and its realism. I don't know enough about genetics to declare that the default ev method is better or worse than Unnamed's, or some other, as yet unproposed selection mechanism.

But, until there's some consensus as to the realism of the ev selection method, you cannot reasonably conclude that ev shows evolution as mathematically impossible, because you don't have all the required components to draw such a conclusion.

[kleinman]

So the nonsensical response that evolutionists give to how the first genes formed without the DNA replicase system is “billions and billions of years”. You have no science, no mathematics, only slogans to support your theory.Oh, you are a hoot! You got that out of what I wrote? (well, no, you didn't--but that didn't stop you.)
Well let’s get these quotes accurately.
Sure. Modern genes have been built upon billions of years of previous genes. To suggest that the simplest current organisms are identical to the earliest replicants is disingenuous at best. There is absolutely no reason to suspect that our current simple life is as simple as it gets. But... if genes are defined functionally, and the function is replication, we can get much much simpler for our early genes.
How many billions of years does abiogenesis take and how many billions of years does it take to get your so-called modern genes?
There are no experiments that demonstrate how the basic components of life formed nonezymatically. Your theory is nothing but gaps.1) Could you please list what you mean here by "basic components of life"? I am curious as to whether you are simply asking the wrong things again, or whether you are making an actual point. 2) Nothing but gaps? Is this one of those deals where, when a gap is filled in, you get to claim that we have merely created two more gaps? These gaps you speak of are shrinking rapidly; soon there may be nowhere left for your god to hide.
Let’s keep it simple for you, 1) ribose and RNA bases or amino acids depending on which fantasy trip you subscribe to and 2) the gaps in your theory are mathematical, chemical and physical, but you have no shortage of slogans. That mathematical gap grew by orders of magnitude with the development of Dr Schneider’s ev program.
Too bad you and other evolutionists don’t accept the results of Dr Schneider’s research, then research money could go to something worthwhile, not your silly, irrational concept of abiogenesis.Hey, "evolutionists" can work just fine with a god-created abiogenesis (and it is not difficult to find examples of evolutionists admitting this; as an aside, my very first school exposure to natural selection was by a visiting entomologist who said that, in his opinion, "god touched the earth" and created life, which then proceeded via natural selection). When you speak of a "silly, irrational concept of abiogenesis", remember that the term applies to your god hypothesis every bit as much as to the tidal pool hypothesis, the thermal vent hypothesis, the volcanic gas hypothesis, Odin's tears, and the Great Green Arkleseizure.
Finally you acknowledge that your concept of abiogenesis has as much validity as Odin's tears and the Great Green Arkleseizure.
So please, in your continuing conflation of natural selection and abiogenesis, be careful which targets you think you are aiming at. Sloppy use of vocabulary might lead some to believe that you don't know what you are talking about.
Since you evolutionists like to define terms, perhaps you would be willing to define when abiogenesis ends and your theory of evolution begins. It will be interesting to see how you define when one fantasy ends and another begins.

[Davidjayjordan]

It used to take millions of years for lucky gene mutations to make lucky beneficial changes, but NOW I think the evolutionists have decided to make the impossible more probable by changing the amount of lucky time needed to billions, and then trillions. And yet as people lose faith in luck and get impatient, I'm sure the evolutionists will say it takes zillions of years for beneficial mutations to chance life for the better.

[Mercutio]

Well let’s get these quotes accurately.Yes, let's.
How many billions of years does abiogenesis take and how many billions of years does it take to get your so-called modern genes?It is not the time, dear, but what happens during that time that is important. The sun has been here billions of years longer than life has been, and yet I doubt very much that abiogenesis will take place upon it. You said that the evolutionist's answer was "billions and billions of years". That is either an ignorant oversimplification or an outright lie.
Let’s keep it simple for you, 1) ribose and RNA bases or amino acids depending on which fantasy trip you subscribe to and 2) the gaps in your theory are mathematical, chemical and physical, but you have no shortage of slogans. That mathematical gap grew by orders of magnitude with the development of Dr Schneider’s ev program.1) Do you think this is the only form that life could have taken? (this is a serious question, not a rhetorical one). 2) You must be looking at different journals than I am. I'd love to see the sources supporting this contention.
Finally you acknowledge that your concept of abiogenesis has as much validity as Odin's tears and the Great Green Arkleseizure.It would be foolish to defend any one abiogenesis hypothesis before there is sufficient evidence for it. The three naturalistic hypotheses mentioned are each being investigated. Even if, however, one of them is shown to create a living thing in the lab, it will not have demonstrated that it is the one that worked billions of years ago. It will merely have been shown to be sufficient. Odin's tears, the Great Green Arkleseizure, and your god hypothesis, however, share the property of being untestable (to the best of my knowledge--I have, however, asked you to report on the evidence you once claimed was abundant). So, I suggest that while none of the listed hypotheses can ever be shown to be "the right one", there is still a meaningful qualitative difference between the naturalistic and the mythical hypotheses. I do, still, encourage you to bring your evidence to bear.
Since you evolutionists like to define terms, perhaps you would be willing to define when abiogenesis ends and your theory of evolution begins. It will be interesting to see how you define when one fantasy ends and another begins. Natural selection requires a replicant. (Some will say that it requires a population of living things; that is a more conservative definition.) Abiogenesis results in a replicant. It is possible that there were several abiogenesis events, but that all current life evolved from the winner. Perhaps another event gave rise to life that was not DNA/RNA based, or that had a different codon (not our three-triplet), or different chirality, or whatever... but this population or populations did not survive the competition with ours. It could even be that one of these new life forms was somehow more efficient than ours, but had a later start and was eaten by a mudskipper.

It is an easy distinction to make. Just look at the definitions of the terms.

[Mercutio]

It used to take millions of years for lucky gene mutations to make lucky beneficial changes, but NOW I think the evolutionists have decided to make the impossible more probable by changing the amount of lucky time needed to billions, and then trillions. And yet as people lose faith in luck and get impatient, I'm sure the evolutionists will say it takes zillions of years for beneficial mutations to chance life for the better.Here (http://www.pnas.org/cgi/content/abstract/0607187104v1), have an example in humans in the past 20,000 years.

ETA: Here (http://www.eurekalert.org/pub_releases/2007-02/ucl-eeu022607.php) is a link to a more user-friendly press release on it.Scientists have known for decades that at some point in the past all humans were lactose intolerant. What was not known was just how recently lactose tolerance evolved.

Dr Thomas said: "To go from lactose tolerance being rare or absent seven to eight thousand years ago to the commonality we see today in central and northern Europeans just cannot be explained by anything except strong natural selection. Our study confirms that the variant of the lactase gene appeared very recently in evolutionary terms and that it became common because it gave its carriers a massive survival advantage. Scientists have inferred this already through analysis of genes in today's population but we've confirmed it by going back and looking at ancient DNA."

[kleinman]

How many billions of years does abiogenesis take and how many billions of years does it take to get your so-called modern genes?It is not the time, dear, but what happens during that time that is important. The sun has been here billions of years longer than life has been, and yet I doubt very much that abiogenesis will take place upon it. You said that the evolutionist's answer was "billions and billions of years". That is either an ignorant oversimplification or an outright lie.
You need to study ev. When you do you will understand that random point mutation and natural selection accomplishes very little in billions of generations. The “billions and billions of years” which is the standard evolutionist answer to how abiogenesis occurs and your answer to how modern genes evolve is neither an ignorant oversimplification nor an outright lie.
Let’s keep it simple for you, 1) ribose and RNA bases or amino acids depending on which fantasy trip you subscribe to and 2) the gaps in your theory are mathematical, chemical and physical, but you have no shortage of slogans. That mathematical gap grew by orders of magnitude with the development of Dr Schneider’s ev program. 1) Do you think this is the only form that life could have taken? (this is a serious question, not a rhetorical one). 2) You must be looking at different journals than I am. I'd love to see the sources supporting this contention.
1) Oh no, I’ve watched Star Trek and Star Wars, there are all different kinds of life forms. 2) Start with Nucleic Acids Research and read EV Evolution of Biological Information by Dr Tom Schneider. His work reveals a huge mathematical gap in your theory.
Finally you acknowledge that your concept of abiogenesis has as much validity as Odin's tears and the Great Green Arkleseizure.It would be foolish to defend any one abiogenesis hypothesis before there is sufficient evidence for it. The three naturalistic hypotheses mentioned are each being investigated. Even if, however, one of them is shown to create a living thing in the lab, it will not have demonstrated that it is the one that worked billions of years ago. It will merely have been shown to be sufficient. Odin's tears, the Great Green Arkleseizure, and your god hypothesis, however, share the property of being untestable (to the best of my knowledge--I have, however, asked you to report on the evidence you once claimed was abundant). So, I suggest that while none of the listed hypotheses can ever be shown to be "the right one", there is still a meaningful qualitative difference between the naturalistic and the mythical hypotheses. I do, still, encourage you to bring your evidence to bear.
Of course there is no evidence for abiogenesis. The chemistry required to accomplish this is impossible and the mathematics and physics to select for the sequences necessary to make genes does not exist. Beside this, you do have billions of years to accomplish this.
Since you evolutionists like to define terms, perhaps you would be willing to define when abiogenesis ends and your theory of evolution begins. It will be interesting to see how you define when one fantasy ends and another begins.Natural selection requires a replicant. (Some will say that it requires a population of living things; that is a more conservative definition.) Abiogenesis results in a replicant. It is possible that there were several abiogenesis events, but that all current life evolved from the winner. Perhaps another event gave rise to life that was not DNA/RNA based, or that had a different codon (not our three-triplet), or different chirality, or whatever... but this population or populations did not survive the competition with ours. It could even be that one of these new life forms was somehow more efficient than ours, but had a later start and was eaten by a mudskipper.
Well, why don’t you tell us how the first replicant came to be? Or is that just another gap in your theory? Here is an abbreviated sequence of the evolutionist concept of how life came to be: abiogenesis->first replicant->mutation and selection->life today or more simply gap->gap->gap->life today.

[Paul C. Anagnostopoulos]

OK, fair enough. So if I understand correctly (and, I probably don't), then with ev's default settings, a perfect creature can arise by chance during nearly any generation, and if it does, that's really the end of the experiment, regardless of the amount of convergence which may have already occured.
I'm not sure I understand you, but I think you're right. A creature with 1 mistake can evolve to one with 0 mistakes by chance, as you say. At that point, Rseq is usually close to Rfreq. But this assumes that the parameters are set so that the creature really is perfect: all bindings sites bound, no spurious bindings. That's because Rfreq is calculated based on that assumption. If you've changed the parameters so that a 0-mistake creature can evolve with spurious bindings, then Rseq will probably be much lower than the calculated Rfreq.

Once a creature with 0 mistakes evolves, then it's pretty much genetic drift after that. It's quite unlikely that a creature that evolves with your parameters will ever drift to Rseq >= Rfreq. There is no pressure to go there.

~~ Paul

[Paul C. Anagnostopoulos]

You need to study ev. When you do you will understand that random point mutation and natural selection accomplishes very little in billions of generations.
With what genome size and population?

~~ Paul

[kleinman]

You need to study ev. When you do you will understand that random point mutation and natural selection accomplishes very little in billions of generations.With what genome size and population?
Let’s see, where did we leave off at? G=100k, Mutation rate=10^-6, Population 1 meg, generations for convergence per your estimate 200,000,000. I still think this is an underestimate but for the sake of discussion we can use that value. So G is still at least a factor of 5 smaller than the smallest G for any free living organism. How many loci evolved in that time? ~100 What is the selection process that would evolve a gene from the beginning? ~gap

[Mercutio]

You need to study ev. When you do you will understand that random point mutation and natural selection accomplishes very little in billions of generations. The “billions and billions of years” which is the standard evolutionist answer to how abiogenesis occurs and your answer to how modern genes evolve is neither an ignorant oversimplification nor an outright lie.Ev, of course, limits population size--it is a model, after all. Your answer is quite consistent with the "ignorant oversimplification" hypothesis... but I am not abandoning the other yet, either.
1) Oh no, I’ve watched Star Trek and Star Wars, there are all different kinds of life forms. 2) Start with Nucleic Acids Research and read EV Evolution of Biological Information by Dr Tom Schneider. His work reveals a huge mathematical gap in your theory.1) Figures. To take this more seriously than is meant, such a definition of "all different kinds" is a tremendous lack of imagination. The vast majority of life forms in these "sources" are bipedal, bilaterally symmetrical, capable of eating what we eat. When you let the media do your imagining for you, you stunt your imagination. 2) Ok, I read Schneider. The ev model quantitatively addresses the question of how life gains information, a valid issue recently raised by creationists (32) (R. Truman, http://www.trueorigin.org/dawkinfo.htm ; 08-Jun-1999) but only qualitatively addressed by biologists (33). The mathematical form of uncertainty and entropy (H = –plog2p, p = 1) implies that neither can be negative (H 0), but a decrease in uncertainty or entropy can correspond to information gain, as measured here by Rsequence and Rfrequency. The ev model shows explicitly how this information gain comes about from mutation and selection, without any other external influence, thereby completely answering the creationists.

The ev model can also be used to succinctly address two other creationist arguments. First, the recognizer gene and its binding sites co-evolve, so they become dependent on each other and destructive mutations in either immediately lead to elimination of the organism. This situation fits Behe’s (34) definition of ‘irreducible complexity’ exactly ("a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning", page 39), yet the molecular evolution of this ‘Roman arch’ is straightforward and rapid, in direct contradiction to his thesis. Second, the probability of finding 16 sites averaging 4 bits each in random sequences is 2–4 x 16 5 x 10–20 yet the sites evolved from random sequences in only ~103 generations, at an average rate of ~1 bit per 11 generations. Because the mutation rate of HIV is only 10 times slower, it could evolve a 4 bit site in 100 generations, ~9 months (35), but it could be much faster because the enormous titer [1010 new virions/day/person (17)] provides a larger pool for successful changes. Likewise, at this rate, roughly an entire human genome of ~4 x 109 bits (assuming an average of 1 bit/base, which is clearly an over estimate) could evolve in a billion years, even without the advantages of large environmentally diverse world-wide populations, sexual recombination and interspecies genetic transfer. However, since this rate is unlikely to be maintained for eukaryotes, these factors are undoubtedly important in accounting for human evolution. So, contrary to probabilistic arguments by Spetner (32,36), the ev program also clearly demonstrates that biological information, measured in the strict Shannon sense, can rapidly appear in genetic control systems subjected to replication, mutation and selection (33).Of course there is no evidence for abiogenesis. The chemistry required to accomplish this is impossible and the mathematics and physics to select for the sequences necessary to make genes does not exist. Beside this, you do have billions of years to accomplish this.The good folks at Nucleic Acids Research seem to disagree with you.
Well, why don’t you tell us how the first replicant came to be? Or is that just another gap in your theory? Here is an abbreviated sequence of the evolutionist concept of how life came to be: abiogenesis->first replicant->mutation and selection->life today or more simply gap->gap->gap->life today.I will wait for the people who are doing the research to answer that question. It certainly is a fascinating question, though. I wonder who will provide a demonstrable abiogenesis event first--the "evolutionists" or the "goddiditists". Time may tell...

[Paul C. Anagnostopoulos]

Let’s see, where did we leave off at? G=100k, Mutation rate=10^-6, Population 1 meg, generations for convergence per your estimate 200,000,000. I still think this is an underestimate but for the sake of discussion we can use that value. So G is still at least a factor of 5 smaller than the smallest G for any free living organism. How many loci evolved in that time? ~100 What is the selection process that would evolve a gene from the beginning? ~gap
How big were the genomes of organisms back when ancient genes were evolving? The populations were certainly many orders of magnitude bigger than a million, but how big?

I'm just asking, cuz you have proven that evolution is mathematically impossible, so you must know.

~~ Paul

[kjkent1]

Let’s see, where did we leave off at? G=100k, Mutation rate=10^-6, Population 1 meg, generations for convergence per your estimate 200,000,000. I still think this is an underestimate but for the sake of discussion we can use that value. So G is still at least a factor of 5 smaller than the smallest G for any free living organism. How many loci evolved in that time? ~100 What is the selection process that would evolve a gene from the beginning? ~gapThis is a frivolous argument. It presumes that only a "perfect creature" as defined by ev is alive and capable of functioning and reproducing in the real world. But, ev makes a different presumption.

We don't know if the ev genome is just part of an already living creature's existing genome, or whether the binding sites that ev presents are just a molecular structure sitting in a pond somewhere. However, what ev does impliedly presume, is that from generation one (1), the "creature" is capable of reproducing itself. Otherwise, there would be no evolution at all.

So, your calculation is irrelevant, because the creature doesn't have to evolve to perfection within some X number of generations to be viable. It's viable at instantiation.

And, during every generation, there are changes -- changes which in the model will cause real-world functionality, but which we cannot actually discuss because we can't observe the creature in its environment.

Suppose that at generation two (2), the DNA sequence creates a different functionality, and then in generation three (3), it develops something else? We don't know what the creature is actually doing -- but we do know that it's alive, and that it's doing something throughout the evolutionary process.

[Dr Adequate]

Since you evolutionists like to define terms, perhaps you would be willing to define when abiogenesis ends and your theory of evolution begins.

You've spent all this time whining about evolution and abiogenesis and you don't even know the meaning of the terms?

I guess that figures. The amount of time people spend whining about science is usually proportional to their ignorance of it.

[Dr Adequate]

I will wait for the people who are doing the research to answer that question. It certainly is a fascinating question, though. I wonder who will provide a demonstrable abiogenesis event first--the "evolutionists" or the "goddiditists". The evolutionists, of course.

See the link in my sig.

[Dr Adequate]

Here is an abbreviated sequence of the evolutionist concept of how life came to be: abiogenesis->first replicant->mutation and selection->life today or more simply gap->gap->gap->life today.

This is a new lie, I believe. Well done!

Tell me, when you pretend that the words "mutation and selection" are the same as the word "gap", whom do you think you're going to fool?

This is even dumber than your other lies.

[kleinman]

You need to study ev. When you do you will understand that random point mutation and natural selection accomplishes very little in billions of generations. The “billions and billions of years” which is the standard evolutionist answer to how abiogenesis occurs and your answer to how modern genes evolve is neither an ignorant oversimplification nor an outright lie. Ev, of course, limits population size--it is a model, after all. Your answer is quite consistent with the "ignorant oversimplification" hypothesis... but I am not abandoning the other yet, either.
If you had run some cases with ev you would find out that the model does not limit population. It is the amount of memory available on the computer which limits the size of the population. Of course you are an expert on ev since you have run as many cases as Adequate has.
1) Oh no, I’ve watched Star Trek and Star Wars, there are all different kinds of life forms. 2) Start with Nucleic Acids Research and read EV Evolution of Biological Information by Dr Tom Schneider. His work reveals a huge mathematical gap in your theory. 1) Figures. To take this more seriously than is meant, such a definition of "all different kinds" is a tremendous lack of imagination. The vast majority of life forms in these "sources" are bipedal, bilaterally symmetrical, capable of eating what we eat. When you let the media do your imagining for you, you stunt your imagination. 2) Ok, I read Schneider.
1) Evolutionists don’t have stunted imaginations, you have stunted mathematical and scientific skills. 2) ok, lets go through what you have read from Dr Schneider’s paper:
Because the mutation rate of HIV is only 10 times slower, it could evolve a 4 bit site in 100 generations, ~9 months (35), but it could be much faster because the enormous titer [1010 new virions/day/person (17)] provides a larger pool for successful changes.
Dr Schneider has made two inaccurate statements here. The first is the mutation rate for HIV is much slower than 1/10 * 1 mutation per 256 bases per generation, look up the value. The second is that Dr Schneider assumes that huge populations markedly accelerate evolution. This view is contradicted by his own computer model.
Likewise, at this rate, roughly an entire human genome of ~4 x 109 bits (assuming an average of 1 bit/base, which is clearly an over estimate) could evolve in a billion years, even without the advantages of large environmentally diverse world-wide populations, sexual recombination and interspecies genetic transfer. However, since this rate is unlikely to be maintained for eukaryotes, these factors are undoubtedly important in accounting for human evolution.
Dr Schneider makes this estimate based on the rate of information gain on a 256 base genome with a mutation rate of 1 mutation per 256 bases per generation. If Dr Schneider simply uses a realistic mutation rate in this case, his estimate of a billion years becomes 4 trillion years. Use a realistic genome length and a realistic mutation rate in the ev model and nothing can evolve in a realistic length of time.
So, contrary to probabilistic arguments by Spetner (32,36), the ev program also clearly demonstrates that biological information, measured in the strict Shannon sense, can rapidly appear in genetic control systems subjected to replication, mutation and selection (33).
Dr Schneider’s superficial analysis with only a single case with unrealistic genome length and mutation rate has erroneously led him to conclude that biological information appears rapidly by this mechanism. In fact, using a realistic genome length and mutation rate in ev shows that the rate of information acquisition by random point mutation and natural selection is profoundly slow, too slow to allow for evolution by this mechanism.
Of course there is no evidence for abiogenesis. The chemistry required to accomplish this is impossible and the mathematics and physics to select for the sequences necessary to make genes does not exist. Beside this, you do have billions of years to accomplish this. The good folks at Nucleic Acids Research seem to disagree with you.
You will find that I agree that the good folks at Nucleic Acids Research were correct in publishing Dr Schneider’s work. Dr Schneider has properly modeled random point mutations and natural selection. What I believe is the folks at Nucleic Acids Research and Dr Schneider did not realize the full ramifications of the mathematics of this model. I did just what Dr Schneider suggested in his paper. Do you remember this paragraph?
Variations of the program could be used to investigate how population size, genome length, number of sites, size of recognition regions, mutation rate, selective pressure, overlapping sites and other factors affect the evolution.
What an interesting surprise this parametric study reveals.
Well, why don’t you tell us how the first replicant came to be? Or is that just another gap in your theory? Here is an abbreviated sequence of the evolutionist concept of how life came to be: abiogenesis->first replicant->mutation and selection->life today or more simply gap->gap->gap->life today. I will wait for the people who are doing the research to answer that question. It certainly is a fascinating question, though. I wonder who will provide a demonstrable abiogenesis event first--the "evolutionists" or the "goddiditists". Time may tell...
What we do know is that evolutiondidn’tdoit. We have the mathematics to show this.
Let’s see, where did we leave off at? G=100k, Mutation rate=10^-6, Population 1 meg, generations for convergence per your estimate 200,000,000. I still think this is an underestimate but for the sake of discussion we can use that value. So G is still at least a factor of 5 smaller than the smallest G for any free living organism. How many loci evolved in that time? ~100 What is the selection process that would evolve a gene from the beginning? ~gap How big were the genomes of organisms back when ancient genes were evolving? The populations were certainly many orders of magnitude bigger than a million, but how big?
I’ll leave this type of fantasizing to you evolutionists.
I'm just asking, cuz you have proven that evolution is mathematically impossible, so you must know.
What I know is that ev shows that when realistic genome lengths and mutation rates are used, the rate of information acquisition is profoundly slow, too slow to explain the theory of information. If you want to fantasize about tiny genomes evolving in some primordial soup, that is fine, just don’t call this science.

[Mercutio]

Have you written to the Journal yet? I searched under "Kleinman", but found nothing. I read your assertions here, but I would like to see what the good folks at the journal say. Your assertion that his rates are unrealistic has taken you a long way from his study, to the point of declaring evolution impossible! I'd kinda like to see more than ... well, just your assertion.

[kleinman]

Have you written to the Journal yet? I searched under "Kleinman", but found nothing. I read your assertions here, but I would like to see what the good folks at the journal say. Your assertion that his rates are unrealistic has taken you a long way from his study, to the point of declaring evolution impossible! I'd kinda like to see more than ... well, just your assertion.
Yes, I contacted the editors of Nucleic Acids Research. Initially they said the typical strawman argument that you evolutionists use. When I told them specifically what happens to Dr Schneider’s model when realistic genome lengths and mutation rates were used in the model and wanted to report these results in a letter to the editor, they said they do not take letters to the editor. This discussion did not come out of nothing; I discussed this issue extensively with Dr Schneider and Paul with hundreds of email communications. Dr Schneider has refused to discuss this issue publicly but Paul has shown willingness to discuss this issue publicly. What you call assertions can easily be replicated in the ev model, plug in the numbers and see the results.

The underlying problem for you evolutionists is that there is no selection process that can evolve a gene from the beginning. When you study ev, you will see the contrive selection process Dr Schneider used in order to carry out the simulation. There is no way to model a selection process that can evolve a gene which doesn’t exist, there is nothing to select for. The ev mathematical model puts the spotlight on this deficiency in your theory.

The ev computer model has put your theory of evolution into a mathematical vise which I don’t think your theory can survive.

[Mercutio]

So write your letter to the editors of the journal--as carefully and well-supported as you would write it to them--and post it here. As is, I see at least two potential problems with your criticism--one a matter of the effects of population size, the other a much more fundamental misunderstanding that presumes a directed evolution aiming for a particular outcome. But without your well-stated argument, it is impossible to evaluate.

And please do not use the construction "a gene is to evolve...". That paragraph, copied and pasted as many times as you have already, has gotten you nowhere. It is that argument that makes me suspect that you have a fundamental misunderstanding. But of course, I could be wrong (it has happened once before, a few years ago); if you focus on your argument, not on the personal sniping, perhaps you can phrase it in such an idiot-proof manner that even I will understand.

If you are willing to do that, I am willing to set aside my request that we evaluate the evidence for your god hypothesis. We can always return to that later.

[kleinman]

So write your letter to the editors of the journal--as carefully and well-supported as you would write it to them--and post it here. As is, I see at least two potential problems with your criticism--one a matter of the effects of population size, the other a much more fundamental misunderstanding that presumes a directed evolution aiming for a particular outcome. But without your well-stated argument, it is impossible to evaluate.
What is the point of doing this? All I would be doing is reiterating what I have posted on this thread and the Evolutionisdead forum. With respects to the population issue, if you examine this data, you would see that only the first few doublings of the population decrease the generations for convergence markedly. The data appears to be rapidly approach an asymptote. This a far stretch from the conclusion Dr Schneider made about the effects of huge populations on the rates of information acquisition, a conclusion he drew with only a single data point. To get a more conclusive answer on this issue requires far more memory than I have on my computer. A G=1000, population=1meg case takes the entire memory available on my PC (1/2 gigabyte). Any realistic genome size with populations of 10^10 would take millions of gigabytes of memory. That said, you can see trends with the smaller genomes and smaller populations that does not bode well for your theory.
And please do not use the construction "a gene is to evolve...". That paragraph, copied and pasted as many times as you have already, has gotten you nowhere. It is that argument that makes me suspect that you have a fundamental misunderstanding. But of course, I could be wrong (it has happened once before, a few years ago); if you focus on your argument, not on the personal sniping, perhaps you can phrase it in such an idiot-proof manner that even I will understand.
If you studied ev, in particular the selection process that Dr Schneider used, you would understand my “a gene is to evolve…” argument. Your theory stands or falls on this definition. I don’t know of a valid definition for selection that would do this and so far no evolutionist has been able to describe such a selection process. Unless you or some other evolutionist can do this, your theory will fail mathematically.
If you are willing to do that, I am willing to set aside my request that we evaluate the evidence for your god hypothesis. We can always return to that later.
I think you should evaluate the evidence for God, especially since your own mathematics shows your theory to be impossible.

[Paul C. Anagnostopoulos]

How big were the genomes of organisms back when ancient genes were evolving? The populations were certainly many orders of magnitude bigger than a million, but how big?

I’ll leave this type of fantasizing to you evolutionists.
...
What I know is that ev shows that when realistic genome lengths and mutation rates are used, the rate of information acquisition is profoundly slow, too slow to explain the theory of information. [emphasis mine]
All righty then.

~~ Paul

[kjkent1]

So write your letter to the editors of the journal--as carefully and well-supported as you would write it to them--and post it here. As is, I see at least two potential problems with your criticism--one a matter of the effects of population size, the other a much more fundamental misunderstanding that presumes a directed evolution aiming for a particular outcome. But without your well-stated argument, it is impossible to evaluate.

And please do not use the construction "a gene is to evolve...". That paragraph, copied and pasted as many times as you have already, has gotten you nowhere. It is that argument that makes me suspect that you have a fundamental misunderstanding. But of course, I could be wrong (it has happened once before, a few years ago); if you focus on your argument, not on the personal sniping, perhaps you can phrase it in such an idiot-proof manner that even I will understand.

If you are willing to do that, I am willing to set aside my request that we evaluate the evidence for your god hypothesis. We can always return to that later.Your suggestions are entirely rational. Why in the world would you try something like that here?

[kjkent1]

All righty then.

~~ PaulI talk to the trees, but they never listen to me... -- Alan J. Lerner, "Paint your Wagon" (1969).

[kleinman]

How big were the genomes of organisms back when ancient genes were evolving? The populations were certainly many orders of magnitude bigger than a million, but how big? I’ll leave this type of fantasizing to you evolutionists.
...
What I know is that ev shows that when realistic genome lengths and mutation rates are used, the rate of information acquisition is profoundly slow, too slow to explain the theory of information. [emphasis Paul’s]All righty then.
Paul, you’ve squeeze out a gnat sized point. Using ev to compute the rate of information acquisition on a 100k genome does not represent a realistic genome length for a free living creature. Do you think the rate of information gain on a 500k genome would be faster or slower than that on a 100k genome? What ev is forcing you to do is take the position that billions of years ago, there were free living organisms with tiny genomes that no longer exist today. As Mercutio said, a mudskipper ate them. This is nothing more than raw speculation. There is no evidence that any such creatures ever existed. How would such creatures carry on metabolic activities and reproduce? How would they code for all the peptides necessary for life? The gap theory strikes again.
If you are willing to do that, I am willing to set aside my request that we evaluate the evidence for your god hypothesis. We can always return to that later. Your suggestions are entirely rational. Why in the world would you try to advance rational suggestions in this forum?
Kjkent1, just how many alternative universes does your string cheese theory of evolution call for?

[Paul C. Anagnostopoulos]

Paul, you’ve squeeze out a gnat sized point. Using ev to compute the rate of information acquisition on a 100k genome does not represent a realistic genome length for a free living creature. Do you think the rate of information gain on a 500k genome would be faster or slower than that on a 100k genome? What ev is forcing you to do is take the position that billions of years ago, there were free living organisms with tiny genomes that no longer exist today. As Mercutio said, a mudskipper ate them. This is nothing more than raw speculation. There is no evidence that any such creatures ever existed. How would such creatures carry on metabolic activities and reproduce? How would they code for all the peptides necessary for life? The gap theory strikes again.
As opposed to the theory that fully-evolved, modern organisms just poofed into existence? Yes, there are gaps in the theory, but at least people are working on it, which is more than we can say for the competing theory.

Do you think that Ev proves that a 500K genome can't evolve a new function, regardless of population and time? If so, could you show us the math?

~~ Paul

[kleinman]

Paul, you’ve squeeze out a gnat sized point. Using ev to compute the rate of information acquisition on a 100k genome does not represent a realistic genome length for a free living creature. Do you think the rate of information gain on a 500k genome would be faster or slower than that on a 100k genome? What ev is forcing you to do is take the position that billions of years ago, there were free living organisms with tiny genomes that no longer exist today. As Mercutio said, a mudskipper ate them. This is nothing more than raw speculation. There is no evidence that any such creatures ever existed. How would such creatures carry on metabolic activities and reproduce? How would they code for all the peptides necessary for life? The gap theory strikes again.As opposed to the theory that fully-evolved, modern organisms just poofed into existence? Yes, there are gaps in the theory, but at least people are working on it, which is more than we can say for the competing theory.
Let’s see if we can figure out your logic. Your own computer model shows your theory to be mathematically impossible but because taxpayers have bamboozled into paying for research into an impossible theory, it makes it a better theory. I wonder how much private money is put into researching your ridiculous theory.
Do you think that Ev proves that a 500K genome can't evolve a new function, regardless of population and time? If so, could you show us the math?
Yes. The mathematical proof is:
Selection process to evolve a new gene from the beginning = f

[kjkent1]

Paul, you’ve squeeze out a gnat sized point. Using ev to compute the rate of information acquisition on a 100k genome does not represent a realistic genome length for a free living creature. Do you think the rate of information gain on a 500k genome would be faster or slower than that on a 100k genome? What ev is forcing you to do is take the position that billions of years ago, there were free living organisms with tiny genomes that no longer exist today. As Mercutio said, a mudskipper ate them. This is nothing more than raw speculation. There is no evidence that any such creatures ever existed. How would such creatures carry on metabolic activities and reproduce? How would they code for all the peptides necessary for life? The gap theory strikes again.

Kjkent1, just how many alternative universes does your string cheese theory of evolution call for?It's not my theory. The theory is proposed by Dr. Leonard Susskind, Ph.D, of Stanford University. It is shared by a large number of the most esteemed high energy physicists and cosmologists on Earth.

To my knowledge, the only person who has adopted your theory of "The failure of the EV program to converge from a random DNA sequence to a human being in under 500,000 generations," is you.

If you want respect from your peers, then you should try to treat their positions with the same respect as you demand of your own. But, you don't. Instead, you make fun of anyone who has an argument which challenges yours. You don't acknowledge that you can't defeat some other reasonable argument, but that you prefer your own. Instead, you pretend that the opposing argument is flat wrong.

I understand why, and so does everyone else. It's because you "know" that God is the only truth, therefore any contradictory argument must be false no matter how well it fits with the facts.

This simply doesn't work when you're arguing with a reasonable opponent, because a reasonable opponent sees through your argument to the reason why you cannot possibly credit anyone else who doesn't see things from your view.

You have no proof of God, and you never will. Using science to prove God is impossible. We all know it, and you know it. The difference is that for those of us who believe in God, we don't interject it into a scientific debate.

You do -- not by expressly stating that God is the truth -- but rather by treating contrary arguments with sarcasm as if you know something that no one else does.

Well, you don't. We're all on the same page, and we find your theory lacking in 100 different ways -- all of which you are content to either avoid, or make fun of.

Yes, this is the annoying creationist thread, and you are the annoying creationist. But, not in the way that someone with a great idea is annoying to someone whose idea is threatened. Rather you are annoying in the way that a 4-year old is annoying when he grabs an egg full of Silly Putty(r) off the "impulse buy" shelf of the checkout counter in the grocery store, and then he cries to high heaven in an effort to avoid any attempt to rationalize with him.

If this is the picture you want to present to your peers, then you have achieved your goal. But, it ain't a pretty picture, Alan.

It's just annoying.

[Paul C. Anagnostopoulos]

Let’s see if we can figure out your logic. Your own computer model shows your theory to be mathematically impossible but because taxpayers have bamboozled into paying for research into an impossible theory, it makes it a better theory. I wonder how much private money is put into researching your ridiculous theory.
As opposed to the coffers of religious organizations, you mean?



Yes. The mathematical proof is:
Selection process to evolve a new gene from the beginning = f
Before you were claiming a mathematical proof based on an incomplete model of evolution. Now you're claiming a mathematical proof based on a gap.

Is there some point where you claim a mathematical proof based on mathematics?

~~ Paul

[kleinman]

Let’s see if we can figure out your logic. Your own computer model shows your theory to be mathematically impossible but because taxpayers have bamboozled into paying for research into an impossible theory, it makes it a better theory. I wonder how much private money is put into researching your ridiculous theory.As opposed to the coffers of religious organizations, you mean?
Paul, is this the best defense of your theory you can muster?
Yes. The mathematical proof is:
Selection process to evolve a new gene from the beginning = fBefore you were claiming a mathematical proof based on an incomplete model of evolution. Now you're claiming a mathematical proof based on a gap.
Now you are defending your theory with the gaps. I guess the more gaps your theory has the better it is. What makes you think you can fill the gap of no selection process to evolve a gene from the beginning? What makes you think you can find a way to speed up the rate of convergence of ev? Do you think modeling multiple simultaneous selection processes in the model will speed up the rate of information gain? Paul you are in denial about the results your computer model show.
Is there some point where you claim a mathematical proof based on mathematics?
Paul, it is Dr Schneider’s and your mathematics upon which my proof is based. Your model reveals the effects of multiple selection process. Your model reveals the flaw in the selection process. It is your model that reveals the mathematical impossibility of the theory of evolution. Now if you want to make a counter argument, change or add features to your model which refute my claims.

[Mercutio]

What is the point of doing this? All I would be doing is reiterating what I have posted on this thread and the Evolutionisdead forum.Then it should be fairly straightforward for you. The point would be that you would have, in one place, the distillation of your argument, honed by criticism by others here and there, in one place where any could see it. If it is worthwhile, at least some here will recognize that; if it is not, you will get more complete criticism. Science progresses this way, not by shying away and coddling your theory.
With respects to the population issue, if you examine this data, you would see that only the first few doublings of the population decrease the generations for convergence markedly. The data appears to be rapidly approach an asymptote. This a far stretch from the conclusion Dr Schneider made about the effects of huge populations on the rates of information acquisition, a conclusion he drew with only a single data point. To get a more conclusive answer on this issue requires far more memory than I have on my computer. A G=1000, population=1meg case takes the entire memory available on my PC (1/2 gigabyte). Any realistic genome size with populations of 10^10 would take millions of gigabytes of memory. That said, you can see trends with the smaller genomes and smaller populations that does not bode well for your theory.If and when you support this, you will put the burden of proof on the other guy. As is, it is as much speculation as assertion. In particular, it may be (I have not seen your argument laid out) that your complaint is easily addressed. After all, you are claiming to have found something that escaped Schneider, his peer reviewers, and the editors. It is possible that something else has escaped you.
If you studied ev, in particular the selection process that Dr Schneider used, you would understand my “a gene is to evolve…” argument. Your theory stands or falls on this definition. I don’t know of a valid definition for selection that would do this and so far no evolutionist has been able to describe such a selection process. Unless you or some other evolutionist can do this, your theory will fail mathematically.See, this is why I want to see the "best, polished for publication" version of your argument. I see a broad expectation of teleology in this argument, and as such dismiss it immediately. Obviously, you must not think it is thus flawed, or you would not continue to present it. One of us is mistaken. If you present it the exact same way each time, I cannot but read it the exact same way. Examine your assumptions--lay them bare, admit them (no theory is without them) so that your readers do not have to assign them.

By my reading of your "a gene is to evolve..." argument, your understanding of natural selection is flawed. Re-write it in such a way that it is clear that it is not your understanding, but natural selection itself, that is flawed.
I think you should evaluate the evidence for God, especially since your own mathematics shows your theory to be impossible.
*sigh* ... for several posts now, I have been asking you *for* the evidence. I am happy to evaluate it. I am even a former born-again christian, so you won't even have to explain your terms. Please, please, give me the evidence in favor of the god hypothesis of abiogenesis.

[Mercutio]

Your suggestions are entirely rational. Why in the world would you try something like that here?

There is a word defining my suggestions. Ask Tricky; he coined it.

[Mr. Scott]

Now if ev only showed what you are proposing. In fact, Dr Schneider’s computer simulation shows the exact opposite of what you are saying.

Paul, is what Alan saying here true? In a large population, when different genes in the same organism duplicate and mutate in parallel, does evolution, as simulated by Ev, slow down?

[Mr. Scott]

Add your gene duplication concept to ev and prove me wrong. Do you see the goalposts?

You are the one with the burden of proof for your hypothesis that evolution is mathematically impossible. You have not met it. I'm quite comfortable with the theory of evolution myself, considering the mountain of consistent evidence that supports it.

The problem with your thesis that evolution is mathematically impossible is that you depend on Ev, which is not a complete simulation of evolution.

I'll give an example to help you understand the fallacy of your procedure:

Suppose I write a computer simulation of bipedal walking, it performs beautifully, and it is well regarded. You take it and change some parameters to try to make it simulate running, and it falls down. You conclude that bipedal motion is therefore mathematically impossible, crow that you used a bipedlist's very program to prove it, and imply that bipedal motion therefore requires divine intervention.

Now, doesn't that sound dumb? Perhaps now you can see how dumb you sound to evolutionists (and, I would surmise, most computer scientists).

BTW: Have you discussed your procedure with any computer scientists who are neutral about evolution? I'd like to know their opinion.

[SomeGuy]

You are the one with the burden of proof for your hypothesis that evolution is mathematically impossible. You have not met it. I'm quite comfortable with the theory of evolution myself, considering the mountain of consistent evidence that supports it.

The problem with your thesis that evolution is mathematically impossible is that you depend on Ev, which is not a complete simulation of evolution.


Well I partially disagree, if there would be a reason to doubt the mathematical possibility of the theory of evolution, the burden of proof would be on us, evolutionists.

However your second argument is spot on, there is no reason to doubt the theory of evolution, but all the more reason to assume Ev doesn't take everything into account that it should.

Naturally this no more invalidates Ev as a helpful tool than the General Theory of Relativity invalidates Newtonian Mechanics as a helpful tool to solve day to day mechanical issues.

editted for omission.

[Taffer]

Kleinmann, I agree with Mercutio. Please provide, in one clear post, your argument along with any evidence you have to support it. As far as I can tell, from reading your posts off and on since the initiation of this thread, your argument goes as follows:

P1) Either evolution and naturalistic abiogenesis is correct, or God is the origin of all life on earth.
P2) The ev simulation shows evolution and naturalistic abiogenesis is impossible.
C) Therefore, God is the origin of all life on earth.

Now, that is a sound argument. If P1 and P2 are both true, then C must be true. However, I have grave problems with both the premises. And no matter how much I read this thread, you are not making yourself any clearer. If you could please provide, in one post, your entire argument and supporting data, I would gladly critically analyse it.

[Paul C. Anagnostopoulos]

Paul, is this the best defense of your theory you can muster?
It's not a defense of any theory, you silly git. It's a sarcastic remark in response to your sarcastic remark:

I wonder how much private money is put into researching your ridiculous theory.

Paul, it is Dr Schneider’s and your mathematics upon which my proof is based.
You have no proof, you silly git. Mathematicians everywhere are gagging at your misuse of the term.

~~ Paul

[Cuddles]

My goodness, is this still here? :popcorn1

[Paul C. Anagnostopoulos]

Paul, is what Alan saying here true? In a large population, when different genes in the same organism duplicate and mutate in parallel, does evolution, as simulated by Ev, slow down?
Ev does not simulate gene duplication. You said:

I don't see the problem with this. In fact, many competing mutation/selection processes makes evolution go even faster because parallel changes are happening within individual organisms. Thanks for pointing this out.
And Alan replied:

Now if ev only showed what you are proposing. In fact, Dr Schneider’s computer simulation shows the exact opposite of what you are saying.
Since Ev only models one mutation/selection process, I'm not sure what Alan means.

~~ Paul

[Mr. Scott]

Well I partially disagree, if there would be a reason to doubt the mathematical possibility of the theory of evolution, the burden of proof would be on us, evolutionists.

Not having a complete mathematical model of bee flight does not mean we have to prove mathematically that bees can fly. We can see they fly.

We have a mountain of physical evidence that confirms evolution is correct. We can see the fact of evolution in the geologic and genetic records. The burden of proof of the claim that goes against this mountain of evidence, that evolution is mathematically impossible, therefore rests with its claimant.

I think only a complete mathematical model of evolution would do that. The burden of developing that model is on the good Doctor Kleinman.

We await his presentation of that model.

[kleinman]

What is the point of doing this? All I would be doing is reiterating what I have posted on this thread and the Evolutionisdead forum.Then it should be fairly straightforward for you. The point would be that you would have, in one place, the distillation of your argument, honed by criticism by others here and there, in one place where any could see it. If it is worthwhile, at least some here will recognize that; if it is not, you will get more complete criticism. Science progresses this way, not by shying away and coddling your theory.
I think I will do what you suggest. Dr Schneider’s work is too important to not be carefully analyzed, something which evolutionists have failed to do.
With respects to the population issue, if you examine this data, you would see that only the first few doublings of the population decrease the generations for convergence markedly. The data appears to be rapidly approach an asymptote. This a far stretch from the conclusion Dr Schneider made about the effects of huge populations on the rates of information acquisition, a conclusion he drew with only a single data point. To get a more conclusive answer on this issue requires far more memory than I have on my computer. A G=1000, population=1meg case takes the entire memory available on my PC (1/2 gigabyte). Any realistic genome size with populations of 10^10 would take millions of gigabytes of memory. That said, you can see trends with the smaller genomes and smaller populations that does not bode well for your theory.If and when you support this, you will put the burden of proof on the other guy. As is, it is as much speculation as assertion. In particular, it may be (I have not seen your argument laid out) that your complaint is easily addressed. After all, you are claiming to have found something that escaped Schneider, his peer reviewers, and the editors. It is possible that something else has escaped you.
Oh, the population data that can be generated with ev obtained by Paul, Myriad and my computer runs has been posted both on this thread and the Evolutionisdead forum. This information would be easier to understand if put in report form rather than this debate format.
If you studied ev, in particular the selection process that Dr Schneider used, you would understand my “a gene is to evolve…” argument. Your theory stands or falls on this definition. I don’t know of a valid definition for selection that would do this and so far no evolutionist has been able to describe such a selection process. Unless you or some other evolutionist can do this, your theory will fail mathematically.See, this is why I want to see the "best, polished for publication" version of your argument. I see a broad expectation of teleology in this argument, and as such dismiss it immediately. Obviously, you must not think it is thus flawed, or you would not continue to present it. One of us is mistaken. If you present it the exact same way each time, I cannot but read it the exact same way. Examine your assumptions--lay them bare, admit them (no theory is without them) so that your readers do not have to assign them.
If you read this thread carefully, you would see my arguments about ev based purely on mathematics. So what if I believe in God? Does that mean 2+2 no longer equals 4? You have got a big mathematical problem with your theory. Ev reveals this.
By my reading of your "a gene is to evolve..." argument, your understanding of natural selection is flawed. Re-write it in such a way that it is clear that it is not your understanding, but natural selection itself, that is flawed.
My “a gene is to evolve…” argument is not the problem. The problem is that you evolutionists have no precise description for selection when using the slogan “mutation and natural selection” for your theory of evolution. You like to say “mutation and selection” when describing how evolution works, well describe selection such that you can put it in ev and evolve a gene from the beginning. Otherwise, your terminology is no more than vague ambiguous hand waving that you try to claim is scientific.
I think you should evaluate the evidence for God, especially since your own mathematics shows your theory to be impossible.*sigh* ... for several posts now, I have been asking you *for* the evidence. I am happy to evaluate it. I am even a former born-again christian, so you won't even have to explain your terms. Please, please, give me the evidence in favor of the god hypothesis of abiogenesis.
Don’t worry, the “Cliff notes” version of this thread will come out so even you can understand that you have embraced a mathematically impossible theory of evolution. Anyone who has studied a basic course in organic chemistry should recognize the impossibility of the evolutionist concept of abiogenesis.
Your suggestions are entirely rational. Why in the world would you try something like that here?There is a word defining my suggestions. Ask Tricky; he coined it.
I said your theory of evolution is irrational and in addition, mathematically unsound. Your suggestion to compile this thread into a coherent report is rational but will take some time. I have 500 pages of discussion in my word processor. Of course if I remove the evolutionists’ whining and complaining, especially about moving goalposts and just discuss the mathematics of ev, that would reduce the volume in half. I do think I should include kjkent1’s string cheese theory of evolution.
Now if ev only showed what you are proposing. In fact, Dr Schneider’s computer simulation shows the exact opposite of what you are saying.Paul, is what Alan saying here true? In a large population, when different genes in the same organism duplicate and mutate in parallel, does evolution, as simulated by Ev, slow down?
Mr Scott, perhaps Paul will address your question below, but if you read back in the thread, Paul proposes a concept of Rcapacity for why ev does not converge when you exceed a certain length of genome. The failure to converge occurs because there are two competing selection processes. One selection condition is the failure to identify a binding site where there should be a binding site and the other condition is locating a binding site where there shouldn’t be a binding site. As you lengthen the genome, the second condition becomes the dominant selection condition and binding sites stop evolving.
Add your gene duplication concept to ev and prove me wrong. Do you see the goalposts? You are the one with the burden of proof for your hypothesis that evolution is mathematically impossible. You have not met it. I'm quite comfortable with the theory of evolution myself, considering the mountain of consistent evidence that supports it.
It is plain from the results of ev that random point mutations and natural selection can evolve nothing in a reasonable length of time (the age of the universe) on a realistic genome length with a realistic mutation rate. Without a selection process nothing can evolve ever, even if you have duplications, insertions, deletions or whatever mechanism of mutation you want. Perhaps you would offer a selection process that can evolve a gene from the beginning?
The problem with your thesis that evolution is mathematically impossible is that you depend on Ev, which is not a complete simulation of evolution.
And the fact that there is no selection process that can evolve a gene from the beginning. How do you select for something that doesn’t exist?
Suppose I write a computer simulation of bipedal walking, it performs beautifully, and it is well regarded. You take it and change some parameters to try to make it simulate running, and it falls down. You conclude that bipedal motion is therefore mathematically impossible, crow that you used a bipedlist's very program to prove it, and imply that bipedal motion therefore requires divine intervention.
The problem with your analogy is that I think Dr Schneider’s model of mutation and selection is basically correct except his selection process is contrived. If you think you can correct Dr Schneider’s model and take it from walking to running, add the selection process that would do this.
Now, doesn't that sound dumb? Perhaps now you can see how dumb you sound to evolutionists (and, I would surmise, most computer scientists).
What sounds dumb is your failure to understand that the results from ev shows that random point mutations and natural selection is a mathematically impossible and yet you think that duplications, insertions, deletions and other mutation mechanisms without a selection process will somehow accomplish mathematically what you claim.
BTW: Have you discussed your procedure with any computer scientists who are neutral about evolution? I'd like to know their opinion.
What question would you have me ask a computer scientist? I think that Dr Schneider properly captured the mathematics of random point mutation and selection (except for the contrived selection process).
Well I partially disagree, if there would be a reason to doubt the mathematical possibility of the theory of evolution, the burden of proof would be on us, evolutionists.

However your second argument is spot on, there is no reason to doubt the theory of evolution, but all the more reason to assume Ev doesn't take everything into account that it should.
What part don’t you agree with that it is evolutionists’ responsibility to prove your own theory?

You are dreaming if you think your theory can stand without an accurate description for selection process that would correct the deficiency that ev reveals.
Naturally this no more invalidates Ev as a helpful tool than the General Theory of Relativity invalidates Newtonian Mechanics as a helpful tool to solve day to day mechanical issues.
Relativity extends Newtonian Mechanics; ev turns the theory of evolution upside down.
Kleinmann, I agree with Mercutio. Please provide, in one clear post, your argument along with any evidence you have to support it. As far as I can tell, from reading your posts off and on since the initiation of this thread, your argument goes as follows:
I will compile these threads into a single document but it will take some time.
P1) Either evolution and naturalistic abiogenesis is correct, or God is the origin of all life on earth.
P2) The ev simulation shows evolution and naturalistic abiogenesis is impossible.
C) Therefore, God is the origin of all life on earth.
I’ll let you work on P2 for a while so that you can convince yourself that this is the case.
Now, that is a sound argument. If P1 and P2 are both true, then C must be true. However, I have grave problems with both the premises. And no matter how much I read this thread, you are not making yourself any clearer. If you could please provide, in one post, your entire argument and supporting data, I would gladly critically analyse it.
I realize that these threads are not easy to wade through and I will produce a single document that summarizes what has already been presented. While I am doing this, I suggest you familiarize yourself with ev and Dr Schneider’s writings.
Paul, is this the best defense of your theory you can muster?It's not a defense of any theory, you silly git. It's a sarcastic remark in response to your sarcastic remark:
I see, you can’t defend the mathematics of your theory so you resort to sarcasm, Mr Rcapacity.
I wonder how much private money is put into researching your ridiculous theory.

Paul, it is Dr Schneider’s and your mathematics upon which my proof is based.You have no proof, you silly git. Mathematicians everywhere are gagging at your misuse of the term.
Oh really, no proof, Mr Ev represents reality but now Mr Ev represents a stylized model of mutation and selection. I think you are going to have to do some work on your evolutionary landscaping. It is starting to look like an evolutionary moonscape; nothing but craters and gaps.
My goodness, is this still here?
Certainly, ev is one of those gifts that keeps on giving.
Paul, is what Alan saying here true? In a large population, when different genes in the same organism duplicate and mutate in parallel, does evolution, as simulated by Ev, slow down? Ev does not simulate gene duplication.
That’s not a very good answer to his question Mr Rcapacity.
I don't see the problem with this. In fact, many competing mutation/selection processes makes evolution go even faster because parallel changes are happening within individual organisms. Thanks for pointing this out. And Alan replied: Now if ev only showed what you are proposing. In fact, Dr Schneider’s computer simulation shows the exact opposite of what you are saying.Since Ev only models one mutation/selection process, I'm not sure what Alan means.
Let’s see if I can explain this to you Mr Rcapacity. When the genome is lengthened beyond a certain point in ev, the errors in the non-binding site region dominate the selection process and stops the evolution of binding sites. So what you call a “one mutation/selection process” in actuality is two selection conditions. One condition is the selection for binding sites on the binding site region of the genome and the other condition is selection for no binding sites on the non-binding site region of the genome. Do you understand what I mean Mr Rcapacity?
We have a mountain of physical evidence that confirms evolution is correct. We can see the fact of evolution in the geologic and genetic records. The burden of proof of the claim that goes against this mountain of evidence, that evolution is mathematically impossible, therefore rests with its claimant.
Too bad that mountain doesn’t include evidence from ev.
I think only a complete mathematical model of evolution would do that. The burden of developing that model is on the good Doctor Kleinman.
Do you think that including gene duplication, insertions and deletions and other forms of mutations in ev is going to correct the problem of now selection process to evolve a gene from the beginning? Describe the selection process and I’ll write the model. I doubt I’ll ever have to do any programming on this problem.

[Taffer]

Thank you, kleinmann. I await your compiled argument. I will look more in depth into ev, when I have time.

[Paul C. Anagnostopoulos]

That’s not a very good answer to his question Mr Rcapacity.
I'm not sure what else to say. Ev does not model gene duplication.


Let’s see if I can explain this to you Mr Rcapacity. When the genome is lengthened beyond a certain point in ev, the errors in the non-binding site region dominate the selection process and stops the evolution of binding sites. So what you call a “one mutation/selection process” in actuality is two selection conditions. One condition is the selection for binding sites on the binding site region of the genome and the other condition is selection for no binding sites on the non-binding site region of the genome. Do you understand what I mean Mr Rcapacity?
Yes, that is a fine way of looking at it. In fact, there are three selection conditions: binding at the sites, spurious binding within the gene, spurious binding outside the gene.

However, your idea of spurious bindings dominating the selection process needs more thought. It certainly has an effect on the evolution, but I very much doubt it "stops" it. The stopping is due to Rcapacity problems. You'll remember I ran some experiments where we crossed the Rcapacity threshold with only a slight increase in the ratio of non-binding-site size to binding-site size, and evolution was thwarted. I very much doubt that's due to the increase in the ratio.

But you can always run some experiments to see if you can get evolution to "stop" without running up against Rcapacity. If this "stopping" is some sort of fundamental feature of evolution, you ought to be able to invoke it without requiring huge genomes.

~~ Paul

[Mercutio]

I, too, look forward to the document. I have a few suspicions about possible flaws in Kleinman's arguments, but it would be pointless to argue against something without that something being well-presented to begin with.

Take your time--edit well...

[kleinman]

Paul, is what Alan saying here true? In a large population, when different genes in the same organism duplicate and mutate in parallel, does evolution, as simulated by Ev, slow down? Ev does not simulate gene duplication.That’s not a very good answer to his question Mr Rcapacity.I'm not sure what else to say. Ev does not model gene duplication.
Your stylized model of random point mutation and natural selection does include two selection conditions operating in parallel. These competing conditions not only cause evolution as simulated by ev to slow down, but it can draw evolution to a complete standstill.
Let’s see if I can explain this to you Mr Rcapacity. When the genome is lengthened beyond a certain point in ev, the errors in the non-binding site region dominate the selection process and stops the evolution of binding sites. So what you call a “one mutation/selection process” in actuality is two selection conditions. One condition is the selection for binding sites on the binding site region of the genome and the other condition is selection for no binding sites on the non-binding site region of the genome. Do you understand what I mean Mr Rcapacity?Yes, that is a fine way of looking at it. In fact, there are three selection conditions: binding at the sites, spurious binding within the gene, spurious binding outside the gene.
You did add the third selection condition to the model since we started our discussion. Did adding the third selection condition speed up evolution or slow down evolution when including all three selection conditions in a simulation?
However, your idea of spurious bindings dominating the selection process needs more thought. It certainly has an effect on the evolution, but I very much doubt it "stops" it. The stopping is due to Rcapacity problems. You'll remember I ran some experiments where we crossed the Rcapacity threshold with only a slight increase in the ratio of non-binding-site size to binding-site size, and evolution was thwarted. I very much doubt that's due to the increase in the ratio.
Your Rcapacity concept needs more thought. What makes you think that the weight matrix will no longer find a match on the genome just because the genome exceeds a particular length? The failure of ev to converge is not due to a failure of the weight matrix finding binding sites, it is due to the weight matrix finding erroneous sites in the non-binding site region which when these errors dominate the selection process, no evolution of binding sites can occur in the binding site region. You have the program set up to count errors. See for yourself which errors are driving the selection process. When the genome is short, errors in the binding site region drives selection and the binding sites rapidly evolve. As errors in the non-binding site region increase, it becomes more and more difficult for ev to select for the evolution of binding sites until ultimately, the errors in the non-binding site region dominates and no evolution of binding sites can occur.
But you can always run some experiments to see if you can get evolution to "stop" without running up against Rcapacity. If this "stopping" is some sort of fundamental feature of evolution, you ought to be able to invoke it without requiring huge genomes.
We already have experiments. We have the original form of ev with two selection conditions which fails to converge with short genome lengths (far shorter than any realistic length for a free living creature). You then introduced a third selection condition, which is spurious binding in the binding site region. Does this third condition speed up or slow down evolution? This concept goes to the core of Mr Scott’s question. Do multiple selection conditions acting in parallel speed up or slow down evolution? Ev shows that multiple selection conditions acting in parallel slows down evolution. There is no reason to believe that this effect would be countered by adding other mutation mechanism such as gene duplication, indels or any other mutation mechanism. So as you take your stylized model of random point mutations and natural selection and make it more realistic, the number of generations for convergence will become larger and larger as your include more and more selection processes. Paul, the theory of evolution is mathematically impossible.

[Paul C. Anagnostopoulos]

Your stylized model of random point mutation and natural selection does include two selection conditions operating in parallel. These competing conditions not only cause evolution as simulated by ev to slow down, but it can draw evolution to a complete standstill.
What does this have to do with whether Ev models gene duplication?


You did add the third selection condition to the model since we started our discussion. Did adding the third selection condition speed up evolution or slow down evolution when including all three selection conditions in a simulation?
Ev has always scored mistake points for missed bindings, spurious bindings within the gene, and spurious bindings outside the gene. What was added in November, 2005, was the ability to specify different mistake points for these three situations.


Your Rcapacity concept needs more thought. What makes you think that the weight matrix will no longer find a match on the genome just because the genome exceeds a particular length?
It's not the length that matters, but Rfrequency and Rsequence. In order to evolve a perfect creature, Rseq must approach Rfreq. But if the binding sites are too narrow relative to the genome size, then they cannot contain a pattern (as shown in the sequence logo) that is unique enough for the transcription factor to match it but nowhere else.

The failure of ev to converge is not due to a failure of the weight matrix finding binding sites, it is due to the weight matrix finding erroneous sites in the non-binding site region which when these errors dominate the selection process, no evolution of binding sites can occur in the binding site region.
It's not that the matrix fails to match binding sites, but that it too easily succeeds in matching elsewhere. This is certainly affected by the genome size, but I see no reason why, barring Rcapacity issues, it should ever halt evolution entirely. What would cause the discontinuity? If you think it does, run some Ev models and find out when and why.

You have the program set up to count errors. See for yourself which errors are driving the selection process. When the genome is short, errors in the binding site region drives selection and the binding sites rapidly evolve. As errors in the non-binding site region increase, it becomes more and more difficult for ev to select for the evolution of binding sites until ultimately, the errors in the non-binding site region dominates and no evolution of binding sites can occur.
I agree with everything except your conclusion.


We already have experiments. We have the original form of ev with two selection conditions which fails to converge with short genome lengths (far shorter than any realistic length for a free living creature).
The only relevant experiments we have are the ones I ran, mentioned above. If you think you have others, present the parameters.

On the other hand, if you are simply going to refuse to accept the fact that there is an Rcapacity issue, no reason to waste our time.

~~ Paul

[Dr Adequate]

Let’s see if we can figure out your logic. Your own computer model shows your theory to be mathematically impossible but because taxpayers have bamboozled into paying for research into an impossible theory, it makes it a better theory. I wonder how much private money is put into researching your ridiculous theory.


I see that kleinman has told Lie #1 again.

No new lies, eh, kleinman?

If you're planning to recite lies until reality disappears, why do it in public? 'Cos, you know, if this strange magical ritual doesn't overturn the laws of nature, people will laugh at you and think you're off your head.

Yes. The mathematical proof is:
Selection process to evolve a new gene from the beginning = f

As a mathematician, I can tell the difference between a mathematical proof and the screaming, gibbering, and twitching of a lunatic trying to hide from reality. That was the latter; and if you are unable to do any maths to back up your crackpot hypothesis, then drooling out nonsense like this is no substitute.

[kleinman]

Your stylized model of random point mutation and natural selection does include two selection conditions operating in parallel. These competing conditions not only cause evolution as simulated by ev to slow down, but it can draw evolution to a complete standstill.What does this have to do with whether Ev models gene duplication?
Again I post Mr Scott’s question.
Paul, is what Alan saying here true? In a large population, when different genes in the same organism duplicate and mutate in parallel, does evolution, as simulated by Ev, slow down?
You evade the key part of his question by simply saying ev does not model gene duplication. The key part of his question is concerns what the effect of multiple selection processes have on the rate of evolution. Ev shows that multiple selection processes slow down evolution.
You did add the third selection condition to the model since we started our discussion. Did adding the third selection condition speed up evolution or slow down evolution when including all three selection conditions in a simulation?Ev has always scored mistake points for missed bindings, spurious bindings within the gene, and spurious bindings outside the gene. What was added in November, 2005, was the ability to specify different mistake points for these three situations.
I stand corrected on this point. What happens when you weight mistakes for missed binding sites to the maximum value while setting spurious binding in an out of the binding site region to 0? Then what happens as you increase the weights for spurious binding sites?
Your Rcapacity concept needs more thought. What makes you think that the weight matrix will no longer find a match on the genome just because the genome exceeds a particular length?It's not the length that matters, but Rfrequency and Rsequence. In order to evolve a perfect creature, Rseq must approach Rfreq. But if the binding sites are too narrow relative to the genome size, then they cannot contain a pattern (as shown in the sequence logo) that is unique enough for the transcription factor to match it but nowhere else.
The following is your first public post concerning your Rcapacity concept from the Evolutionisdead forum:
What's happening is that Rfrequency is approaching Rcapacity, the information capacity of the binding sites. In this experiment, Rcapacity = 12 bits. At Rfrequency = Rcapacity, the number of generations to evolve a perfect creature is infinite. This is what we're seeing in our data sets.
This issue has nothing to do with the “transcription factor” (weight matrix) to match a binding site but nowhere else. The weight matrix will find matches anywhere on the genome where the sequence of bases is appropriate. As you lengthen the non-binding site region, you have more potential sites for a match. It is this increase in potential sites on the non-binding site region which slows down and ultimately stops evolution of the binding sites.
The failure of ev to converge is not due to a failure of the weight matrix finding binding sites, it is due to the weight matrix finding erroneous sites in the non-binding site region which when these errors dominate the selection process, no evolution of binding sites can occur in the binding site region.It's not that the matrix fails to match binding sites, but that it too easily succeeds in matching elsewhere. This is certainly affected by the genome size, but I see no reason why, barring Rcapacity issues, it should ever halt evolution entirely. What would cause the discontinuity? If you think it does, run some Ev models and find out when and why.
The weight matrix does not find matches more easily on the non-binding site region of the genome as you lengthen the genome; you simply have more potential sites for erroneous binding. Set the weighting factor for errors in the non-binding site region to 0 and your Rcapacity problem disappears.
You have the program set up to count errors. See for yourself which errors are driving the selection process. When the genome is short, errors in the binding site region drives selection and the binding sites rapidly evolve. As errors in the non-binding site region increase, it becomes more and more difficult for ev to select for the evolution of binding sites until ultimately, the errors in the non-binding site region dominates and no evolution of binding sites can occur. I agree with everything except your conclusion.
So what did you mean when you said this?
At Rfrequency = Rcapacity, the number of generations to evolve a perfect creature is infinite. This is what we're seeing in our data sets.
We already have experiments. We have the original form of ev with two selection conditions which fails to converge with short genome lengths (far shorter than any realistic length for a free living creature).
The only relevant experiments we have are the ones I ran, mentioned above. If you think you have others, present the parameters.
I’m talking about the experiments you ran varying the parameters which shows that erroneous binding slows down evolution. Those are good experiments. I think I’ll co-opt the results.
On the other hand, if you are simply going to refuse to accept the fact that there is an Rcapacity issue, no reason to waste our time.
Oh, there is an “Rcapacity” issue, but the explanation is that competing selection processes slow down and ultimately stop evolution in the ev model. This phenomenon that ev is demonstrating also occurs in reality.

Now Paul, it is not my aim to waste your time, my aim is to annoy you.

[Gargoyle]

So kleinman is trying to "annoy" us?

I find him rather like a soap opera - dull and repetative, but you just can't stop watching because of the stilted acting and laughable script.
A human perpetuum mobile of circular argumentation.
Great entertainment!

[kjkent1]

You evade the key part of his question by simply saying ev does not model gene duplication. The key part of his question is concerns what the effect of multiple selection processes have on the rate of evolution. Ev shows that multiple selection processes slow down evolution.

I stand corrected on this point. What happens when you weight mistakes for missed binding sites to the maximum value while setting spurious binding in an out of the binding site region to 0? Then what happens as you increase the weights for spurious binding sites?We can't use zero for a mistake value.

Zeroing one of the weight variables in ev prevents ev from evaluating the existence of that type of mistake, during selection. But, the mistake remains in the genome. So, by zeroing out a mistake, we would be introducing a programming error.

The only way to evolve towards a "perfect creature" is to permit ev's selection method to find all the mistakes. Reweighting the mistake values will change the importance of a particular mistake in determining survival fitness. But, if we set a mistake to zero, we are allowing that mistake to be completely ignored, which means it has no importance to survival.

In the former case, eventually all mistakes will be eliminated via selection and a legitimate "perfect creature" will appear. In the latter case, the mistake will be ignored, and the perfect creature which appears isn't actually perfect. It's still full of the mistake(s) which have been set to zero.

[kleinman]

So kleinman is trying to "annoy" us?
Trying? Ask Paul whether I’m successful at annoying evolutionists. The only thing I am better at is showing that the theory of evolution is mathematically impossible using the ev computer model.
I find him rather like a soap opera - dull and repetative, but you just can't stop watching because of the stilted acting and laughable script.
A human perpetuum mobile of circular argumentation.
Great entertainment!
I’m looking for something in Gargoyle’s post that breaks the pattern of dull and repetitive in this thread but it just isn’t there. Perhaps you should try something new and unusual, for example claim moving goalposts, or try yelling strawman? Oh, wait, there it is, you post gifs and jpegs. That certainly breaks the dull and repetitive nature of this thread. How clever you evolutionists are.
You evade the key part of his question by simply saying ev does not model gene duplication. The key part of his question is concerns what the effect of multiple selection processes have on the rate of evolution. Ev shows that multiple selection processes slow down evolution.

I stand corrected on this point. What happens when you weight mistakes for missed binding sites to the maximum value while setting spurious binding in an out of the binding site region to 0? Then what happens as you increase the weights for spurious binding sites? We can't use zero for a mistake value.
Sure you can kjkent1, it’s just a computer program. Don’t tell me you are a member of ASPCPC, the American Society for the Prevention of Cruelty to Perfect Creatures.
Zeroing one of the weight variables in ev prevents ev from evaluating the existence of that type of mistake, during selection. But, the mistake remains in the genome. So, by zeroing out a mistake, we would be introducing a programming error.
Set the value to 10^-10. We don’t want you to divide by zero. Your theory might blow up.
The only way to evolve towards a "perfect creature" is to permit ev's selection method to find all the mistakes. Reweighting the mistake values will change the importance of a particular mistake in determining survival fitness. But, if we set a mistake to zero, we are allowing that mistake to be completely ignored, which means it has no importance to survival.
Just what is the function of the “perfect creature”?
In the former case, eventually all mistakes will be eliminated via selection and a legitimate "perfect creature" will appear. In the latter case, the mistake will be ignored, and the perfect creature which appears isn't actually perfect. It's still full of the mistake(s) which have been set to zero.
I thought you were arguing the Rsequence -> Rfrequency is how convergence should be measured?

[kjkent1]

Sure you can kjkent1, it’s just a computer program. Don’t tell me you are a member of ASPCPC, the American Society for the Prevention of Cruelty to Perfect Creatures.

Set the value to 10^-10. We don’t want you to divide by zero. Your theory might blow up.This is not a divide by zero or a limit of a function issue. It's a programming state issue. The program selects by evaluating mistakes based on their weight. A mistake with a very small value will still be evaluated -- albeit with less selective weight than a mistake with a higher value -- but a mistake with a zero value will not be evaluated at all.Just what is the function of the “perfect creature”?A perfect creature for ev purposes is a genetic sequence with neither missing nor spurious bindings.I thought you were arguing the Rsequence -> Rfrequency is how convergence should be measured?I was indeed arguing that Rseq->Rfreq is how evolution should be measured. However, Paul explained that ev doesn't select for convergence, but rather that convergence is an artifact of ev selecting against missing and spurious bindings.

I believe that Paul's explanation is correct, and it further explains what you would describe as micro vs. macro-evolution, because a perfect creature can either evolve slowly over time, or it can simply appear by random chance between generations. And, when the latter state occurs, that creature's improvements quickly takes over the entire population (in ev, at the rate of 2generation(s)).

If we presume that ev is modeling a binding site region contained within the genome of an already existing creature (and we must, because otherwise, the ev creatures are all already alive and functioning at the start of every program run, even though none have yet evolved any genetic material), then such random accidents would explain how new functionality can appear rapidly, and thereby avoid the slower micro-evolutionary process, which you argue proves evolution mathematically impossible.

Also, it's worth noting that there is no requirement in nature that Rseq->Rfreq. It happens to be that "on average," Rseq->Rfreq is an attribute of genes in functioning organisms. But, it's just an average, which doesn't mean that a gene must have a perfect set of bindings to function. As far as I'm aware, no one has expressed the minimum requirements for a functioning gene. It could be that convergence may be sufficient, but not necessary for viable life functions.

[Paul C. Anagnostopoulos]

Let's run a little experiment to demonstrate the Rcapacity problem.

population 64
genome size 1024
binding sites 8
mutations/generation 4

This makes Rfrequency = 7.

Now, let's vary the weight and binding site widths, starting with 2 and 1, and increasing by 1. Here are the results:

weight/site width, Rcapacity, generations to perfect creature

1/2, 2, ---
2/3, 4, ---
3/4, 6, ---
5/4, 8, 19137
6/5, 10, 2742

Notice that the genome size is constant and the ratio of nonbinding-site genome to binding-site genome is roughly constant. We can keep it more constant by increasing the genome size to 2048, making Rfrequency = 8. The mutations/generation is 8.

weight/site width, Rcapacity, generations to perfect creature

1/2, 2, ---
2/3, 4, ---
3/4, 6, ---
5/4, 8, ---
6/5, 10, 4105
7/6, 12, 4117

It's an amazing thing, don't you think?

~~ Paul

[Paul C. Anagnostopoulos]

Oh, there is an “Rcapacity” issue, but the explanation is that competing selection processes slow down and ultimately stop evolution in the ev model. This phenomenon that ev is demonstrating also occurs in reality.
Convince us by running a series of experiments that shows evolution stopping, but not at the Rcapacity boundary.

The problem, see, is that you refuse to acknowledge that a binding site too narrow to contain a unique sequence logo simply cannot evolve a perfect creature, regardless of the size of the genome.

~~ Paul

[kleinman]

Sure you can kjkent1, it’s just a computer program. Don’t tell me you are a member of ASPCPC, the American Society for the Prevention of Cruelty to Perfect Creatures.

Set the value to 10^-10. We don’t want you to divide by zero. Your theory might blow up.This is not a divide by zero or a limit of a function issue. It's a programming state issue. The program selects by evaluating mistakes based on their weight. A mistake with a very small value (the program only allows integers) will still be evaluated -- albeit more slowly than a mistake with a higher value -- but a mistake with a zero value will not be evaluated at all.
What you need to consider is what the program is evaluating. What is the selection pressure that has been defined by Dr Schneider? It is this definition which is applied to increase the information content in the genome by the mutation and selection process and it is this definition which is the contrivance required in order to make the genomes evolve. There may be a basis in reality to include a selection condition that says the identification of a binding site where one should not exist represents a harmful mutation because an inappropriate protein would be transcribed. But as a basis for studying the mathematics of mutation and selection, setting these mistakes in the non-binding site region to 0 to illustrate why ev won’t converge is useful for identifying how this process works.
Just what is the function of the “perfect creature”?A perfect creature for ev purposes is a genetic sequence with neither missing nor spurious bindings.
And that function of the “perfect creature” is based on two selection conditions you have just described. If you add another selection condition on the perfect creatures (such as evolving a different set of binding sites), what do you think would happen?
I thought you were arguing the Rsequence -> Rfrequency is how convergence should be measured? I was indeed arguing that Rseq->Rfreq is how evolution should be measured. However, Paul explained that ev doesn't select for convergence, but rather that convergence is an artifact of ev selecting against missing and spurious bindings.
You can use either “perfect creature” or Rseq->Rfreq convergence criterion and neither will converge when you use Dr Schneider’s selection conditions and the genome exceeds the length defined by Paul’s Rcapacity variable. The reason is the spurious bindings dominate the selection process and no binding sites evolve.
I believe that Paul's explanation is correct, and it further explains what you would describe as micro vs. macro-evolution, because a perfect creature can either evolve slowly over time, or it can simply appear by random chance between generations. And, when the latter state occurs, that creature's improvements quickly takes over the entire population (in ev, at the rate of 2generation(s)).
If you are going to take the position the life appeared strictly by random chance, you better stick with your string cheese theory and 10^500 alternative universes.
If we presume that ev is modeling a binding site region contained within the genome of an already existing creature (and we must, because otherwise, the ev creatures are all already alive and functioning at the start of every program run, even though none have yet evolved any genetic material), then such random accidents would explain how new functionality can appear rapidly, and thereby avoid the slower micro-evolutionary process, which you argue proves evolution mathematically impossible.
Nothing appears rapidly in ev when you use realistic genome lengths and mutation rates. Nothing appears in ev at all without a selection process. And there is no selection process that can evolve a gene from the beginning. You can’t select for something that doesn’t exist.
Also, it's worth noting that there is no requirement in nature that Rseq->Rfreq. It happens to be that "on average," Rseq->Rfreq is an attribute of genes in functioning organisms. But, it's just an average, which doesn't mean that a gene must have a perfect set of bindings to function. As far as I'm aware, no one has expressed the minimum requirements for a functioning gene. It could be that convergence may be sufficient, but not necessary for viable life functions.
I don’t believe what you are saying is physiologically or biologically true. The rates of chemical reactions in living things can be affected by how well enzymes bind to reactants. Differences in binding sites can affect the affinity of binding proteins. A realistic selection process would take into account these differences. So not only do you have competing selection processes that would slow down the evolutionary process, you have subtle differences in a given selection process that would have to be taken into account to make a realistic mathematical model. Each of these conditions reveals the mathematical impossibility for the theory of evolution. You have no selection process that can evolve a gene from the beginning and competing selection processes stop the evolutionary process.
Oh, there is an “Rcapacity” issue, but the explanation is that competing selection processes slow down and ultimately stop evolution in the ev model. This phenomenon that ev is demonstrating also occurs in reality.Convince us by running a series of experiments that shows evolution stopping, but not at the Rcapacity boundary.
Paul, you have already run the experiment. Don’t you recall having difficulty in understanding why the generations for convergence does not go up linearly with increasing genome length and a fixed mutation rate as a function of a number of bases? You raised this question on the following thread: http://forums.randi.org/showthread.php?t=67488 (http://forums.randi.org/showthread.php?t=67488)

When you ignore the errors in the non-binding site region, you uncouple the rate of convergence from the genome length.
The problem, see, is that you refuse to acknowledge that a binding site too narrow to contain a unique sequence logo simply cannot evolve a perfect creature, regardless of the size of the genome.
The problem is you can’t remember the experiments you have done. Why did Unnamed’s selection process converge for much larger genomes than Dr Schneider’s selection process? Both selection processes use the same weight matrix and site widths.

[Paul C. Anagnostopoulos]

Paul, you have already run the experiment. Don’t you recall having difficulty in understanding why the generations for convergence does not go up linearly with increasing genome length and a fixed mutation rate as a function of a number of bases?
Alan! Kleinman! You're claiming that evolution will stop dead. I'm not arguing that its speed varies. Demonstrate that it stops dead.


The problem is you can’t remember the experiments you have done. Why did Unnamed’s selection process converge for much larger genomes than Dr Schneider’s selection process? Both selection processes use the same weight matrix and site widths.
Because the selection procedure was not as discrete as the standard one, allowing for selection among creatures with the same mistake counts.

~~ Paul

[Paul C. Anagnostopoulos]

You can use either “perfect creature” or Rseq->Rfreq convergence criterion and neither will converge when you use Dr Schneider’s selection conditions and the genome exceeds the length defined by Paul’s Rcapacity variable. The reason is the spurious bindings dominate the selection process and no binding sites evolve.
Rcapacity is not a function of genome size!

Hey Alan, care to comments on the experiments I reported above?

~~ Paul

[kjkent1]

Why did Unnamed’s selection process converge for much larger genomes than Dr Schneider’s selection process? Both selection processes use the same weight matrix and site widths.Unnamed's selection process weighted mistakes by the sum of their strengths, rather than by their aggregate number. This effectively made a creature with more mistakes much less fit and a creature with less mistakes much more fit for for the purpose of determining whether or not to select it for survival.

That's all the algorithm does, although you've consistently claimed otherwise.

[kleinman]

Paul, you have already run the experiment. Don’t you recall having difficulty in understanding why the generations for convergence does not go up linearly with increasing genome length and a fixed mutation rate as a function of a number of bases? Alan! Kleinman! You're claiming that evolution will stop dead. I'm not arguing that its speed varies. Demonstrate that it stops dead.
Paul, it is already demonstrated. You call it Rcapacity affect but it is due to the dominance of spurious binding in the non-binding site region.
The problem is you can’t remember the experiments you have done. Why did Unnamed’s selection process converge for much larger genomes than Dr Schneider’s selection process? Both selection processes use the same weight matrix and site widths.Because the selection procedure was not as discrete as the standard one, allowing for selection among creatures with the same mistake counts.
How does that differ from varying the weight on the different errors in your model? Weight the errors for missed binding sites different than spurious binding errors and see whether your estimate for Rcapacity changes. Post your version on the evjava web page and I’ll generate the data to show this.
You can use either “perfect creature” or Rseq->Rfreq convergence criterion and neither will converge when you use Dr Schneider’s selection conditions and the genome exceeds the length defined by Paul’s Rcapacity variable. The reason is the spurious bindings dominate the selection process and no binding sites evolve.Rcapacity is not a function of genome size!
It is if you vary the weights for the different types of errors.
Hey Alan, care to comments on the experiments I reported above?
Let's run a little experiment to demonstrate the Rcapacity problem.

population 64
genome size 1024
binding sites 8
mutations/generation 4

This makes Rfrequency = 7.

Now, let's vary the weight and binding site widths, starting with 2 and 1, and increasing by 1. Here are the results:

weight/site width, Rcapacity, generations to perfect creature

1/2, 2, ---
2/3, 4, ---
3/4, 6, ---
5/4, 8, 19137
6/5, 10, 2742

Notice that the genome size is constant and the ratio of nonbinding-site genome to binding-site genome is roughly constant. We can keep it more constant by increasing the genome size to 2048, making Rfrequency = 8. The mutations/generation is 8.

weight/site width, Rcapacity, generations to perfect creature

1/2, 2, ---
2/3, 4, ---
3/4, 6, ---
5/4, 8, ---
6/5, 10, 4105
7/6, 12, 4117

It's an amazing thing, don't you think?
I’m not sure what you are trying to demonstrate here. You’ve run one series with 5 cases, only two converged and another series with 6 cases, only two converged. The last two cases in the first series have a weight width greater than the site width and the last three cases in the second series have weight widths greater than the site width. I expect you transposed your numbers. Assuming that is the case, all you have shown is that your Rcapacity value gives a good estimate when the spurious binding errors dominate with Dr Schneider’s selection process. Change the weights for the different errors and you will find that Rcapacity value will change.

[Paul C. Anagnostopoulos]

Paul, it is already demonstrated. You call it Rcapacity affect but it is due to the dominance of spurious binding in the non-binding site region.
How large do I have to make the genome before you'll agree that the trivial difference in the ratios of nonbinding-site size to binding-site size is irrelevant? See below.


How does that differ from varying the weight on the different errors in your model? Weight the errors for missed binding sites different than spurious binding errors and see whether your estimate for Rcapacity changes. Post your version on the evjava web page and I’ll generate the data to show this.
Unnamed took into account how close each organism was to matching another binding site. The current model does not do that, regardless of parameters.


It is if you vary the weights for the different types of errors.
$R_\mathrm{capacity} = 2 \cdot \mathit{bindingsitewidth}$


I’m not sure what you are trying to demonstrate here. You’ve run one series with 5 cases, only two converged and another series with 6 cases, only two converged.
Note carefully at what point each converged: just after Rcapacity was large enough to accommodate Rfrequency. And in each set of experiments, the genome size is constant.

~~ Paul

[kleinman]

Paul, it is already demonstrated. You call it Rcapacity affect but it is due to the dominance of spurious binding in the non-binding site region.How large do I have to make the genome before you'll agree that the trivial difference in the ratios of nonbinding-site size to binding-site size is irrelevant? See below.
I don’t understand what you are asking. The ratio of the non-binding site region size to the binding site region size will always affect the rate of convergence with Dr Schneider’s selection process.
How does that differ from varying the weight on the different errors in your model? Weight the errors for missed binding sites different than spurious binding errors and see whether your estimate for Rcapacity changes. Post your version on the evjava web page and I’ll generate the data to show this. Unnamed took into account how close each organism was to matching another binding site. The current model does not do that, regardless of parameters.
So what? When you weight the errors in the binding site region differently than those in the non-binding site region you will affect the rate of convergence of ev. If you give no weight to the errors in the non-binding site region, you will uncouple the convergence of ev from the genome length and your Rcapacity problem will disappear.
It is if you vary the weights for the different types of errors.http://www.randi.org/latexrender/latex.php?$R_\mathrm{capacity} = 2 \cdot \mathit{bindingsitewidth}$
Nice use of fonts. It’s also an interesting coincidence that 2*bindingsitewidth gives a value that matches the point where ev no longer converges with Dr Schneider’s selection process, but it is the errors in the non-binding site region which is preventing convergence.
I’m not sure what you are trying to demonstrate here. You’ve run one series with 5 cases, only two converged and another series with 6 cases, only two converged. Note carefully at what point each converged: just after Rcapacity was large enough to accommodate Rfrequency.
So your equation gives an interesting estimate of where ev fails to converge with Dr Schneider’s selection process but your equation does not explain why ev does not converge. That explanation is the non-binding site errors dominate the calculation and prevent binding sites from evolving.

The point here is that it is the competition of the two selection processes (spurious binding in the non-binding site region and unlocated binding sites in the binding site region) that causes the failure of convergence when the first selection condition dominates.

I’ll go around on this topic as many times as you want. You already understand that if you rewrote ev such that you tried to evolve two independent sets of binding sites with two different sets of selection processes on each genome that you would slow down the evolutionary process. Selection processes by their very nature are competitive phenomena. A good mutation and a bad mutation occurring on the same genome would have countering effects. Unless you insure that you have two different good mutations on the same genome at the same time, selection processes will be working against each other. The more selection processes in action on a population at a given time, the more likely they evolutionary process will be stymied.

[Taffer]

I’ll go around on this topic as many times as you want. You already understand that if you rewrote ev such that you tried to evolve two independent sets of binding sites with two different sets of selection processes on each genome that you would slow down the evolutionary process. Selection processes by their very nature are competitive phenomena. A good mutation and a bad mutation occurring on the same genome would have countering effects. Unless you insure that you have two different good mutations on the same genome at the same time, selection processes will be working against each other. The more selection processes in action on a population at a given time, the more likely they evolutionary process will be stymied.

Evolution is not nearly that simple. If two mutations arrise in a genome, their value to the organism is independantly calculated, and the sum of that calculation is used to determine the overall fitness of the organism. For example, if 10 mutations arrise, 9 on which are deletarious, but the last mutation adds a large evolutionary benefit, then the overall fitness of the organism will be higher then the wild type.

[Paul C. Anagnostopoulos]

I don’t understand what you are asking. The ratio of the non-binding site region size to the binding site region size will always affect the rate of convergence with Dr Schneider’s selection process.
If you'll look at the experiments I ran, you'll see that some produce a perfect creature and some do not, even with the same size genome. You are claiming that it is the increasing size of the genome that eventually stops evolution, but I have shown a counterexample.

Perhaps I don't understand what you're actually claiming, in which case you could present your claim in greater detail.


So what? When you weight the errors in the binding site region differently than those in the non-binding site region you will affect the rate of convergence of ev. If you give no weight to the errors in the non-binding site region, you will uncouple the convergence of ev from the genome length and your Rcapacity problem will disappear.
I agree, but this has nothing to do with what Unnamed did.


Nice use of fonts. It’s also an interesting coincidence that 2*bindingsitewidth gives a value that matches the point where ev no longer converges with Dr Schneider’s selection process, but it is the errors in the non-binding site region which is preventing convergence.
No, it's not. In each of those experiments I outlined above, the mistake count drops to 8, which is the number of binding sites, and then never budges. It is precisely the errors at the binding sites that prevent improvement.


So your equation gives an interesting estimate of where ev fails to converge with Dr Schneider’s selection process but your equation does not explain why ev does not converge. That explanation is the non-binding site errors dominate the calculation and prevent binding sites from evolving.
No, see above.


The point here is that it is the competition of the two selection processes (spurious binding in the non-binding site region and unlocated binding sites in the binding site region) that causes the failure of convergence when the first selection condition dominates.
No.

Your problem of large genomes making evolution of binding sites more difficult is a valid issue, it's just not the Rcapacity problem. Nor would it cause evolution to stop dead.

~~ Paul

[kleinman]

I’ll go around on this topic as many times as you want. You already understand that if you rewrote ev such that you tried to evolve two independent sets of binding sites with two different sets of selection processes on each genome that you would slow down the evolutionary process. Selection processes by their very nature are competitive phenomena. A good mutation and a bad mutation occurring on the same genome would have countering effects. Unless you insure that you have two different good mutations on the same genome at the same time, selection processes will be working against each other. The more selection processes in action on a population at a given time, the more likely they evolutionary process will be stymied.Evolution is not nearly that simple. If two mutations arrise in a genome, their value to the organism is independantly calculated, and the sum of that calculation is used to determine the overall fitness of the organism. For example, if 10 mutations arrise, 9 on which are deletarious, but the last mutation adds a large evolutionary benefit, then the overall fitness of the organism will be higher then the wild type.
Not quite Taffer, you can have hundreds of beneficial mutations arising on a genome but one fatal mutation will cancel out the effects of those hundreds of beneficial mutations. You can not apply the principle of superposition to a non-linear system.
I don’t understand what you are asking. The ratio of the non-binding site region size to the binding site region size will always affect the rate of convergence with Dr Schneider’s selection process. If you'll look at the experiments I ran, you'll see that some produce a perfect creature and some do not, even with the same size genome. You are claiming that it is the increasing size of the genome that eventually stops evolution, but I have shown a counterexample.
What you are seeing with your data is that smaller binding sites (and the smaller weight matrix) are more likely to identify spurious binding sites. As you increase the size of the weight matrix, the less likely you are to identify spurious binding sites and the larger the non-binding site region on the genome can be used and convergence still attained.
Perhaps I don't understand what you're actually claiming, in which case you could present your claim in greater detail.
What I am claiming and what the data from ev is showing is that convergence is slowed when you have competing selection conditions. The selection in ev is based on two possible errors, identification of spurious binding sites and the failure to identify binding sites. When the identification of spurious binding sites is driving the selection process in ev, binding sites will not evolve.
So what? When you weight the errors in the binding site region differently than those in the non-binding site region you will affect the rate of convergence of ev. If you give no weight to the errors in the non-binding site region, you will uncouple the convergence of ev from the genome length and your Rcapacity problem will disappear. I agree, but this has nothing to do with what Unnamed did.
Unnamed did two things with his selection process. He allowed for a graded identification of binding sites and he weighted the selection towards failed identification of binding sites. This is why your Rcapacity equation does not give a good estimate for when ev will fail to converge with Unnamed’s selection process. Unnamed’s selection process can evolve binding sites on much larger genomes than Dr Schneider’s selection process. This is due to the fact that Unnamed’s selection process almost completely ignores spurious binding errors. The only problem with Unnamed’s selection process is that it has nothing to do with reality.
Nice use of fonts. It’s also an interesting coincidence that 2*bindingsitewidth gives a value that matches the point where ev no longer converges with Dr Schneider’s selection process, but it is the errors in the non-binding site region which is preventing convergence. No, it's not. In each of those experiments I outlined above, the mistake count drops to 8, which is the number of binding sites, and then never budges. It is precisely the errors at the binding sites that prevent improvement.
The total mistake count may remain at 8 but track each of the individual mistakes counts, that is, errors due to spurious binding and errors due to missed binding sites. When you do, you will find that spurious binding errors are driving the selection, not the missed binding site errors.
So your equation gives an interesting estimate of where ev fails to converge with Dr Schneider’s selection process but your equation does not explain why ev does not converge. That explanation is the non-binding site errors dominate the calculation and prevent binding sites from evolving. No, see above.
Paul, it is not the failure of the weight matrix to be able to identify binding sites. What difference does genome length make to the weight matrix? All that you do with the weight matrix is walk it along the genome and if value computed exceeds the threshold, you have a match for a binding site. The only thing that changes with the lengthening of the genome is the number of potential sites for spurious binding increases. As you increase the number of potential sites for spurious binding, you increase the effect of this selection condition. When this spurious binding condition selection process becomes the dominant selection condition, the failed identification of binding site condition no longer can select for the evolution of the binding sites. Ev will only evolve binding sites when the failed identification of binding site condition drives the selection of creatures.
The point here is that it is the competition of the two selection processes (spurious binding in the non-binding site region and unlocated binding sites in the binding site region) that causes the failure of convergence when the first selection condition dominates. No.

Your problem of large genomes making evolution of binding sites more difficult is a valid issue, it's just not the Rcapacity problem. Nor would it cause evolution to stop dead.
Paul, evolution stops dead when the wrong selection condition is driving the evolution. In the case of the ev model, when you lengthen the genome, spurious binding errors become the dominant selection condition. When that happens, you no longer see the evolution of binding sites. Competing selection conditions slow and as ev shows ultimately can stop evolution. This effect is seen in reality and is another reason why the theory of evolution is mathematically impossible.

[cyborg]

Seriously people, put him on ignore. It really is a waste of time trying to argue with him. As far as he's concerned he's lashing evolution to a cross using ev as nails. He will hear nothing else.

[delphi_ote]

You can not apply the principle of superposition to a non-linear system.
Right! Just like you you can't apply mathematical terms in an irrelevant context and expect people to think you know what you're talking about!

[Paul C. Anagnostopoulos]

You're right Cyborg, I'm tired. And what purpose is my fatigue serving? None.

~~ Paul

[Taffer]

[FONT=Times New Roman]Not quite Taffer, you can have hundreds of beneficial mutations arising on a genome but one fatal mutation will cancel out the effects of those hundreds of beneficial mutations. You can not apply the principle of superposition to a non-linear system.

Not all deletarious mutations are fatal, kleinman.

[kjkent1]

Not quite Taffer, you can have hundreds of beneficial mutations arising on a genome but one fatal mutation will cancel out the effects of those hundreds of beneficial mutations. You can not apply the principle of superposition to a non-linear system.Disagree. Very few mutations are immediately fatal, so as to prevent future reproduction. Life evolves when an organism reproduces, so even if there is a "fatal" mutation, this doesn't necessarily prevent beneficial mutations from being inherited by successors. Nor, is it necessarily true that a "fatal" mutation in one generation may not be overcome or replaced by later neutral or beneficial mutations.

The raw odds overwhelmingly favor reproduction of all mutations -- beneficial, neutral, or harmful. And, as long as an organism can survive to reproduce, natural selection will eliminate the weakest members in favor of the stronger, until the harmful mutations are minimized.What I am claiming and what the data from ev is showing is that convergence is slowed when you have competing selection conditions. The selection in ev is based on two possible errors, identification of spurious binding sites and the failure to identify binding sites. When the identification of spurious binding sites is driving the selection process in ev, binding sites will not evolve.Try changing the three mistake weights in the java program, but, don't set any to zero. As long as all three mistake weights are non-zero, binding sites will evolve. And, contrary to your claim that failing to give substantial weight to non-binding site region spurious bindings will speed up evolution, the fastest convergence appears to occur when mistakes in the non-binding site region are overweighted.Unnamed did two things with his selection process. He allowed for a graded identification of binding sites and he weighted the selection toward failed identification of binding sites. This is why your Rcapacity equation does not give a good estimate for when ev will fail to converge with Unnamed’s selection process. Unnamed’s selection process can evolve binding sites on much larger genomes than Dr Schneider’s selection process. This is due to the fact that Unnamed’s selection process almost completely ignores spurious binding errors. The only problem with Unnamed’s selection process is that it has nothing to do with reality.Totally false. You don't know how the algorithm works -- otherwise, you would not draw this conclusion. The algorithm overweights both mistakes and successful bindings, regardless of where they occur in the genome. So, the real reason why the algorithm speeds up evolution is because a mistake in the non-binding site region is treated as more harmful to the creature -- and because there is so much more non-binding site space in the genome, more mistakes will occur therein, and be overly harmful, which leads to the destruction of that creature.

This, is not realistic, in my opinion, but also isn't what you are claiming, i.e., that Unnamed's selection process ignores spurious binding errors. It's exactly the reverse: Unnamed's selection process gives greater selective power to any mistake, but it also gives greater selective power to correct bindings. The algorithm doesn't count the mistakes and compare them to the correct bindings -- it adds the weights of the mistakes and compares them to the weights of the correct bindings and then sorts on that comparison. This makes selection much more powerful. Whether this is actually more realistic, I have no idea.

I would like to see a graph of the values of the sorted creatures immediately prior to ev's killing by copying function, for both the original selection method and for Unnamed's. This would show how dramatically different the selective power is between the two methods. However, it doesn't tell us much about reality.

The issue always comes back to the question of what sort of selective power (benefit v. harm) is most realistic. Until this can be quantified, ev's ability to evolve at any particular generational rate is pure speculation.

[Mr. Scott]

Seriously people, put him on ignore. It really is a waste of time trying to argue with him. As far as he's concerned he's lashing evolution to a cross using ev as nails. He will hear nothing else.

Good suggestion, but I don't find Dr. Kleinman annoying. I find him amusing, as a cat finds a mouse amusing. I play until he bores me, then come back later to play again when I think of another way swat at him so I can watch him jump.

What these fanatical biblarians do, is when they come across a scientific development they think contradicts their bronze age manuscript, they attempt to undermine the science. They never consider questioning their manuscipt, written thousands of years ago by demonstrably ignorant authors. Where are microbes in the bible? Genes? Where is micro-evolution??? The bible reports nothing but what ordinary people knew when it was written. Nothing only observable with telescopes or microscopes was reported in the bible.

When science contradicts the bible, it's the bible we should dismatle, not the science. The developments of science work and bring us the bounties of modern life. The dead hand of religon wants to trap us in the bronze age. The harping of creationists is, except when it helps evolutionarians improve their science and their arguments, a pathetic waste.

[kleinman]

You can not apply the principle of superposition to a non-linear system.Right! Just like you you can't apply mathematical terms in an irrelevant context and expect people to think you know what you're talking about!
Oh really Delphi? Are you going to claim that the mathematics of mutation and selection is linear? Are you going to claim that selection processes can be superimposed and you obtain the same evolutionary events when the selection processes are applied independently? Perhaps you could explain to us when triple anti-HIV medications are used, it is much less likely to evolve drug resistant strains of HIV than when using the same drugs used in sequence, one at a time.

I’m pretty sure I have more experience and training in solving non-linear mathematical problems than you.

Stick with your gene duplication argument for your theory of evolution, even though you can’t explain how the original gene evolved. You have no selection process for this. And lay off the sterno.
You're right Cyborg, I'm tired. And what purpose is my fatigue serving? None.
The reason why you are fatigued is you now understand what your model shows and rather than face up to this reality, you are quitting. Your computer model doesn’t show how evolution works; it shows why evolution doesn’t work.
Not quite Taffer, you can have hundreds of beneficial mutations arising on a genome but one fatal mutation will cancel out the effects of those hundreds of beneficial mutations. You can not apply the principle of superposition to a non-linear system. Not all deletarious mutations are fatal, kleinman.
They don’t have to be fatal, they just have to interfere with the other selection processes and slow down evolution. That is what happens with ev with its simple two selection conditions as the genome length is increased until the spurious selection condition dominates and stops evolution of the binding sites.
Not quite Taffer, you can have hundreds of beneficial mutations arising on a genome but one fatal mutation will cancel out the effects of those hundreds of beneficial mutations. You can not apply the principle of superposition to a non-linear system. Disagree. Very few mutations are immediately fatal, so as to prevent future reproduction. Life evolves when an organism reproduces, so even if there is a "fatal" mutation, this doesn't necessarily prevent beneficial mutations from being inherited by successors. Nor, is it necessarily true that a "fatal" mutation in one generation may not be overcome or replaced by later neutral or beneficial mutations.
None of ev’s mutations are fatal on their own. It is the sum of mistakes which determines selection. Yet evolution is slowed and ultimately stopped as you increase the genome length and potential spurious binding mistakes.
The raw odds overwhelmingly favor reproduction of all mutations -- beneficial, neutral, or harmful. And, as long as an organism can survive to reproduce, natural selection will eliminate the weakest members in favor of the stronger, until the harmful mutations are minimized.
The difference between what you are saying and what Dr Schneider did is he applied rigorous mathematics to his argument and you have not. Dr Schneider’s model shows that with competing selection processes, evolution can be brought to a standstill.
What I am claiming and what the data from ev is showing is that convergence is slowed when you have competing selection conditions. The selection in ev is based on two possible errors, identification of spurious binding sites and the failure to identify binding sites. When the identification of spurious binding sites is driving the selection process in ev, binding sites will not evolve. Try changing the three mistake weights in the java program, but, don't set any to zero. As long as all three mistake weights are non-zero, binding sites will evolve. And, contrary to your claim that failing to give substantial weight to non-binding site region spurious bindings will speed up evolution, the fastest convergence appears to occur when mistakes in the non-binding site region are overweighted.
I haven’t run the java version of ev for a while. Has Paul posted the version that allow weighting of different errors?
Unnamed did two things with his selection process. He allowed for a graded identification of binding sites and he weighted the selection toward failed identification of binding sites. This is why your Rcapacity equation does not give a good estimate for when ev will fail to converge with Unnamed’s selection process. Unnamed’s selection process can evolve binding sites on much larger genomes than Dr Schneider’s selection process. This is due to the fact that Unnamed’s selection process almost completely ignores spurious binding errors. The only problem with Unnamed’s selection process is that it has nothing to do with reality. Totally false. You don't know how the algorithm works -- otherwise, you would not draw this conclusion. The algorithm overweights both mistakes and successful bindings, regardless of where they occur in the genome. So, the real reason why the algorithm speeds up evolution is because a mistake in the non-binding site region is treated as more harmful to the creature -- and because there is so much more non-binding site space in the genome, more mistakes will occur therein, and be overly harmful, which leads to the destruction of that creature.
Do you want to explain to us how increasing the weights of both spurious binding and successful binding equally will alter selection?
This, is not realistic, in my opinion, but also isn't what you are claiming, i.e., that Unnamed's selection process ignores spurious binding errors. It's exactly the reverse: Unnamed's selection process gives greater selective power to any mistake, but it also gives greater selective power to correct bindings. The algorithm doesn't count the mistakes and compare them to the correct bindings -- it adds the weights of the mistakes and compares them to the weights of the correct bindings and then sorts on that comparison. This makes selection much more powerful. Whether this is actually more realistic, I have no idea.
The way to address this issue is to put counters in the program and keep track of which of the two errors (spurious binding sites and missed binding sites) are driving the selection process. Selection based on spurious binding site errors will not help evolve binding sites, this selection condition is only required to evolve a perfect creature.
I would like to see a graph of the values of the sorted creatures immediately prior to ev's killing by copying function, for both the original selection method and for Unnamed's. This would show how dramatically different the selective power is between the two methods. However, it doesn't tell us much about reality.
The values you need are which errors are determining selection. If the spurious errors are determining selection, it doesn’t matter how far along the evolution of the binding sites are in these creatures, they get selected out because of spurious binding errors.
The issue always comes back to the question of what sort of selective power (benefit v. harm) is most realistic. Until this can be quantified, ev's ability to evolve at any particular generational rate is pure speculation.
It is not just the defining of realistic selection process, even Dr Schneider’s contrived selection process with two selection conditions demonstrates an important mathematical principle for mutation and selection, that is two different selection conditions leads to a slowing and ultimately the stopping of the evolutionary process. This effect is seen in reality.
Seriously people, put him on ignore. It really is a waste of time trying to argue with him. As far as he's concerned he's lashing evolution to a cross using ev as nails. He will hear nothing else.Good suggestion, but I don't find Dr. Kleinman annoying. I find him amusing, as a cat finds a mouse amusing. I play until he bores me, then come back later to play again when I think of another way swat at him so I can watch him jump.
Mr Scott, I particularly like when you play like this:
Paul, is what Alan saying here true? In a large population, when different genes in the same organism duplicate and mutate in parallel, does evolution, as simulated by Ev, slow down?
You have asked a crucial question here. Let me rephrase it a little. Do selection processes which when acting in parallel, does evolution, as simulated by ev, slow down? Paul side stepped your question by saying that ev does not model gene duplication. Ask him the same question without your gene duplication condition and let’s see how he answers, that is if he is not too fatigued.

By the way, one of my cats is sitting on my shoulder as I type this. You don’t want to be a mouse around this cat.
What these fanatical biblarians do, is when they come across a scientific development they think contradicts their bronze age manuscript, they attempt to undermine the science. They never consider questioning their manuscipt, written thousands of years ago by demonstrably ignorant authors. Where are microbes in the bible? Genes? Where is micro-evolution??? The bible reports nothing but what ordinary people knew when it was written. Nothing only observable with telescopes or microscopes was reported in the bible. [/quote]
Well, your rust age theory doesn’t have a mathematical basis. As it becomes clearer what the mathematics of parallel selection processes leads to, you will have to get yourself a new manuscript because evolutiondidn’tdoit.
When science contradicts the bible, it's the bible we should dismatle, not the science. The developments of science work and bring us the bounties of modern life. The dead hand of religon wants to trap us in the bronze age. The harping of creationists is, except when it helps evolutionarians improve their science and their arguments, a pathetic waste.
The problem for you is your own mathematics is contradicting your theory. In fact your own mathematics is showing why your theory is impossible. You have no selection process to evolve a gene from the beginning and competing selection processes operating in parallel interfere with evolution, initially slowing down the process and ultimately stopping evolution. This is shown in ev and in reality.

[articulett]

Seriously people, put him on ignore. It really is a waste of time trying to argue with him. As far as he's concerned he's lashing evolution to a cross using ev as nails. He will hear nothing else.

Now, now--

You have to admire his tenacity and the way at which religion has demented him. There is entertainment value in participating in his delusion and reading the responses. This is why creationism must not be taught in schools--it makes you positively unteachable and arrogant on top of that. You can only compute that which proves the belief you've been told leads to salvation. All else is stuff from that evil tree of knowledge...

[kleinman]

Seriously people, put him on ignore. It really is a waste of time trying to argue with him. As far as he's concerned he's lashing evolution to a cross using ev as nails. He will hear nothing else. Now, now--

You have to admire his tenacity and the way at which religion has demented him. There is entertainment value in participating in his delusion and reading the responses. This is why creationism must not be taught in schools--it makes you positively unteachable and arrogant on top of that. You can only compute that which proves the belief you've been told leads to salvation. All else is stuff from that evil tree of knowledge...
What is particularly entertaining is that your own computer model shows why the theory of evolution is mathematically impossible. You evolutionary dogmatists have nothing to counter these mathematical facts so you retreat to playground tactics. Your theory of evolution by mutation and natural selection has no selection process to evolve a gene from the beginning and ev shows that selection processes acting in parallel slow and ultimately stop evolution. This effect is seen in reality. The theory of evolution is mathematically impossible despite all your evolutionary indoctrination you have been taught. Cyborg would like to ignore these facts but thanks to Dr Schneider and Paul’s good mathematical and computer programming work, the theory of evolution by mutation and selection is now much better understood and refuted. Cyborg, I would really like to co-opt your cruft theory of evolution but I think I will let you keep that idea.

[kjkent1]

The difference between what you are saying and what Dr Schneider did is he applied rigorous mathematics to his argument and you have not. Dr Schneider’s model shows that with competing selection processes, evolution can be brought to a standstill.It shows nothing of the kind, and Dr. Schneider's paper suggests no such competition. Ev slows down as the genome lengthens, because there is more space for spurious binding mistakes to exist within a longer genome. Humorously, this was your original argument, back in the evolutionisdead forum. Somewhere along the line, you've invented a completely unsupported hypothesis suggesting that there is some inhibiting competition taking place within the ev genome. Why you decided that you need this additional argument is beyond me. Regardless, it's just your imagination.I haven’t run the java version of ev for a while. Has Paul posted the version that allow weighting of different errors?I've never seen the java version when it didn't have this weighting option, so yes.Do you want to explain to us how increasing the weights of both spurious binding and successful binding equally will alter selection?There are three mistakes in the java version -- not two. You can overweight spurious bindings inside the binding site region, or outside. When you overweight the mistakes outside the binding site region, it means that the area of the genome into which more mistakes will randomly fall, simply because of its greater size, will obtain greater negative weight, and thus creatures with more non-binding site mistakes will be killed off quicker. If you add Unnamed's algorithm, that will kill them off even quicker, because the mistake weight is increased by the sum of the weights of the mistakes. And that is why Unnamed's algorithm converges faster -- not because it ignores mistakes in the non-binding site region -- but because it overemphasizes their importance.It is not just the defining of realistic selection process, even Dr Schneider’s contrived selection process with two selection conditions demonstrates an important mathematical principle for mutation and selection, that is two different selection conditions leads to a slowing and ultimately the stopping of the evolutionary process. This effect is seen in reality.Well, your audience would very much like you to state this mathematical principle in mathematical symbols, rather than just repeating it continuously, in the hope that we will all suddenly fall to our knees with a "Praise Jesus!"

[fishbob]

What is particularly entertaining is that your own computer model shows why the theory of evolution is mathematically impossible.

All the other evidence supporting evolution means that your math might just be wrong. Refusal to even consider this possibility means that your arguments are weaselly. Tenacity in dementia is not an admirable trait.

[Mr. Scott]

The problem for you is your own mathematics is contradicting your theory. In fact your own mathematics is showing why your theory is impossible.

I don't know why you keep repeating this when it's been explained repeatedly and with perfectly logical clarity that it's incorrect.

If you don't come up with some new lies I'll have to start wacking at that crumbling manuscript again. Every time creationists lie, they make the baby Jesus cry, for it is the devil that is the inventor of all lies. Look it up!

[Taffer]

They don’t have to be fatal, they just have to interfere with the other selection processes and slow down evolution. That is what happens with ev with its simple two selection conditions as the genome length is increased until the spurious selection condition dominates and stops evolution of the binding sites.

Evolution works on phenotypes. If the overall phenotype of a range of mutations is beneficial, then it doesn't matter how harmful any of the individual mutations are. What matters is the sum total of the organism's fitness.

[Dr Adequate]

Where are microbes in the bible? Genes? Where is micro-evolution??? The bible reports nothing but what ordinary people knew when it was written. Nothing only observable with telescopes or microscopes was reported in the bible. Oh, come on, there's lots of good science in the Bible:

* God makes thunder by shouting.
* God makes earthquakes by shaking the Earth.
* God makes rainbows by magic.
* The Earth is supported on pillars.
* The Earth doesn't move.
* Insects have four legs.

[Dr Adequate]

Lie #1. Truth #1.

See how much easier my way is?

[Paul C. Anagnostopoulos]

I just don't want to see any Truth #1.3.2(D).iii.q. I hate those deep truths!

~~ Paul

[kleinman]

The difference between what you are saying and what Dr Schneider did is he applied rigorous mathematics to his argument and you have not. Dr Schneider’s model shows that with competing selection processes, evolution can be brought to a standstill. It shows nothing of the kind, and Dr. Schneider's paper suggests no such competition. Ev slows down as the genome lengthens, because there is more space for spurious binding mistakes to exist within a longer genome. Humorously, this was your original argument, back in the evolutionisdead forum. Somewhere along the line, you've invented a completely unsupported hypothesis suggesting that there is some inhibiting competition taking place within the ev genome. Why you decided that you need this additional argument is beyond me. Regardless, it's just your imagination.
The reason Dr Schneider’s paper says nothing about such competition is that Dr Schneider published only a single case which used an extremely short genome. If you carefully read Dr Schneider’s web site you would have seen this quote from his http://www.lecb.ncifcrf.gov/~toms/paper/ev/faq-for-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/faq-for-ev.html) page”
If you had a reasonable sized genome would you find that there won't be an information gain? No. Don't be lazy, go try it yourself (http://www.lecb.ncifcrf.gov/~toms/delila/ev.html)! But notice that it will take a lot more computation, and the runs may take some years unless you write a version that uses parallel processors.
Why does it take more time to run a reasonable length genome? It is the competing selection processes in his model that profoundly slow the rate of information gain.
I haven’t run the java version of ev for a while. Has Paul posted the version that allow weighting of different errors? I've never seen the java version when it didn't have this weighting option, so yes.
Now isn’t that interesting. Paul’s online version does not have this feature. I guess Paul is too fatigued to put that version up on the net.
Do you want to explain to us how increasing the weights of both spurious binding and successful binding equally will alter selection?There are three mistakes in the java version -- not two. You can overweight spurious bindings inside the binding site region, or outside. When you overweight the mistakes outside the binding site region, it means that the area of the genome into which more mistakes will randomly fall, simply because of its greater size, will obtain greater negative weight, and thus creatures with more non-binding site mistakes will be killed off quicker. If you add Unnamed's algorithm, that will kill them off even quicker, because the mistake weight is increased by the sum of the weights of the mistakes. And that is why Unnamed's algorithm converges faster -- not because it ignores mistakes in the non-binding site region -- but because it overemphasizes their importance.
Now why don’t we have Paul put the same version up on the net so we can all generate identical data and compare results?
It is not just the defining of realistic selection process, even Dr Schneider’s contrived selection process with two selection conditions demonstrates an important mathematical principle for mutation and selection, that is two different selection conditions leads to a slowing and ultimately the stopping of the evolutionary process. This effect is seen in reality. Well, your audience would very much like you to state this mathematical principle in mathematical symbols, rather than just repeating it continuously, in the hope that we will all suddenly fall to our knees with a "Praise Jesus!"
The failure of ev to converge is demonstrated in what calls the Rcapacity problem. This problem occurs when spurious bindings dominate the selection process. This effect is seen and used in reality when physicians use multiple antimicrobials to prevent the evolution of resistant strains of microbes. A particular example of this is the use of triple anti-HIV drugs for the treatment of this disease. If you want to see this written in mathematical symbols, read Dr Schneider’s papers, he did this properly. The only thing he did not do is a thorough analysis of his equations. Why should I expect that showing you the mathematical truth about your theory should make you fall on your knees with a “Praise Jesus”?
What is particularly entertaining is that your own computer model shows why the theory of evolution is mathematically impossible.All the other evidence supporting evolution means that your math might just be wrong. Refusal to even consider this possibility means that your arguments are weaselly. Tenacity in dementia is not an admirable trait.
This is not my mathematics. This is Dr Schneider’s mathematics and it was peer reviewed and published in Nucleic Acids Research. I only did what Dr Schneider called for in his publication and the results show that your theory is mathematically impossible.

With respects to your other evidence, perhaps you better start reconsidering your interpretation of this evidence since your foundation concept of mutation and selection is mathematically impossible. Isn’t your theory in a sad state when a demented person can show that your theory is mathematically impossible with your own mathematics.
The problem for you is your own mathematics is contradicting your theory. In fact your own mathematics is showing why your theory is impossible.I don't know why you keep repeating this when it's been explained repeatedly and with perfectly logical clarity that it's incorrect.
I keep repeating it because it is true. You have two basic reasons why your theory is mathematically impossible. You don’t have a selection process that can evolve a gene from the beginning and competing selection processes is what slows and ultimately stops evolution in ev. This effect is seen and used in reality.
If you don't come up with some new lies I'll have to start wacking at that crumbling manuscript again. Every time creationists lie, they make the baby Jesus cry, for it is the devil that is the inventor of all lies. Look it up!
You only wish these were lies that I am saying about ev but these results are easily reproducible. You don’t have a selection process that can evolve a gene from the beginning and multiple selection process slow and ultimately stop evolution. This is shown by ev and exists in reality. Evolutiondidn’tdoit.
They don’t have to be fatal, they just have to interfere with the other selection processes and slow down evolution. That is what happens with ev with its simple two selection conditions as the genome length is increased until the spurious selection condition dominates and stops evolution of the binding sites.Evolution works on phenotypes. If the overall phenotype of a range of mutations is beneficial, then it doesn't matter how harmful any of the individual mutations are. What matters is the sum total of the organism's fitness.
Do you want to explain how the overall fitness will evolve a gene from the beginning? How do you include what you have just said in a mathematical model of mutation and selection?

What ev reveals about competing selection processes is demonstrated with the use of multiple antimicrobials. Evolution is slowed if not halted in the HIV by using the three antimicrobials. The prevention of the changes in the genotype prevent the change in the phenotype.
I just don't want to see any Truth #1.3.2(D).iii.q. I hate those deep truths!
Especially when those truths contradict your belief system.

What happen, did you find enough strength to post again on this thread, Mr Rcapacity?

[Paul C. Anagnostopoulos]

Now isn’t that interesting. Paul’s online version does not have this feature. I guess Paul is too fatigued to put that version up on the net.
Lie #39. Look harder, dude.

~~ Paul

[fishbob]

This is not my mathematics. This is Dr Schneider’s mathematics and it was peer reviewed and published in Nucleic Acids Research. I only did what Dr Schneider called for in his publication and the results show that your theory is mathematically impossible.

Weaselry incarnate.

[kleinman]

Now isn’t that interesting. Paul’s online version does not have this feature. I guess Paul is too fatigued to put that version up on the net.Lie #39. Look harder, dude.
I see you’ve added a new button since I last used your java version of ev. I’m going to enjoy co-opting this new feature to prove your Rcapacity problem has nothing to do with the weight matrix being able to locate binding sites and that the failure of the program to converge has everything to do with spurious binding sites controlling the selection process. Paul, how does it feel to have your own computer programming work used to disprove the theory of evolution? When are you going to simulate the evolution of two sets of different binding sites simultaneously? Or will that make the stylized ev computer model to realistic for the theory of evolution? You better take some vitamins or start taking power naps because the new features you have put in ev gives a new direction for parametric studies. I like number crunching with ev. Every time I run a case with ev I hear the theory of evolution go crunch. Ev is that gift that keeps on giving. Thank you, Paul.
This is not my mathematics. This is Dr Schneider’s mathematics and it was peer reviewed and published in Nucleic Acids Research. I only did what Dr Schneider called for in his publication and the results show that your theory is mathematically impossible. Weaselry incarnate.
Stop being such a cry baby just because someone can take your mathematics and do a parametric study and show your silly theory is mathematically impossible.

[Paul C. Anagnostopoulos]

I see you’ve added a new button since I last used your java version of ev.
You haven't used it since November 2005?


I’m going to enjoy co-opting this new feature to prove your Rcapacity problem has nothing to do with the weight matrix being able to locate binding sites and that the failure of the program to converge has everything to do with spurious binding sites controlling the selection process.
Alan, if the binding sites are too narrow to allow a unique sequence logo, then spurious bindings are controlling the selection process. I agree with that. What you have to demonstrate is your claim that (a) at some point evolution abruptly stops; and (b) this stoppage is not due to Rcapacity. Simply run some experiments where evolution stops when Rcapacity is not an issue.

If you refuse to acknowledge that there is any Rcapacity problem at all, then you're just being silly. Obviously, for example, a binding site width of 1 base will not allow a unique sequence logo to emerge at binding sites. It's also gonna be awfully tough for 2-base sites to work. You need enough capacity in the sites to form a pattern that isn't present anywhere else.

Also, keep in mind that the Rcapacity problem is an artifact of the Ev model and is not a problem in nature.

~~ Paul

[Paul C. Anagnostopoulos]

These parameters show a cool result:

population 64
genome size 256
bindings sites 16
weight/site width 2/2
Rcapacity = Rfrequency = 4

After about 171,000 generations, the perfect creature evolves with a sequence logo of GG. There is not a single GG anywhere in the genome except at the binding sites.

Let's increase the genome size to 512 and see if we can conquer Rcapacity ...

No luck after 2,500,000 generations.

~~ Paul

[kleinman]

I see you’ve added a new button since I last used your java version of ev. You haven't used it since November 2005?
What can I say Paul, I’m not perfect. If I had noticed that feature, this discussion would have been much shorter. Anyway, it’s fun talking with you guys. It reminds me of my elementary school playground days.
I’m going to enjoy co-opting this new feature to prove your Rcapacity problem has nothing to do with the weight matrix being able to locate binding sites and that the failure of the program to converge has everything to do with spurious binding sites controlling the selection process. Alan, if the binding sites are too narrow to allow a unique sequence logo, then spurious bindings are controlling the selection process. I agree with that. What you have to demonstrate is your claim that (a) at some point evolution abruptly stops; and (b) this stoppage is not due to Rcapacity. Simply run some experiments where evolution stops when Rcapacity is not an issue.
Paul, I’m going to write this as plainly as I can. It is the competing selection processes which halt the convergence of ev. The exact reason it occurs at genome lengths with your Rcapacity value, I don’t know but a more careful study of the model should give this answer. What I suspect is happening is as one selection condition is being satisfied, another selection condition is being overwhelmed and the system oscillates between the different selection conditions, never being able to satisfying all three at once. So since you pointed out that you could vary the weights for mistakes a chose a case which does not converge with all three selection conditions imposed.

Wow, am I fatigued. It took me 3 cases to demonstrate that it is competing selection conditions that slow ev’s convergence. The case I used consists of G=16384, binding sites=6, weight width=5, Rfreq=10, Paul’s infamous Rcapacity=2*site width=10. With the weights for each mistake, (missed site, spurious binding in gene, spurious binding outside gene), set to 1, this case fails to converge. But for varying weights you get the following results:
missed site/spurious binding-gene/spurious binding outside gene/gens to perfect creature
1/0/0/7
0/1/0/223
0/0/1/233
So, a case with three different selection conditions will not converge when all three conditions must be satisfied simultaneously. While if you select based on one condition at a time it takes only 7 generations to evolve the binding sites, 223 generations to eliminate spurious binding within the gene and only 233 generations to eliminate spurious binding outside the gene. These cases take so few generations to evolve, it is instructive to step through the evolution and watch the mistakes go to zero. Combining these three selection conditions is exactly analogous to using triple anti-HIV drugs to prevent the evolution of drug resistant strains. Paul’s this is the explanation for your Rcapacity problem. I appreciate your fine programming work.
If you refuse to acknowledge that there is any Rcapacity problem at all, then you're just being silly. Obviously, for example, a binding site width of 1 base will not allow a unique sequence logo to emerge at binding sites. It's also gonna be awfully tough for 2-base sites to work. You need enough capacity in the sites to form a pattern that isn't present anywhere else.
Paul, certainly there is an Rcapacity problem for the theory of evolution. What that Rcapacity problem is competing selection conditions.
Also, keep in mind that the Rcapacity problem is an artifact of the Ev model and is not a problem in nature.
Paul, you couldn’t be more wrong. Competing selection processes occur all the time in nature. The problem for you evolutionists is understanding that these competing selection processes stop evolution. Dr Schneider’s model has accurately captured a real physical phenomenon with his three different selection condition.

Perhaps if you consider the question from the opposite point of view, you may find a way of understanding this Rcapacity issue. Why do small genomes still evolve despite three selection conditions?
These parameters show a cool result:

population 64
genome size 256
bindings sites 16
weight/site width 2/2
Rcapacity = Rfrequency = 4

After about 171,000 generations, the perfect creature evolves with a sequence logo of GG. There is not a single GG anywhere in the genome except at the binding sites.

Let's increase the genome size to 512 and see if we can conquer Rcapacity ...

No luck after 2,500,000 generations.
Paul, run the case I have shown above setting 2 of the three selection conditions weights to zero and then step through all three cases and watch the mistakes disappear. Perhaps then you will understand why your theory of evolution is mathematically impossible. The mistakes do not disappear when you apply all three selection conditions simultaneously. Competing selection conditions stop evolution. Your model shows this and this is also seen in the real world.

[Paul C. Anagnostopoulos]

Wow, am I fatigued. It took me 3 cases to demonstrate that it is competing selection conditions that slow ev’s convergence.
Alan, please, stop spewing this claim over and over. I agree that a simpler selection requirement is likely to result in a faster convergence. Whoopie crap.

Your interesting claim is that evolution stops dead even when Rcapacity isn't an issue. Demonstrate it.


Paul’s this is the explanation for your Rcapacity problem.
Rcapacity is irrelevant in the experiments you ran, because the calculation of Rfrequency assumes all three mistake points greater than 0. Rfrequency, Rsequence, and Rcapacity are all irrelevant.


Paul, you couldn’t be more wrong. Competing selection processes occur all the time in nature.
But they have nothing to do with Rcapacity.

~~ Paul

[delphi_ote]

Oh really Delphi? Are you going to claim that the mathematics of mutation and selection is linear? Are you going to claim that selection processes can be superimposed and you obtain the same evolutionary events when the selection processes are applied independently? Perhaps you could explain to us when triple anti-HIV medications are used, it is much less likely to evolve drug resistant strains of HIV than when using the same drugs used in sequence, one at a time.
Wow. More irrelevant word salad. You can't arbitrarily use technical jargon from another field out of context to describe whatever you like and expect people to respect you. Once again, it doesn't make you sound intelligent. It's patently obvious you're trying to claim authority on a subject you don't understand by using terminology from your own field as a smoke screen.
I’m pretty sure I have more experience and training in solving non-linear mathematical problems than you.
Congratulations. You're an engineer. That's fantastic. Despite that elitist feeling that came packaged with your diploma, you are not omniscient. While you can probably snowball the other nontechnical people at your office with this behavior, we're not falling for it here.

Also, while I'm not going to get into a credentials pissing contest with you, you should be probably be careful saying things like that. Especially on this forum. You're talking to a lot of very educated people.

[Paul C. Anagnostopoulos]

In fairness to Kleinman, I ran one more experiment with his parameters, and here is the result:

missed site/spurious binding-gene/spurious binding outside gene/gens to perfect creature
0/0/0/1

Extraordinary! Exploring this in greater depth, I increased the genome size to 256,000 bases:

0/0/0/1

Absolutely amazing! We have just shown that if there are no selective pressures at all, a perfect creature evolves immediately, regardless of genome size and Rcapacity.

~~ Paul

[kjkent1]

Paul, I’m going to write this as plainly as I