Annoying creationists

[joobz]

No comment is necessary.

:dl:

Joobz, add this one to your list, it's priceless.
Done and done.
1.)Thermodynamics is a study of kinetics, "dynamics is in the name!"
2.)Natural Selection is a restatement of the First Law of Thermodynamics.
3.)Probability can exceed 1.
4.)A failure of a model proves that the natural, observed event is impossible5) Anyone thinks that H. Sapiens evolved from a random gigabase genome with only point mutations.
6.)ev demonstrates decreasing rates of convergence with increasing population

[Yahzi]

You may believe that faith is a mindless act of self-deception and immune to reason but that describes science almost as well as it does religion.
Up is down!

Black is white!

I have declared it; therefore, it must be so.

In this brave new world of argument-by-vacuous assertion, I shall issue the ultimate challenge: I double-dog dare ya!

[articulett]

I guess that's why I still look at this thread now and then.

He's mostly a bore, 'cos he keeps reciting the same lies over and over, but when he comes out with a new lie, his self-righteous self-importance does make it funny.

Well it's not technically a lie if he actually believes it--that is, it's self deception--a confabulation--but not a lie. Of course if he knows he's lying (and one would imagine that would be the case given the number of times he's been told), then he's a liar. For now, I'll give him the benefit of the doubt (cognitive dissonance). It's hard when your eternal salvation rests on how well you believe a certain fairytale.

[articulett]

Up is down!

Black is white!

I have declared it; therefore, it must be so.

In this brave new world of argument-by-vacuous assertion, I shall issue the ultimate challenge: I double-dog dare ya!

It's not his fault--clearly this is a mind damaged from childhood by the notion that there are higher truths that can be found by twisting primitive texts into meaningful truths--a mind that can't help but think upside down (top down "design"--cannot comprehend bottom up evolution)...a mind told that faith is good--it's bad to doubt--arrogant to ask questions--and wicked to lose faith.
It truly is brain damaging to tell trusting children that their eternity depends on how much they can make themselves believe a particular version of the truth.

And John, I think your intelligent designer can fight his own battle. He's free to present his evidence at any time--if you religionists would get your story straight about what name the intelligent designer wants to be called and what he does and what he wants and why he didn't mention DNA in the bible (or any other future scientifically established facts) it would help. It's hard to take an invisible immeasurable entity seriously--and you guys can't even agree as to who is or isn't a Christian--or who and/or what goes to heaven, hell, limbo, purgatory, and/or reincarnates. You can't even tell us what a soul is or does or feels or thinks or how it does so without a body or brain (or how your god does it). The fact that everyone truly believes all sorts of different variations on the theme (for example virgins in the afterlife) and many of them are clearly false...and none of them have more evidence for them than any other--how in the world can you imagine we would care about your "opinion" on the topic more than you care about ours? If the evidence for your beliefs is the same as for the beliefs you mock (Scientology perhaps?), then your beliefs deserve the same mockery. But believers never seem to see that. That's why I stick to evidence. Got any?

[kleinman]

There are many creatures that have gone extinct. The issues I have raised here about the ev program is that your contention that these creatures are evolving from one to the next does not have a mathematical basis. You are extrapolating the similarities of animals to your concept of evolution. If you are correct about the theory of evolution, you must have some mechanism(s) that allow the transformation of genomes from one species to the next. Ev shows that the process of random point mutation and natural selection is profoundly slow, too slow to account for these changes. Hard science requires this type of accounting and it doesn’t appear that the theory of evolution can pass this type of test. If not by evolution, then by what process which satisfies the rigorous mathematical basis which you apparently require, have the myriad of past and present lifeforms come to exist on Earth?

State your hypothesis and supporting mathematics.
I have made no scientific claims to origins of life and explanation for all the different life forms we observe. It is you evolutionarians that claim you have the scientific explanation for these observations. I am showing how unscientific your explanations are and that your views are simply another faith and belief system without scientific basis despite all your claims.
Up is down!

Black is white!

I have declared it; therefore, it must be so.

In this brave new world of argument-by-vacuous assertion, I shall issue the ultimate challenge: I double-dog dare ya!
What are you squealing about? Don’t you like the mathematics of ev?

Here’s something for Paul and the rest of you evolutionarians to consider. Paul has extrapolated a value for the case of a 100k genome with 16 binding sites each 6 bases wide and a population of 1,000,000 to take 200,000,000 generations to evolve. Now the data for the human and chimpanzee genome are now becoming available. The initial estimate is that there about 20,000 genes in the human genome. I haven’t seen an estimate for the number of genes in the chimpanzee genome. Since according to evolutionarian estimates there are about 500,000 generations separating the two species and ev shows that it takes 4000 times as many generations to evolve 96 loci on a genome that is 30,000 times shorter by random point mutations and natural selection. How are you going to explain even one single gene difference between the two species?

You have about as much chance of giving a scientific explanation for this as joobz has for explaining abiogenesis. I’ll help you out, joobz explanation is anything is possible and if it sounds good it must be true. He is a modern Leonardo joobinzi.

The auditors are here and the evolutionarian books do not balance. You had better pray more and louder to your natural selection god, he doesn’t seem to be listening.

[cyborg]

I am showing how unscientific your explanations are and that your views are simply another faith and belief system without scientific basis despite all your claims.

YEAH! Because only idiots would participate in silly old belief systems that are without scientific basis! Like the Bible!

You had better pray more and louder to your natural selection god, he doesn’t seem to be listening.

You first. Get Yahweh to make me into a pillar of salt. Go on, you know you want to.

[John Hewitt]

And John, I think your intelligent designer can fight his own battle. He's free to present his evidence at any time--if you religionists would get your story straight about what name the intelligent designer wants to be called and what he does and what he wants and why he didn't mention DNA in the bible (or any other future scientifically established facts) it would help. It's hard to take an invisible immeasurable entity seriously--and you guys can't even agree as to who is or isn't a Christian--or who and/or what goes to heaven, hell, limbo, purgatory, and/or reincarnates. You can't even tell us what a soul is or does or feels or thinks or how it does so without a body or brain (or how your god does it). The fact that everyone truly believes all sorts of different variations on the theme (for example virgins in the afterlife) and many of them are clearly false...and none of them have more evidence for them than any other--how in the world can you imagine we would care about your "opinion" on the topic more than you care about ours? If the evidence for your beliefs is the same as for the beliefs you mock (Scientology perhaps?), then your beliefs deserve the same mockery. But believers never seem to see that. That's why I stick to evidence. Got any?
Is this addressed to me?

[drkitten]

Is this addressed to me?

No, it's not. That's why the section you quoted begins "And John,"

This also explains the rest of your scientific illiteracy. Because you can't figure out what words mean.

[Paul C. Anagnostopoulos]

Paul has extrapolated a value for the case of a 100k genome with 16 binding sites each 6 bases wide and a population of 1,000,000 to take 200,000,000 generations to evolve.
If I said that, I was an idiot. Rfrequency > Rcapacity in that situation, so I doubt it would ever converge.

I'm currently running a series of experiments varying the genome size, but with wide binding sites that will allow a million base genome. I estimate it will take about a month to run the experiments. Stay tuned.

~~ Paul

[I less than three logic]

If I said that, I was an idiot. Rfrequency > Rcapacity in that situation, so I doubt it would ever converge.

I'm currently running a series of experiments varying the genome size, but with wide binding sites that will allow a million base genome. I estimate it will take about a month to run the experiments. Stay tuned.

~~ Paul
Not that I doubt you were being an idiot ( :D ), but I attempted a search of this thread and couldn't find where you'd made such a claim. Of course, my search may be been inaccurate or you may have made the claim in another place. Perhaps Kleinman can post a link to where you made the claim, instead of just saying you did.

[John Hewitt]

No, it's not. That's why the section you quoted begins "And John,"

I inquired whether or not Articulette's posting was addressed to me because I seem to be the only "John" on this thread while his comments seem unrelated to anything I have posted.

This also explains the rest of your scientific illiteracy. Because you can't figure out what words mean.I fail to see how this inquiry could lead you to think that I am scientifically illiterate.

[drkitten]

I fail to see how this inquiry could lead you to think that I am scientifically illiterate.

Nor could you see that a posting beginning "And John," was addressed to you.

Which leads me to believe that your failure to see something is independent of whether or not it's there, and of no concern to me.

[Paul C. Anagnostopoulos]

Not that I doubt you were being an idiot ( ), but I attempted a search of this thread and couldn't find where you'd made such a claim. Of course, my search may be been inaccurate or you may have made the claim in another place.
I think I may have said it over at evolutionisdead.

~~ Paul

[John Hewitt]

Nor could you see that a posting beginning "And John," was addressed to you.

Which leads me to believe that your failure to see something is independent of whether or not it's there, and of no concern to me.
I infer that you felt the posting was addressed to me, though I cannot understand why you do not just say so. As you know, my analysis of evolution, bioepistemic evolution, is based on on data, which describes pattern rather than concrete objects. Thus it considers evolution as an IT proocess often involving software rather than mere hardware. These concepts can be tricky, which may explain why you have difficulty grasping them.

Articulette's note read
And John, I think your intelligent designer can fight his own battle. He's free to present his evidence at any time--if you religionists would get your story straight about what name the intelligent designer wants to be called and what he does and what he wants and why he didn't mention DNA in the bible (or any other future scientifically established facts) it would help. It's hard to take an invisible immeasurable entity seriously--and you guys can't even agree as to who is or isn't a Christian--or who and/or what goes to heaven, hell, limbo, purgatory, and/or reincarnates. You can't even tell us what a soul is or does or feels or thinks or how it does so without a body or brain (or how your god does it). The fact that everyone truly believes all sorts of different variations on the theme (for example virgins in the afterlife) and many of them are clearly false...and none of them have more evidence for them than any other--how in the world can you imagine we would care about your "opinion" on the topic more than you care about ours? If the evidence for your beliefs is the same as for the beliefs you mock (Scientology perhaps?), then your beliefs deserve the same mockery. But believers never seem to see that. That's why I stick to evidence. Got any?I have not identified myself as a religious person, the only intelligent designer I have considered was Francis Crick's aliens with a consideration of how such an alien could be distinguished from God.

I have not discussed the bible, heaven, hell, limbo, purgatory, reincarnates, souls, the variability of religion, virgins in the afterlife or scientology. What I deal in and would like to see is evidence. I am asking Articulette what any of the above has to do with me.

[Yahzi]

I fail to see how this inquiry could lead you to think that I am scientifically illiterate.
Not in the obvious way: we are not so narrow-minded as to assume that one must be literate in order to be scientifically literate. Common sense knows no educational boundries.

However, the fact that you are illiterate, and unaware of it, strongly implies that you are unaware of even your grossest deficiencies. The ability to recognize what one does not know is crucial to science and common sense. Hence, your willingness to participate in a textual discussion even while you are functionally illiterate suggests you lack that most basic capacity for education, learning, and productive discourse: self-awareness.

[joobz]

Not that I doubt you were being an idiot ( :D ), but I attempted a search of this thread and couldn't find where you'd made such a claim. Of course, my search may be been inaccurate or you may have made the claim in another place. Perhaps Kleinman can post a link to where you made the claim, instead of just saying you did.
Why can't you go and look for it, huh???

Are you too lazy of an evolutionarian to go and do research. or are you just afraid to having your weak evolutionary ideas disproven?!?!? :rolleyes: :rolleyes:

-----
Oh my, It's way to easy to write this wakazoolian junk. :D :D

[dv82matt]

No, it's not. That's why the section you quoted begins "And John,"

This also explains the rest of your scientific illiteracy. Because you can't figure out what words mean.
Seriously, could you possibly be more of a jerk? This is flawed logic and an example of exactly the kind of thing that gives people like John the impression that science is a dogma that cannot tolerate dissent.

[hammegk]

State your hypothesis and supporting mathematics.
Actually, evolution being the theory (lots & lots of hypotheses -- no doubt about that) with proponents here, it would be appropriate for them to provide 'supporting mathematics' to add needed rigour to the current just-so-story. :)



FYI to those who don't already know; drkitten & articulette are 'jerkettes' rather than 'jerks'.

[dv82matt]

FYI to those who don't already know; drkitten & articulette are 'jerkettes' rather than 'jerks'.
Thanks for clearing that up for me. :o
Actually, evolution being the theory (lots & lots of hypotheses -- no doubt about that) with proponents here, it would be appropriate for them to provide 'supporting mathematics' to add needed rigour to the current just-so-story. :)
It's disingenuous to say evolution is a just so story as there is plenty of evidence that it is real. Are you referring to a particular aspect of evolution, or are you of the persuasion that since we don't know everything we don't know anything?

[John Hewitt]

Not in the obvious way: we are not so narrow-minded as to assume that one must be literate in order to be scientifically literate. Common sense knows no educational boundries.

However, the fact that you are illiterate, and unaware of it, strongly implies that you are unaware of even your grossest deficiencies. The ability to recognize what one does not know is crucial to science and common sense. Hence, your willingness to participate in a textual discussion even while you are functionally illiterate suggests you lack that most basic capacity for education, learning, and productive discourse: self-awareness.

Nonetheless, I am scientifically literate, more so I suspect than you. What is more, and as I have mentioned to you previously, what I look for is an intelligent discussion directed to the subject. I am sorry you feel unable to deliver that.

[joobz]

It's disingenuous to say evolution is a just so story as there is plenty of evidence that it is real. Are you referring to a particular aspect of evolution, or are you of the persuasion that since we don't know everything we don't know anything?
nicely stated, I look forward to seeing more of your posts.

[John Hewitt]

It's disingenuous to say evolution is a just so story as there is plenty of evidence that it is real. Are you referring to a particular aspect of evolution, or are you of the persuasion that since we don't know everything we don't know anything?
It is not, of course, for me to speak for Hammegk, but I do not have the impression that he doubts evolution as a historical fact, I certainly do not. The problem people have with evolutionary explanation is that so many such explanations are not really amenable to test. Hence, people pursue the alternative of rudeness, presumably to avoid answering embarrassing questions.
I, personally, am unhappy with the general structure of evolutionary theory. I would like to hope that applying a more logically structured theory might reduce the number of those just so stories.

[kleinman]

Paul has extrapolated a value for the case of a 100k genome with 16 binding sites each 6 bases wide and a population of 1,000,000 to take 200,000,000 generations to evolve. If I said that, I was an idiot. Rfrequency > Rcapacity in that situation, so I doubt it would ever converge.

I'm currently running a series of experiments varying the genome size, but with wide binding sites that will allow a million base genome. I estimate it will take about a month to run the experiments. Stay tuned.
I wouldn’t judge you so harshly. You published the following series previously using a wider site width.
Here's some data I collected:

population 36
site width 8
1 mutation per 512 bases

genome size, generations
512, 3763
722, 4950
1024, 9866
1448, 11446
2048, 11189
2887, 13037
4096, 38731
5775, 34424
8192, 61365
11550, 68696
16384, 73915
23101, 136762
32768, 177424
46202, 344124
65536, 526545
92406, 707871
If you assume that the mutation rate affects the generations for convergence linearly (which it does not), then your generations for convergence for the last point in this series using a mutation rate of 1 mutation per 1,000,000 bases would take about 2000 times as many generations or about 1.4 billion generations. If you then increase the population to 1,000,000, you should get about 140 million generations which is still in the same ball park as your previous extrapolation. I think you are going to find that back peddling on your extrapolation of 200,000,000 generations to evolve 16 binding sites, 6 bases wide on a 100k genome with a mutation rate of 10^-6 and a population of a million is one of your few fairly accurate extrapolations and now you are retracting it. Your other fairly accurate extrapolation was that ev models reality and then you retracted that as well. The only extrapolations you make that I agree with you retract. When are you going to retract the entire ev program?

What parameters are you using anyway? Do we really have to wait a month? Well, it will give joobz a chance to increase his insult vocabulary. For someone so grammatically challenged, any increase in his vocabulary we have to look on as progress. Now if we could only have him apply his skills as an alchemist to showing us how ribose is formed in the primordial world.

You all have a fun weekend.

[Paul C. Anagnostopoulos]

FYI to those who don't already know; drkitten & articulette are 'jerkettes' rather than 'jerks'.
I think you may be wrong about at least one of them.

~~ Paul

[hammegk]

Evidence?

[Paul C. Anagnostopoulos]

I think you are going to find that back peddling on your extrapolation of 200,000,000 generations to evolve 16 binding sites, 6 bases wide on a 100k genome with a mutation rate of 10^-6 and a population of a million is one of your few fairly accurate extrapolations and now you are retracting it.
Actually, it's an absurd extrapolation, although you like it because "ooh, it's a long time and I want evolution to take a long time."

The Rfrequency for that experiment is 13, while the Rcapacity is 12. It is quite unlikely ever to evolve a perfect creature. Either I did not notice the Rcapacity problem or I made that extrapolation before I understood Rcapacity.

You have one criterion for liking an extrapolation: It makes evolution take a long time. Of course, in other circumstances you renounce extrapolation completely. Well, here's a case where you, unlike me, could have done your homework and noted the absurdity.

~~ Paul

[Paul C. Anagnostopoulos]

Evidence?
Right, like I'm going to state publicly how I know the gender of an anonymous poster.

~~ Paul

[hammegk]

Nothing like a good Paulie-The-Greek anecdote substituted for fact.

[dv82matt]

nicely stated, I look forward to seeing more of your posts.
Thanks. Fun thread. :)
It is not, of course, for me to speak for Hammegk, but I do not have the impression that he doubts evolution as a historical fact, I certainly do not. The problem people have with evolutionary explanation is that so many such explanations are not really amenable to test. Hence, people pursue the alternative of rudeness, presumably to avoid answering embarrassing questions.
I, personally, am unhappy with the general structure of evolutionary theory. I would like to hope that applying a more logically structured theory might reduce the number of those just so stories.
There are certainly some practical difficulties with testing evolution directly, however, as you are probably aware many predictions (or retrodictions if you prefer) of evolution have been tested. In cases where predictions are not feasible we may need to be content, at least temporarily, with the explanation that best explains the available evidence.

There is plenty of guesswork and hypothesizing on the cutting edge of evolutionary research as there is in any active scientific discipline. Many of these speculative theories will eventually be found wanting and discarded regardless of the esteem they are held in today.

I certainly agree that any human endeavor including science is vulnerable human foibles and that science depends on the free exchange of ideas as much as it does on evidence and reason.

Could you provide an example of an evolutionary explanation that you feel lacks convincing evidence yet is unquestioned by experts in the field?

[joobz]

Actually, evolution being the theory (lots & lots of hypotheses -- no doubt about that) with proponents here, it would be appropriate for them to provide 'supporting mathematics' to add needed rigour to the current just-so-story. :)


I thought ev was part of that. Maybe I am mistaken, but so far Paul has demonstrated that there is a definite parameter space within which a binding site could evolve. Meaning that as genome sizes increase, point mutations alone cannot effectively generate a wholly new binding site.

There doesn't seem to be a lack of evidence for evolution just a lack in putting it all together. If there was a viable contrary theory that could experimentally support all existing evidence, I would be very interested in hearing it. But ID doesn't attempt to explain any of the known data mechanistically, which makes it impossible to test and rather worthless as a counterhypothesis.

[hammegk]

Maybe I am mistaken, but so far Paul has demonstrated that there is a definite parameter space within which a binding site could evolve. Meaning that as genome sizes increase, point mutations alone cannot effectively generate a wholly new binding site.
Or we could stick with Sh.it Happens as being equally informative ... :)


There doesn't seem to be a lack of evidence for evolution just a lack in putting it all together.
See, we agree after all. In few more decades we may bring Modern Evolutionary Theory up to pre-Newtonion preciseness. :p


If there was a viable contrary theory that could experimentally support all existing evidence, I would be very interested in hearing it. But ID doesn't attempt to explain any of the known data mechanistically, which makes it impossible to test and rather worthless as a counterhypothesis.
Umm, yes, I'd also state 'Worthless Is As Worthless Does' is a fair charcterization the Mod. Ev. Th., today's version. :)

[joobz]

Or we could stick with Sh.it Happens as being equally informative ... :)
Really? I think you're being deliberately obtuse here.


See, we agree after all. In few more decades we may bring Modern Evolutionary Theory up to pre-Newtonion preciseness. :p
I think we're more at the Boyle's Law, charle's Law state in the development of equations of state. We have aspects and theories in evolution and genetics that provide useful, predictive relationships. But there is obviously more to the story.


Umm, yes, I'd also state 'Worthless Is As Worthless Does' is a fair charcterization the Mod. Ev. Th., today's version. :)
This is an unfair characterization. Modern theory has provided us the ability to predict Flu vacination effectiveness as a function of evolving mutations(see the work of Michael Deem).
ID has provided us with undue legal issues.

[hammegk]

Alternatively, Modern theory trumpets the Fact of (Mendelian) modification with descent and with great fanfare and arm-waving pretends all of the Theory has equal basis in fact. :)

[dv82matt]

Or we could stick with Sh.it Happens as being equally informative ... :)
So you don't think evolution is informative. Do you hold this position because in comparison to physics evolution is a less exact predictor of future events?
See, we agree after all. In few more decades we may bring Modern Evolutionary Theory up to pre-Newtonion preciseness. :p
All that this means is that simple physical processes are more easily modeled than complex ones.
Umm, yes, I'd also state 'Worthless Is As Worthless Does' is a fair charcterization the Mod. Ev. Th., today's version. :)So you don't think evolution is useful for describing the changes in the traits of a population over successive generations, right?

I'm still not completely clear on your position. Do you believe that evolution is:
a: false
b: reserve judgement
c: true but completly useless
d: trivially true, a tautology
e: other, please describe

If you could nail it down for me it wouldn't seem so much like a moving target, thanks.

[joobz]

Alternatively, Modern theory trumpets the Fact of (Mendelian) modification with descent and with great fanfare and arm-waving pretends all of the Theory has equal basis in fact. :)
Mendelian modification, DNA/RNA genetic theory, inter and intraspecies protein polymorphisms... But who's counting?;)

Fair enough. Which aspects of the Theory are you most in doubt of? Specifically, which aspects of the Theory (that is taken as undoubted fact) do you consider unscientific?

BTW, I hold you and your comments with the highest respect. I've seen you egg people on, but i have yet to you to be down right offensive. :)

[Paul C. Anagnostopoulos]

Nothing like a good Paulie-The-Greek anecdote substituted for fact.
Hammy, I really don't give a crap whether you take my warning seriously or not. I was simply pointing out that your fact-filled statement "FYI to those who don't already know; drkitten & articulette are 'jerkettes' rather than 'jerks'." might not be accurate in spite of the mass quantity of evidence contained therein.

~~ Paul

[Paul C. Anagnostopoulos]

Alternatively, Modern theory trumpets the Fact of (Mendelian) modification with descent and with great fanfare and arm-waving pretends all of the Theory has equal basis in fact.
Hmm. Why do scientists keep working on it, then? I never understand that. I also don't understand why scientists keep working when science is just a social construct with established hegemonic dogma.

~~ Paul

[John Hewitt]

There are certainly some practical difficulties with testing evolution directly, however, as you are probably aware many predictions (or retrodictions if you prefer) of evolution have been tested. In cases where predictions are not feasible we may need to be content, at least temporarily, with the explanation that best explains the available evidence.

There is plenty of guesswork and hypothesizing on the cutting edge of evolutionary research as there is in any active scientific discipline. Many of these speculative theories will eventually be found wanting and discarded regardless of the esteem they are held in today.
<snip>
Could you provide an example of an evolutionary explanation that you feel lacks convincing evidence yet is unquestioned by experts in the field?
"Yet is unquestioned by experts?" I am tempted to say their own theories - there are a great many DrKittens in science. However, to be more serious, I would say most of the subject matter of evolutionary psychology, (excepting my own work on sexuality and humour) most of social evolution (including all of memetics), most ideas about the origins of sense organs and nervous systems and all theories about the origin of life - apart my own work.

Really, the only evolutionary fields in which I find the reasoning and supportive data compelling are those that concern the relatedness between species. There you have serious evidence from the correlations between sequence data, Linnaean classification, geology and biological functions. One could not deny the quality of those results but so much of the rest is handwaving and it can never be more than handwaving because evolutionary theory gives no guide - predictively, it is a very weak theory.

The reasons for the weaknesses, as I said, I consider to be the erroneous construction that is placed on evolutionary theory itself. Evolutionary theory should be based on data, not genes, and should recognise all data pools, not just the data in DNA sequence. Construct it properly and I believe evolutionary theory would do better.

[Paul C. Anagnostopoulos]

The reasons for the weaknesses, as I said, I consider to be the erroneous construction that is placed on evolutionary theory itself. Evolutionary theory should be based on data, not genes, and should recognise all data pools, not just the data in DNA sequence. Construct it properly and I believe evolutionary theory would do better.
As you said, the origin of species does rely on multiple data pools. What data pools are the evo psych, memetics, sensory systems, nervous system, and origins scientists overlooking? Are the evo devo folks overlooking any data pools?

Let's take the origins scientists as an example. Clearly they are looking at fossils, at clues in genomes (DNA, RNA, and proteins), at chemistry, at crystals, at early environments, at existing extreme environments, and at extraterrestrial possibilities. What are they overlooking?


... and it can never be more than handwaving because evolutionary theory gives no guide - predictively, it is a very weak theory.
Wait a minute, now you appear to be saying they have no hope anyway.

~~ Paul

[kjkent1]

If not by evolution, then by what process which satisfies the rigorous mathematical basis which you apparently require, have the myriad of past and present lifeforms come to exist on Earth? State your hypothesis and supporting mathematics.
I have made no scientific claims to origins of life and explanation for all the different life forms we observe. It is you evolutionarians that claim you have the scientific explanation for these observations. I am showing how unscientific your explanations are and that your views are simply another faith and belief system without scientific basis despite all your claims.
If you make no scientific claims, then the alternative is that life is the product of magic, right? If that’s what you believe, then you should have the courage to state it, so that no one can mistake your position.

You decry all existing scientific investigations, you offer no other scientific hypotheses, and as an alternative, you offer nothing.

Something from nothing = magic.

I think you’ve been living out in Clovis for too long.

[dv82matt]

"Yet is unquestioned by experts?" I am tempted to say their own theories - there are a great many DrKittens in science. However, to be more serious, I would say most of the subject matter of evolutionary psychology, (excepting my own work on sexuality and humour) most of social evolution (including all of memetics), most ideas about the origins of sense organs and nervous systems and all theories about the origin of life - apart my own work.
I was thinking in terms of biological evolution. I agree that evolutionary psychology and the rest are less robust. Regarding the origins of sense organs and nervous systems my understanding is that, although they may be quite detailed, these explanations are generally proofs of concept rather than precise descriptions. As to abiogenisis I don't know of any theory that has gained widespead acceptance.
Really, the only evolutionary fields in which I find the reasoning and supportive data compelling are those that concern the relatedness between species. There you have serious evidence from the correlations between sequence data, Linnaean classification, geology and biological functions. One could not deny the quality of those results but so much of the rest is handwaving and it can never be more than handwaving because evolutionary theory gives no guide - predictively, it is a very weak theory.It seems to me that there's room for some parts of evolutionary theory to be less compelling than other parts without becoming mere handwaving.
The reasons for the weaknesses, as I said, I consider to be the erroneous construction that is placed on evolutionary theory itself. Evolutionary theory should be based on data, not genes, and should recognise all data pools, not just the data in DNA sequence. Construct it properly and I believe evolutionary theory would do better.
I take it that you mean that the gene should not be considered as the fundamental unit of selection, at least not to the exclusion of other factors. What factors do you think are being overlooked?

[hammegk]

There doesn't seem to be a lack of evidence for evolution just a lack in putting it all together.
We sure agree on that.

And my problem with the modern theory is not it as such; rather it is the misuse by it's strongest proponents to pretend Science (and evolution) provide evidence for or against the existence of god.

I'd find more charm in physicists who proclaimed "We now have the Standard Model; therefore God is Dead.".

[Foster Zygote]

My problem with the modern theory is not it as such; rather it is the misuse by it's strongest proponents to pretend Science (and evolution) provide evidence for or against the existence of god.

Which scientists do that? Science can only tell us about the physical universe. If a religious claim contradicts scientific knowledge then all scientists can say is that the claim contradicts what we know of reality. The claim that the universe is about 6000 years old is contradicted by science. Scientists can say that the claim that God made the universe 6000 years ago is contradicted by observable facts. No good scientist would then add "Therefor, God does not exist".

[hammegk]

The 6000 year comment is your strawman, not mine. And as many have pointed out, even that stance cannot be 'absolutely' ruled out; the Tricky God scenario is bulletproof albeit unappetizing to most.

And some Scientists go out of their way to proclaim God is Dead. See Dawkins for the latest example, and read others here who at least proclaim themselves to be scientists/100% atheists.

[John Hewitt]

I was thinking in terms of biological evolution. I agree that evolutionary psychology and the rest are less robust. Regarding the origins of sense organs and nervous systems my understanding is that, although they may be quite detailed, these explanations are generally proofs of concept rather than precise descriptions.
I am not sure what you mean by proof of concept.

As to abiogenisis I don't know of any theory that has gained widespead acceptance.Indeed not but my point is that none of the theories being advanced are evolutionary, or even sensible. Genes are plainly products of evolution and one cannot have an evolutionary theory for the origin of life without dispensing with genes as a foundation for evolution.


It seems to me that there's room for some parts of evolutionary theory to be less compelling than other parts without becoming mere handwaving.

I take it that you mean that the gene should not be considered as the fundamental unit of selection, at least not to the exclusion of other factors. What factors do you think are being overlooked?
As I said before, evolutionary theory should be based on data not genes. Genes should not be considered as the fundamental unit of selection but as formatting some of the data in DNA. If data is recognised as the fundamental basis for evolution then one must also recognise other forms of data as legitimate inputs into evolutionary selection. These would include the prebiotic data, sensory data and social data that encode those levels of knowledge.

[John Hewitt]

As you said, the origin of species does rely on multiple data pools. What data pools are the evo psych, memetics, sensory systems, nervous system, and origins scientists overlooking? Are the evo devo folks overlooking any data pools? I think understanding evolution requires a recognition that multiple data pools were involved. The "modern sythesis" is built around Fisher's analysis of population genetics, which only considers evolution based on genes. All other data pools are left unanalysed.


Let's take the origins scientists as an example. Clearly they are looking at fossils, at clues in genomes (DNA, RNA, and proteins), at chemistry, at crystals, at early environments, at existing extreme environments, and at extraterrestrial possibilities. What are they overlooking?The laws of physics and chemistry and the principles of information technology. In other words, what is needed is a rational analysis, not random guesses.

Wait a minute, now you appear to be saying they have no hope anyway.

~~ Paul
No, you generate rational theories by analysing the problem.

[Foster Zygote]

The 6000 year comment is your strawman, not mine.
Yes, I'm familiar with your strawmen.;) I was simply pointing out an example of what science does and does not do.
And as many have pointed out, even that stance cannot be 'absolutely' ruled out; the Tricky God scenario is bulletproof albeit unappetizing to most.
You seem to be implying that all scenarios are equally likely. The Tricky God scenario is just as "bulletproof" as any other untestable claim about the supernatural. Science doesn't claim to give the only possible answer, only the answer that is most likely based on the available evidence. Just because I can't disprove the existence of an utterly immeasurable being that can only be shown to exist in the minds of humans is not a good reason to assume that the being's existence or non-existence are equally probable. And anyway, Tricky is a great guy but I'd hardly call him a "god".
And some Scientists go out of their way to proclaim God is Dead. See Dawkins for the latest example,...
Well, Dawkins has stated openly that it would be unreasonable to claim absolute certainty that no gods exist. His claim is simply that the existence of gods is extremal unlikely.
...and read others here who at least proclaim themselves to be scientists/100% atheists.
OK, so you can point to a few people who claim to be 100% certain of the unknowable. I don't intend this to sound aggressive, but you seem to be making generalizations about atheists, scientists etc. based on a few characteristics that can only be found in a handful of people.

[Paul C. Anagnostopoulos]

If data is recognised as the fundamental basis for evolution then one must also recognise other forms of data as legitimate inputs into evolutionary selection. These would include the prebiotic data, sensory data and social data that encode those levels of knowledge.
I'm not sure what you mean by "prebiotic data," but scientists studying abiogenesis are certainly considering the prebiotic state of the Earth.

What do you mean by "sensory data"?

I'm not sure what you mean by "social data," but scientists are certainly considering the effects of social organization on evolution, and the effects of evolution on social organization. Here's an interesting article:

http://adb.sagepub.com/cgi/content/abstract/14/3/223


All other data pools are left unanalysed.
So you said. What are the data pools that evo psych, memetics, sensory systems, nervous system, abiogenesis, and evo devo are overlooking?

Are you sure you're not just painting a charicature of evolutionary biology using the scare term "modern synthesis"?

~~ Paul

[Paul C. Anagnostopoulos]

If data is recognised as the fundamental basis for evolution then one must also recognise other forms of data as legitimate inputs into evolutionary selection. These would include the prebiotic data, sensory data and social data that encode those levels of knowledge.
Perhaps I didn't understand what you meant by these pools of data. Regarding social data, do you mean the data that is embodied in the social habits that are passed from parent to child, not encoded in the genome? If so, I certainly agree that this is important data, but so do scientists. Witness interest in the Baldwin effect, for example. And investigation of social learning in monkeys.

~~ Paul

[hammegk]

You seem to be implying that all scenarios are equally likely.
Not as such; just a question of degree.


The Tricky God scenario is just as "bulletproof" as any other untestable claim about the supernatural.
Except there would be nothing supernatural about it if it were fact.


Science doesn't claim to give the only possible answer, only the answer that is most likely based on the available evidence.
Now if scientists would just do the same ...


Just because I can't disprove the existence of an utterly immeasurable being that can only be shown to exist in the minds of humans is not a good reason to assume that the being's existence or non-existence are equally probable.
Who does?


And anyway, Tricky is a great guy but I'd hardly call him a "god".
Aww, isn't that special, but no I don't think the Tricky who posts here fits the bill.


Well, Dawkins has stated openly that it would be unreasonable to claim absolute certainty that no gods exist. His claim is simply that the existence of gods is extremal unlikely.
The problem for Dawkins, and anyone else who buys that pap, is that it's a worldview that cannot be defended logically by wannabe materialists.


OK, so you can point to a few people who claim to be 100% certain of the unknowable.
Exactly one I'm sure of. He does the rest of you mealy-mouths proud by taking a stand.


I don't intend this to sound aggressive, but you seem to be making generalizations about atheists, scientists etc. based on a few characteristics that can only be found in a handful of people.
Yeah, I generalize that most self-described atheists/scientists/materialists accept an illogical worldview that is none of those positions and whine when they get called on it.

[joobz]

Not as such; just a question of degree.


The problem for Dawkins, and anyone else who buys that pap, is that it's a worldview that cannot be defended logically by wannabe materialists.

Exactly one I'm sure of. He does the rest of you mealy-mouths proud by taking a stand.

Yeah, I generalize that most self-described atheists/scientists/materialists accept an illogical worldview that is none of those positions and whine when they get called on it.

Why would an uncertainty in a god be viewed as illogical world view when uncertainty in the evolutionary theory isn't?

[joobz]

As I said before, evolutionary theory should be based on data not genes. Genes should not be considered as the fundamental unit of selection but as formatting some of the data in DNA. If data is recognised as the fundamental basis for evolution then one must also recognise other forms of data as legitimate inputs into evolutionary selection. These would include the prebiotic data, sensory data and social data that encode those levels of knowledge.
I curious to know what "data" you are talking about here. It seems odd to use a more nebulous/indisctinct term without providing reasons to do so. How does this changing of word usage better fit the observations we have?

[dv82matt]

I am not sure what you mean by proof of concept.
Proof that a concept, eye evolution for example, is feasible rather than a precise description of how the eye actually evolved.
Indeed not but my point is that none of the theories being advanced are evolutionary, or even sensible.
Oh, well that's a seperate issue from what we were discussing. At least I don't see the relevance.
Genes are plainly products of evolution and one cannot have an evolutionary theory for the origin of life without dispensing with genes as a foundation for evolution.I don't see that the second part must follow from the first part.
As I said before, evolutionary theory should be based on data not genes. Genes should not be considered as the fundamental unit of selection but as formatting some of the data in DNA. If data is recognised as the fundamental basis for evolution then one must also recognise other forms of data as legitimate inputs into evolutionary selection.Hmmm... I don't know. It seems like a distinction without a difference. Why not simply propose that genes are not the sole unit of selection?
These would include the prebiotic data, sensory data and social data that encode those levels of knowledge.
Leaving open the question of whether prebiotic data would be relevant, it seems to me that we would need to have a pretty good understanding of abiogenesis before we could identify it.

I'm not sure what is to be gained by including sensory data. The senses are determined by the genes so a selection mechanism that has genes as its fundamental unit automatically considers sensory data.

Social data could very well be relevant in species that are able to pass on learned behaviours. The brain would be encoding data independent of the genes. It doesn't strike me as a very robust data set however. I think that theories that utilize this data set, such as social evolution, will tend to be more conjectural. And there is also the problem of collecting social data. In most cases it's only feasible with living species.

[John Hewitt]

I'm not sure what you mean by "prebiotic data," but scientists studying abiogenesis are certainly considering the prebiotic state of the Earth.

What do you mean by "sensory data"?

I'm not sure what you mean by "social data," but scientists are certainly considering the effects of social organization on evolution, and the effects of evolution on social organization. Here's an interesting article:

http://adb.sagepub.com/cgi/content/abstract/14/3/223


So you said. What are the data pools that evo psych, memetics, sensory systems, nervous system, abiogenesis, and evo devo are overlooking?

Are you sure you're not just painting a charicature of evolutionary biology using the scare term "modern synthesis"?

~~ Paul
I am not into developmental biology, so I shall not comment upon it.

There was, I presume, an evolutionary process that led to the apparatus of an evolved molecular genetics that uses nucleotide bases etc. I take the data used in that prebiotic evolution to be prebiotic data and I take that evolutionary process to have been rank0 evolution. Rank1 evolution is DNA based evolution. Sensory data is data acquired through the sense organs and I take the evolution associated with it, which occurs in the brain, to be rank2 evolution.

I take social data to be the data that codes for communally inherited knowledge, such as language and shared skills. That leads to rank3 evolution.

Edelman does give an analysis of neural Darwinism for rank2 but it does not generalize to other ranks. I am not aware of any evolutionary analysis of these other levels of evolution. Workers don't overlook those topics, they just don't analyse them. My work aims for general anaysis of evolution applicable to all those levels and also to rank4. Prebiotic theories are mostly random hypotheses and discussions of social evolution tend to be empty verbiage - memetics being a case in point.

Until very recently, most biologists entirely dismissed multilevel selection theories and insisted on reducing every analysis to the "fundamental genes." Since genes cannot possibly be fundamental to any evolution but rank1, that is not sensible. So far as I know, I am the only person who has yet identified data as the foundation of all evolution and as the basis from which you can generalise evolutionary theory.

[John Hewitt]

I curious to know what "data" you are talking about here. It seems odd to use a more nebulous/indisctinct term without providing reasons to do so. How does this changing of word usage better fit the observations we have?
The word "data" is well defined. It arises from statistical mechanics - for example Shannon. (As an aside, Shannon used the word "information" but this is now incorrect in modern usage; his definition would now be of the word "data," whicle information is "interpreted data."

Genes, on the other hand, are not well defined at all. The fundamental theory of evolution comes from Fisher, whose work was inspired by statistical mechanics. Fisher tried to apply the statistics of genes and selection to organisms in much the same statistical way that Boltzmann applied atomic physics to the macroscopic properties of materials. However, the atom was well defined but the gene wasn't - Fisher's genes were independent atoms of evolution. Molecular biology shows that genes are not independent and are not atoms. It also shows that population genetics is just an approximation. I do argue that the more non-genetic data is being inherited, the less accurate population genetic analyses will become.

Sagan estimated that humans inherit about 1000 times more social data than biological data. He did not say where that estimate came from, but I think you get the point. To me, population genetics looks like a very dubious tool to apply to our understanding of human evolution.

[John Hewitt]

Oh, well that's a seperate issue from what we were discussing. At least I don't see the relevance.
I don't see that the second part must follow from the first part.
Hmmm... I don't know. It seems like a distinction without a difference. Why not simply propose that genes are not the sole unit of selection?

Well, there are two theories for the origin of life, ID and evolution. So, find an evolutionary theory that comes from chemistry and physics or consider ID. My work proposes an evolutionary mechanism that comes from chemistry and physics. In addition, either
1. genes arose by an evolutionary process from non-genes, or
2. genes arose by chance or
3. genes were created by design.

My work suggests that genes arose by an evolutionary process from non-genes. On that basis, an evolutionary process must exist that does not take genes as an input.

Because I prefer not to use the word "unit" without defining it. A unit of evolution is a self-bounding data set.


Leaving open the question of whether prebiotic data would be relevant, it seems to me that we would need to have a pretty good understanding of abiogenesis before we could identify it.The first step is to identify the prebiotic data source and then apply what we already know about chemistry.

I'm not sure what is to be gained by including sensory data. The senses are determined by the genes so a selection mechanism that has genes as its fundamental unit automatically considers sensory data.

Social data could very well be relevant in species that are able to pass on learned behaviours. The brain would be encoding data independent of the genes. It doesn't strike me as a very robust data set however. I think that theories that utilize this data set, such as social evolution, will tend to be more conjectural. And there is also the problem of collecting social data. In most cases it's only feasible with living species.The data acquired by the senses is not determined by the sense organs. One cannot ignore sensory data while including social data. Social data is spread using sense organs.
However, I am not concerned with analysing social data itself, only with attempting to understand the biological consequences of its existence.

[Paul C. Anagnostopoulos]

Sensory data is data acquired through the sense organs and I take the evolution associated with it, which occurs in the brain, to be rank2 evolution.
Huh? I have no idea what you're talking about here. Are you treating how I learn over my lifetime as some sort of single-organism evolutionary process?


Until very recently, most biologists entirely dismissed multilevel selection theories and insisted on reducing every analysis to the "fundamental genes." Since genes cannot possibly be fundamental to any evolution but rank1, that is not sensible. So far as I know, I am the only person who has yet identified data as the foundation of all evolution and as the basis from which you can generalise evolutionary theory.
I think you are making a sweeping statement here that is not entirely accurate. Scientists are considering data from all your levels. However, if you can come up with a general mathematical model that covers all these levels, one that is not simply window dressing on existing theories, that would be pretty cool.

~~ Paul

[dv82matt]

Well, there are two theories for the origin of life, ID and evolution. So, find an evolutionary theory that comes from chemistry and physics or consider ID. My work proposes an evolutionary mechanism that comes from chemistry and physics. In addition, either
1. genes arose by an evolutionary process from non-genes, or
2. genes arose by chance or
3. genes were created by design.

My work suggests that genes arose by an evolutionary process from non-genes. On that basis, an evolutionary process must exist that does not take genes as an input.
Indeed. This may be a naive question but how do you know that rank0 evolution has data as its fundamental unit?
Because I prefer not to use the word "unit" without defining it. A unit of evolution is a self-bounding data set.
I'm not sure what you're getting at here but from your post to Paul I got the impression that it was to facilitate the unification of the seperate 'ranks' of evolution into a single overarching theory.
The first step is to identify the prebiotic data source and then apply what we already know about chemistry.
Of course. The problem is in identifying a prebiotic data source.
The data acquired by the senses is not determined by the sense organs.And the foods available to be eaten are not determined by the digestive system. What is the process for inheriting sensory data?
One cannot ignore sensory data while including social data. Social data is spread using sense organs.It is also spread using speech organs. Does speech now require its own evolutionary rank?
However, I am not concerned with analysing social data itself, only with attempting to understand the biological consequences of its existence.Wouldn't the biological consequences of social data depend on the specifics of that data?

One last question, what is rank4 evolution?

[hammegk]

Why would an uncertainty in a god be viewed as illogical world view when uncertainty in the evolutionary theory isn't?
God (not science) vs ev theory (science) comparisons start with a category error.

Uncertainty in a god is not apriori illogical; it's only illogical for a materialist who should be 100% certain god cannot exist. Dualism -- the stance materialism reaches iff the existence of god is only uncertain -- is itself apriori illogical.

Or, iff you can answer my question to Darat, you can place dualism on a logical footing. :)

[Paul C. Anagnostopoulos]

God (not science) vs ev theory (science) comparisons start with a category error.
By whose fiat is god not science? Is this the damn category error you keep mentioning?

Uncertainty in a god is not apriori illogical; it's only illogical for a materialist who should be 100% certain god cannot exist.
And if you say to a materialist "assume god is not material" then I'm sure he would agree that god cannot exist. Unless, of course, he is only taking materialism as a reasonable assumption, pending some evidence that distinguishes materialism from idealism.

Dualism -- the stance materialism reaches iff the existence of god is only uncertain -- is itself apriori illogical.
Again, this statement is based on your dogmatic pseudo-definition of god.

~~ Paul

[hammegk]

By whose fiat is god not science? Is this the damn category error you keep mentioning?
Yes. I believe you finally got it. :D


And if you say to a materialist "assume god is not material" then I'm sure he would agree that god cannot exist. Unless, of course, he is only taking materialism as a reasonable assumption, pending some evidence that distinguishes materialism from idealism.
Paulie, you are free to embrace dualism as it apparently please you (unless materialism is True; then none of us may have any choice in our 'private behaviors'). ;)


Again, this statement is based on your dogmatic pseudo-definition of god.

Who can define god? I can't. You may choose to (or be forced to) as the case may be.

[joobz]

The word "data" is well defined.

I take the data used in that prebiotic evolution to be prebiotic data and I take that evolutionary process to have been rank0 evolution. Rank1 evolution is DNA based evolution. Sensory data is data acquired through the sense organs and I take the evolution associated with it, which occurs in the brain, to be rank2 evolution.

I take social data to be the data that codes for communally inherited knowledge, such as language and shared skills. That leads to rank3 evolution.

I do not see how one statement follows the other. I stated that "Data" is a more nebulous catch-all compared to a gene, which has a specific known biological context. Your statement is an effect saying that evolution had to occur prior to the gene formation, which is self understood.


Until very recently, most biologists entirely dismissed multilevel selection theories and insisted on reducing every analysis to the "fundamental genes." Since genes cannot possibly be fundamental to any evolution but rank1, that is not sensible. So far as I know, I am the only person who has yet identified data as the foundation of all evolution and as the basis from which you can generalise evolutionary theory.
This isn't true now. Again, you gave a term to a concept that's been "evolving" in the literature already. Your complaint of genes may have been accurate 20 years ago, but I do not think you'll find anyone claiming that genes must be the beginning or sole portion of evolutionary theory.

If your theory can provide some weighting effect that each rank has. Or if your theory has an ability to differentiate what defines the different ranks or when the different ranks evolve ( I assume in your theory we can't have rank1 without rank0, or rank2 without rank1 or rank0...) it may be quite interesting. But if it just a vocabulary change you are inacting, I'd be a little suspect in it's utility.

[joobz]

God (not science) vs ev theory (science) comparisons start with a category error.

Uncertainty in a god is not apriori illogical; it's only illogical for a materialist who should be 100% certain god cannot exist. Dualism -- the stance materialism reaches iff the existence of god is only uncertain -- is itself apriori illogical. Isn't this only the case of god is unknowable. If we are simply uncertain, I do not see how that can be considered an illogical stance. If we allow for the fact that god isn't supernatural.

[Paul C. Anagnostopoulos]

God (not science) vs ev theory (science) comparisons start with a category error.
...
Who can define god? I can't.
All righty then. You contradicted yourself in the space of two posts.

~~ Paul

[kjkent1]

Who can define god? I can't. You may choose to (or be forced to) as the case may be.

Why do you interject God into a scientific discussion? You're smart enough to know that God is not measurable via any scientific methodology, so how is God relevant, except as a distraction?

[John Hewitt]

I do not see how one statement follows the other. I stated that "Data" is a more nebulous catch-all compared to a gene, which has a specific known biological context. Your statement is an effect saying that evolution had to occur prior to the gene formation, which is self understood.
Understood by whom? Most theories of prebiosis just speculate that genes emerge by one form or another of chance. I know of no work apart from my own that proposes any prebiotic selective process at all.


This isn't true now. Again, you gave a term to a concept that's been "evolving" in the literature already. Your complaint of genes may have been accurate 20 years ago, but I do not think you'll find anyone claiming that genes must be the beginning or sole portion of evolutionary theory.
No? Come on, they reduce evolution to fundamental genes - which is the same thing.

If your theory can provide some weighting effect that each rank has. Or if your theory has an ability to differentiate what defines the different ranks or when the different ranks evolve ( I assume in your theory we can't have rank1 without rank0, or rank2 without rank1 or rank0...) it may be quite interesting. But if it just a vocabulary change you are inacting, I'd be a little suspect in it's utility.
This is getting way of topic but here's a little bit of a reply.

All data, in all ranks is subject to interpretation into information and selection into knowledge, which is encoded as data for transmission to the next generation.
I categorize ranks of evolution on the basis of where the selective process takes place. Rank0, is a catch-all for prebiotic chemistry; rank1 is evolution that selects data encoded on DNA. Rank2 arises from sensory data and when interpretations are selected with a receiving organism. Rank3 occurs when the selection is performed by the transmitter - thus leading to social knowledge. Rank4 evolution and occurs when selection is determined by neither a transmitter nor a receiver but by the mandate of a shared body of selective rules. This is subcultural evolution and, among other things, leads to professional bodies of knowledge.

This description implies that there can be more than one evolution at each rank - for example, rank2 evolution in humans involves two Darwinian machines, the brain and the immune system. These I refer to are separate orders of evolution within the same evolutionary rank.

Evolving data sets must be interpreted in such a way as to make them self-bounding and therefore competitively separable.

I am always interested in identifying more properties that are generally required for evolving data sets. Suggestions are welcome.

Its utilty is in what it can do.

[joobz]

Understood by whom? Most theories of prebiosis just speculate that genes emerge by one form or another of chance. I know of no work apart from my own that proposes any prebiotic selective process at all.
I've just started looking into the literature (hence the reason for the delay in answering your former question). But i haven't seen the concept proposed as a pure chance development of genes. It seems that self-propagating chemstry in the development of genes is the most commonly considered avenue of speculation. The one that comes to mind first is the RNA directed formation of ribose, but I just pulled the article.

[Foster Zygote]

Uncertainty in a god is not apriori illogical; it's only illogical for a materialist who should be 100% certain god cannot exist. Dualism -- the stance materialism reaches iff the existence of god is only uncertain -- is itself apriori illogical.

Only if your materialist is 100% certain of materialism. If he is provisionally 99.99% convinced that materialism is the correct explanation of the state of the universe then your word-game argument falls apart. As is usually the case, you are dueling a dualist straw man.

[John Hewitt]

I've just started looking into the literature (hence the reason for the delay in answering your former question). But i haven't seen the concept proposed as a pure chance development of genes. It seems that self-propagating chemstry in the development of genes is the most commonly considered avenue of speculation. The one that comes to mind first is the RNA directed formation of ribose, but I just pulled the article.

And, just by CHANCE, this self-propagating chemistry (the details of which I look forward to reading) happens to produce a ribozyme, a piece of RNA which has the amazing property of being able to copy itself, from precursors that had the equally amazing properties of being present in the first place and of not diffusing off into the prebiotic soup.

Sorry, I think maybe I'm in a bad mood today.

[Yahzi]

What is more, and as I have mentioned to you previously, what I look for is an intelligent discussion directed to the subject.

I would say most of the subject matter of evolutionary psychology, (excepting my own work on sexuality and humour) most of social evolution (including all of memetics), most ideas about the origins of sense organs and nervous systems and all theories about the origin of life - apart my own work.
See, again we stumble over your basic illiteracy.

The word you were looking for was not "discussion;" but rather, "monologue."

[Yahzi]

Why would an uncertainty in a god be viewed as illogical world view when uncertainty in the evolutionary theory isn't?
Hey! Hey! Are you using logic?

None of that stuff in here, buster! Take it outside!

:D

[Yahzi]

And, just by CHANCE,
Remember when you asserted you were more scientifically literate than me?

I know that evolution doesn't happen by chance. I learned this from granola.

Shake a box of granola gently, and what happens? The the little flakes sink to the bottom, and the big pieces float to the top where you can eat them by hand. Some time ago I noticed this sorting effect happens every single time. And, not being scientifically illiterate, I realized it wasn't because of chance.

I'm not sure how to characterize your scientific expertise, given that apparently my breakfast habits have yielded superior insights.

Sorry, I think maybe I'm in a bad mood today.
That's a good thing. It's the first sign that your cognitive dissonance is breaking down. It's like taking out a splinter; it hurts coming out, but afterwards there's a huge sense of relief.

Just take a big breath and admit that order can arise from simplicity if energy is injected into the system. Just let that fact lie there, like your granola, until it gets mushy. Just accept it for today.

And then, tomorrow, you can start working out what it means for everything else.

[hammegk]

Only if your materialist is 100% certain of materialism. If he is provisionally 99.99% convinced that materialism is the correct explanation of the state of the universe then your word-game argument falls apart.
No, that's what causes the problem ... unless you'd like to contend that 99.99=100. :)


As is usually the case, you are dueling a dualist straw man.
In this case, you are wrong; but keep trying ... you may eventually get it. ;)

[Paul C. Anagnostopoulos]

And, just by CHANCE, this self-propagating chemistry (the details of which I look forward to reading) happens to produce a ribozyme, a piece of RNA which has the amazing property of being able to copy itself, from precursors that had the equally amazing properties of being present in the first place and of not diffusing off into the prebiotic soup.
Come on. No one is saying that a ribozyme appeared by chance. Just Google "evolution of ribozymes". And search for it at PubMed, too.

I really think you've got a narrow view of the modern synthesis.

~~ Paul

[John Hewitt]

Remember when you asserted you were more scientifically literate than me?

I know that evolution doesn't happen by chance. I learned this from granola.

Shake a box of granola gently, and what happens? The the little flakes sink to the bottom, and the big pieces float to the top where you can eat them by hand. Some time ago I noticed this sorting effect happens every single time. And, not being scientifically illiterate, I realized it wasn't because of chance.

I'm not sure how to characterize your scientific expertise, given that apparently my breakfast habits have yielded superior insights.

That's a good thing. It's the first sign that your cognitive dissonance is breaking down. It's like taking out a splinter; it hurts coming out, but afterwards there's a huge sense of relief.

Just take a big breath and admit that order can arise from simplicity if energy is injected into the system. Just let that fact lie there, like your granola, until it gets mushy. Just accept it for today.

And then, tomorrow, you can start working out what it means for everything else.


The problem with understanding the origin of life is not that of understanding the orgin of inanimate order but that of biological complexity. I am sorry you are unable to understand that distinction.

I repeat that what I would like is a dialogue directed to the topic. I think you just engage in ad hominems all the time.

[John Hewitt]

Come on. No one is saying that a ribozyme appeared by chance. Just Google "evolution of ribozymes". And search for it at PubMed, too.

I really think you've got a narrow view of the modern synthesis.

~~ Paul
No, I don't need to google it. I've read up on this field and attended a recent conference on it. Scientists may avoid those exact words, but chance is pretty much exactly what they are saying.

All these experiments on catalysed RNA sythesis begin with energy activated precursors, whose origin is not specified. In the laboratory, these precursors are kept together in containers, to stop them diffusing away. The clay cataysts are selected and treated to remove impurities that would stop the catalysis. Such carefully controlled conditions could never appear by chance in the prebiotic oceans and yet, even under those conditions, nothing resembling an autocatalytic ribozyme has been produced.

Consider Monod's options - chance or necessity - he could have added design but, so far as science is concerned, there are two options - origin by necessity, which means selection, or origin by chance. These studies on RNA synthesis do not specify a selective mechanism which leaves just chance as the origin of ribozymes - chance that we must happened not in a carefully controlled test tube but in the wide expanses of the prebiotic oceans.

I think the whole thing is a complete fantasy. My preference is to look for a selective mechanism.

[joobz]

And, just by CHANCE, this self-propagating chemistry (the details of which I look forward to reading) happens to produce a ribozyme, a piece of RNA which has the amazing property of being able to copy itself, from precursors that had the equally amazing properties of being present in the first place and of not diffusing off into the prebiotic soup.

Sorry, I think maybe I'm in a bad mood today.
No need to apologize, always happy to hear your thoughts.:)

But I again think it strange you acknowledge a rank0 form of selection that had to precede the rank1(gene based evolution). But you dismiss attempts to define what this rank0 as mere chance descriptions. Again, unless we know what data means in a physical sense, saying data is the basic unit of evolution doesn't add any "information".

[Paul C. Anagnostopoulos]

No, I don't need to google it. I've read up on this field and attended a recent conference on it. Scientists may avoid those exact words, but chance is pretty much exactly what they are saying.

All these experiments on catalysed RNA sythesis begin with energy activated precursors, whose origin is not specified. In the laboratory, these precursors are kept together in containers, to stop them diffusing away. The clay cataysts are selected and treated to remove impurities that would stop the catalysis. Such carefully controlled conditions could never appear by chance in the prebiotic oceans and yet, even under those conditions, nothing resembling an autocatalytic ribozyme has been produced.
When I search around, I seem to find a more varied selection of experiments.

So what's your first step in discovering the selection pressures that you're talking about?

~~ Paul

[articulett]

John, you say: "The problem with understanding the origin of life is not that of understanding the origin of inanimate order but that of biological complexity. I am sorry you are unable to understand that distinction" to Yahtzi's clever explanation. But biological complexity arises from atoms...matter that responds to forces. There is no single point where we can say this is alive and this isn't when we go along the evolutionary path--some things have some properties of life but not others...sperm for example--viruses--prions--amino acides--blood cells--stem cells--the brain dead, tumors, fungi spores, etc. There really isn't a dividing line where something becomes alive just as speciation takes years and there is no moment where we can say--that is the first "human". You seem to think there is something added to the continuum of natural events to make life different than non life because on a macroscopic level the two seem very different--you seem to think there needs to be intelligence behind replication--that natural laws couldn't account for it--but that just means that you stop looking for the answer. All of our greatest scientific knowledge were powers once attributed to gods--we were told we couldn't understand--and yet we do--weather, inheritance, atoms, gravity, etc.

The ancestors of you didn't plan for or know you--and the further you go back in time the more you understand how true that is--they don't need to...it turns out that life can get made without anyone intending it and does so all the time. There's so much that came before you and so much that will come after and stuff in the bottom of the ocean that we are still discovering and so many weird viruses in the ocean that there are theories that viruses lead to life and not the other way around. What good does it do to believe that it's special or mysterious or beyond human understanding--other than make you feel more self important, I mean.

Yahtzi's point was merely that you are purposely and artificially making a difference between that which we call alive and that which is not so that you can point to a lack of knowledge as argument that an "intelligent designer" must be added to the "alive" side of the equation. But there is no such dividing line between alive and unalive--between conscious and unconscious...between awareness and lack thereof. It's a continuum.

[articulett]

And isn't the "selective mechanism" you are looking for always your "intelligent designer"--it's never chance coupled with natural selection...the way mountains get built and planets get formed and so forth? You won't allow yourself to even imagine this as a possibility because life is too different than those things--but it's not so different when you look at all the life-ish things mentioned above. It's ratcheting...one teeny tiny change on top of another and endless opportunities for experimentation just so long as energy is coming into the system...

[hammegk]

... there is no such dividing line between alive and unalive--between conscious and unconscious...between awareness and lack thereof. It's a continuum.
You finally typed something worthwhile. It's too bad you don't understand what it means.

[cyborg]

You finally typed something worthwhile.

Maybe you will too one day.

[Foster Zygote]

No, that's what causes the problem ... unless you'd like to contend that 99.99=100. :)


In this case, you are wrong; but keep trying ... you may eventually get it. ;)

Yes, maybe someday we'll all be as smart as you.:rolleyes:

[Paul C. Anagnostopoulos]

I opened the 8 December issue of Science and what did I find? An article by Martin Nowak titled "Five Rules for the Evolution of Cooperation." The final sentence:

Thus, we might add "natural cooperation" as a third fundamental principle of evolution beside mutation and natural selection.

~~ Paul

[Yahzi]

The problem with understanding the origin of life is not that of understanding the orgin of inanimate order but that of biological complexity.
What's the difference?

Life is made out of inanimate substances, arranged in a particular order. Indeed, the sole difference between inanimacy and life is the order in which the materials are arranged.

I am sorry you are unable to understand that distinction.
I am sorry you are unaware that vitalism (http://skepdic.com/vitalism.html) is really, really out of date.

I repeat that what I would like is a dialogue directed to the topic. I think you just engage in ad hominems all the time.
It's not ad hominem; it's an insult. I did not assert that your arguments were worthless because you were stupid; I concluded that you were stupid because your arguments are worthless.

I offered you a rational discourse; I presented my case with flair and clarity. I demonstrated that your use of the word "chance" was wholly inappropriate. Your response was to assert that there is some magical difference between biological order and chemical order, while insinuating that I was too stupid to respond to. This is a case of both "ad hominen" and "moving the goal posts."

[John Hewitt]

Yahtzi's point was merely that you are purposely and artificially making a difference between that which we call alive and that which is not
I note that you and Yahzi feel there is no difference between alive and not alive.

[John Hewitt]

When I search around, I seem to find a more varied selection of experiments.

So what's your first step in discovering the selection pressures that you're talking about?

~~ Paul
So do I, I was just quoting the most popular. I begin with data, the data flow from the sun. It might be best if you read what I wrote.

http://www.sexandphilosophy.co.uk/pe00_prebiotic_index.htm

and subsequent files, which include a review of the main existing ideas.

[hammegk]

Maybe you will too one day.
I'll keep watching to see if you ever understand my point. If you do, I'll probably be wrong.

Yes, maybe someday we'll all be as smart as you.:rolleyes:
If you care to live as though 0.01=0.00 go right ahead.


Thanks for playing, though.

[kjkent1]

I'll keep watching to see if you ever understand my point. If you do, I'll probably be wrong.


If you care to live as though 0.01=0.00 go right ahead.


Thanks for playing, though.

Hello, Z.

[kleinman]

You all have been very busy this weekend.

I think you are going to find that back peddling on your extrapolation of 200,000,000 generations to evolve 16 binding sites, 6 bases wide on a 100k genome with a mutation rate of 10^-6 and a population of a million is one of your few fairly accurate extrapolations and now you are retracting it. Actually, it's an absurd extrapolation, although you like it because "ooh, it's a long time and I want evolution to take a long time."

The Rfrequency for that experiment is 13, while the Rcapacity is 12. It is quite unlikely ever to evolve a perfect creature. Either I did not notice the Rcapacity problem or I made that extrapolation before I understood Rcapacity.

You have one criterion for liking an extrapolation: It makes evolution take a long time. Of course, in other circumstances you renounce extrapolation completely. Well, here's a case where you, unlike me, could have done your homework and noted the absurdity.
That’s why I posted your series with Rcapacity of 16 which gives about the same number of generations to evolve a perfect creature. There is a small gain in doing this for the evolutionarian argument, instead of evolving only 96 loci; you are evolving 128 loci on the 100k genome. Perhaps next month you will post the data which shows how absurd these extrapolations are but I doubt it.

I have two criterions for liking an extrapolation, one is that it makes evolution take a long time and the other is that it annoys evolutionarians.
I thought ev was part of that. Maybe I am mistaken, but so far Paul has demonstrated that there is a definite parameter space within which a binding site could evolve. Meaning that as genome sizes increase, point mutations alone cannot effectively generate a wholly new binding site.
Well stated.
There doesn't seem to be a lack of evidence for evolution just a lack in putting it all together. If there was a viable contrary theory that could experimentally support all existing evidence, I would be very interested in hearing it. But ID doesn't attempt to explain any of the known data mechanistically, which makes it impossible to test and rather worthless as a counterhypothesis.
There also wasn’t a lack of evidence for the flat earth theory; however that evidence was overwhelmed by further discoveries.
Umm, yes, I'd also state 'Worthless Is As Worthless Does' is a fair charcterization the Mod. Ev. Th., today's version. This is an unfair characterization. Modern theory has provided us the ability to predict Flu vacination effectiveness as a function of evolving mutations(see the work of Michael Deem).
ID has provided us with undue legal issues.
The field of immunology advances despite the theory of evolution, not because of the theory of evolution. Stop trying to teach grade school children the theory of evolution is truth and I think most evolutionarian legal problems would disappear.
Alternatively, Modern theory trumpets the Fact of (Mendelian) modification with descent and with great fanfare and arm-waving pretends all of the Theory has equal basis in fact. Fair enough. Which aspects of the Theory are you most in doubt of? Specifically, which aspects of the Theory (that is taken as undoubted fact) do you consider unscientific?
It’s the mathematics joobz, the theory does not add up.
If not by evolution, then by what process which satisfies the rigorous mathematical basis which you apparently require, have the myriad of past and present lifeforms come to exist on Earth? State your hypothesis and supporting mathematics.I have made no scientific claims to origins of life and explanation for all the different life forms we observe. It is you evolutionarians that claim you have the scientific explanation for these observations. I am showing how unscientific your explanations are and that your views are simply another faith and belief system without scientific basis despite all your claims.If you make no scientific claims, then the alternative is that life is the product of magic, right? If that’s what you believe, then you should have the courage to state it, so that no one can mistake your position.

You decry all existing scientific investigations, you offer no other scientific hypotheses, and as an alternative, you offer nothing.

Something from nothing = magic.

I think you’ve been living out in Clovis for too long.
Don’t confuse that I am not making any scientific claims about the origin of life with a claim that it occurs by magic. Neither have I decried any scientific investigations we have been discussing. On numerous occasions I have applauded Dr Schneider’s work in developing ev. I am only critical of the superficial analysis he did with his model but I believe he did a good job applying the fundamental theories involved.

I haven’t lived in Clovis for years but now you can easily verify my medical credentials. With that piece of information and the title and publisher of my PhD thesis you can verify my engineering credentials. You are really trying to find the exit to your cubicle.
As I said before, evolutionary theory should be based on data not genes. Genes should not be considered as the fundamental unit of selection but as formatting some of the data in DNA. If data is recognised as the fundamental basis for evolution then one must also recognise other forms of data as legitimate inputs into evolutionary selection. These would include the prebiotic data, sensory data and social data that encode those levels of knowledge.
John, a synonym for the word “data” is the word “information”. I believe in order to take this discussion into the hard scientific arena, you must define your data (information) in a way which can be quantified and then apply accepted mathematical rules to this data and see whether the theory can be supported. In addition, the concept of evolutionary selection needs to be accurately defined and quantified in order to apply mathematical rules to test its validity. Dr Schneider did both of these things with his ev model.
Who can define god? I can't. You may choose to (or be forced to) as the case may be.Why do you interject God into a scientific discussion? You're smart enough to know that God is not measurable via any scientific methodology, so how is God relevant, except as a distraction?
Hammegk wasn’t the only one to interject God into a scientific discussion. You did this yourself when you said:
I presume that your alternative theory is that all life on Earth is the product of instantaneous materialization by application of the divine will of an almighty and limitless creator?
You can not aggressively challenge the theory of evolution without having evolutionarians accusing the opposition of being religious fanatics.
... there is no such dividing line between alive and unalive--between conscious and unconscious...between awareness and lack thereof. It's a continuum.
Don’t you know that we live in a quantized world?

[Paul C. Anagnostopoulos]

I have two criterions for liking an extrapolation, one is that it makes evolution take a long time and the other is that it annoys evolutionarians.
I stand corrected.

~~ Paul

[Yahzi]

I note that you and Yahzi feel there is no difference between alive and not alive.
Um.

It's not just me and Articulett.

It's the entire scientific establishment.

Vitalism is dead, dude.

Perhaps the rest of the people in this thread could explicitly state whether they endorse the vitalist principle or not.

[Foster Zygote]

I'll keep watching to see if you ever understand my point. If you do, I'll probably be wrong.


If you care to live as though 0.01=0.00 go right ahead.


Thanks for playing, though.

You may read the following as an ad hominem if you like, but it is not intended as such. It is simply an honest appraisal of your forum behavior based on my observations.

When it comes right down to it you're not much different from Lifegazer. Your motive for participation in this forum seems to be little more than ego-masturbation. I've noticed that you are deliberately vague about your own position while demanding others define their's with great precision. I suspect this is because you are simply a troll who wishes to belittle others intellect (and imply the superiority of your own) without having to defend your own dubious position. If this game amuses you you are welcome to it. I'm sure there will always be those who will be willing to play it with you. I, however, find it puerile and boring. Have a nice life.

[John Hewitt]

John, a synonym for the word “data” is the word “information”. I believe in order to take this discussion into the hard scientific arena, you must define your data (information) in a way which can be quantified and then apply accepted mathematical rules to this data and see whether the theory can be supported. In addition, the concept of evolutionary selection needs to be accurately defined and quantified in order to apply mathematical rules to test its validity. Dr Schneider did both of these things with his ev model.

Data and information are no longer synonymous. Information is "interpreted data," or that is the definition taught in schools. However, you are correct in implying that a great many people treat them as synonymous and they were indeed so treated in Shannon's day. It would certainly help to define selection rigidly and treat it quantitatively but I think that is easier to say than do. It would be much easier in computer simulations than in models that attempt to mimic the real world.

[John Hewitt]

Um.

It's not just me and Articulett.

It's the entire scientific establishment.

Vitalism is dead, dude.

Perhaps the rest of the people in this thread could explicitly state whether they endorse the vitalist principle or not.
I, like most people, believe that living things are subject to the laws of chemistry and physics but that does not mean or even imply that there is no difference between alive and dead.

[kleinman]

I note that you and Yahzi feel there is no difference between alive and not alive.Um.

It's not just me and Articulett.

It's the entire scientific establishment.

Vitalism is dead, dude.

Perhaps the rest of the people in this thread could explicitly state whether they endorse the vitalist principle or not.
Yahzi, I guess the medical, legal and insurance community has not been informed of this scientific breakthrough. If you like, when you die, I’ll fill out your death certificate and under cause of death, I’ll put “Not dead, rapidly devolving”.

Calling someone “dude” really dates you. You aren’t a 60’s hippie are you? If you have any hair left, do you still wear a head band? The theory of evolution is really a bad trip man, heavy dude, heavy.
John, a synonym for the word “data” is the word “information”. I believe in order to take this discussion into the hard scientific arena, you must define your data (information) in a way which can be quantified and then apply accepted mathematical rules to this data and see whether the theory can be supported. In addition, the concept of evolutionary selection needs to be accurately defined and quantified in order to apply mathematical rules to test its validity. Dr Schneider did both of these things with his ev model.Data and information are no longer synonymous. Information is "interpreted data," or that is the definition taught in schools. However, you are correct in implying that a great many people treat them as synonymous and they were indeed so treated in Shannon's day. It would certainly help to define selection rigidly and treat it quantitatively but I think that is easier to say than do. It would be much easier in computer simulations than in models that attempt to mimic the real world.
If you want to engage in a scientific discussion on this topic, you have to come up with a workable definition that people can agree on. I think I see the distinction you are making between the words “data” and “information”. For example data could be the measured state of a system while the degree of order of the data would represent the information content.

If selection is as powerful as to be able to organize atoms and molecules to create the genetic molecules and proteins necessary for life and then evolve these complex molecules to the life forms we observe today you should be able to mathematically model such a profound force. Dr Schneider’s use of a binding protein (weight matrix) which imposes a very stringent selection process yet is still profoundly slow in evolving binding sites.

[hammegk]

You may read the following as an ad hominem if you like ....
Nah, I read it as useless psycobabble posted by a useless nobody.


Have a nice life.
I do, thanks.

[kjkent1]

Don’t confuse that I am not making any scientific claims about the origin of life with a claim that it occurs by magic.Why not? You refuse to state your hypothesis. If not by magic and not by evolution, then by what? Either life is a process of matter which occurs under suitable conditions or it's the product of some supernatural force.

And, if you have developed some third alternative, then tell us all what it is.Otherwise, I will assume that you are just dodging the issue, so you don't have to reveal that you do indeed believe in magic. Which is juvenile.

Neither have I decried any scientific investigations we have been discussing. On numerous occasions I have applauded Dr Schneider’s work in developing ev. I am only critical of the superficial analysis he did with his model but I believe he did a good job applying the fundamental theories involved.You have yet to answer his three responses posted on his blog. You won't model anything further to see if it affects the outcome of EV. You're content to merely pound on your one point as if it is self evident that no selection mechanism, other than the artificial mechanism found in EV, has any effect on information gain.

Schneider doesn't think it's self evident. So if you actually respect him, then prove he's wrong. Until you do, you're just demanding that the evolutionary proponents exclude all possible alternatives to God, before you will concede that God is not the cause. Also juvenile.

I haven’t lived in Clovis for years but now you can easily verify my medical credentials. With that piece of information and the title and publisher of my PhD thesis you can verify my engineering credentials. You are really trying to find the exit to your cubicle.I just needed to identify your county of residence. Thanks for making it so easy, by taking the bait and admitting you're licensed to practice in California. Doubtless your PO Box is located in the same county.

As for the exit to my cubical, I know where that is, too.

Hammegk wasn’t the only one to interject God into a scientific discussion. You did this yourself...Your statement demonstrates your disingenuousness. You're smart enough to know that I only raised the God issue to question why someone else would raise it. So, what you're really doing is nothing more than juvenile baiting. Try to stick to what you know, and leave sarcasm to the professional comedians.

[I less than three logic]

Nah, I read it as useless psycobabble posted by a useless nobody.
So you're saying it reads the same as most of your posts. ;)

[hammegk]

So you're saying it reads the same as most of your posts. ;)
Actually, no I didn't.

Sorry your ability to comprehend failed you. Happen often?

[I less than three logic]

Actually, no I didn't.

Sorry your ability to comprehend failed you. Happen often?
What distinguishes your useless psycobabble from his?

[joobz]

There also wasn’t a lack of evidence for the flat earth theory; however that evidence was overwhelmed by further discoveries.
Actually, there wasn't a ton of evidence for flat earth. I do agree with the further discoveries point though. As we discover and know more we fit the data to the most logical models. But I'm still waiting for the evidence to be "stacked against" evolutionary theory. It needs work hammering out the details. (I think Paul's presentation of the cooperative effect represents this).

But saying, point mutation and natural selection isn't enough doesn't equate into evoution it wrong.
The field of immunology advances despite the theory of evolution, not because of the theory of evolution. Please explain this statement? Do you have some interesting examples where this is the case?

It’s the mathematics joobz, the theory does not add up.
You keep saying this, but the evidence has argued against it. All simulations that have been presented agree with Paul's analysis of the data. If you feel that the Rcapacity limitation in the model has a meaningful real world significance and is not a simulation oddity, that would be one thing. But as it stands, you are more interested in pretending to have found the proof against evolution than remaining within the bounds of reality. I would place more weight on your ideas/theories if you stopped contridicting hard data and stopped engaging in personal attacks.

[joobz]

Nah, I read it as useless psycobabble posted by a useless nobody.

Not that you would care, but this post disappoints me a bit. I have enjoyed greatly your participation on the threads I've read. Admittedly, Foster Zygote had directly attacked the presentation style to your posts, but presented reasons for that attack. You countered with a single line personal value judgement that provided no reason for that statement.

Now, I don't expect every post to possess lengthy explanations, but something with this much ire should contain some justification. Otherwise it seems to come from pure emotion and devalues many of the interesting comments you've made up til now.

[hammegk]

What distinguishes your useless psycobabble from his?
In your case, perhaps it's an in-ability to separate his meaningless psychobabble from my meaningful commentary. :D

[hammegk]

Not that you would care, but this post disappoints me a bit.
Actually, I would care.


I have enjoyed greatly your participation on the threads I've read.
Thank you.


Admittedly, Foster Zygote had directly attacked the presentation style to your posts, but presented reasons for that attack. You countered with a single line personal value judgement that provided no reason for that statement.
Yeah, I find little value in glib personal analysis, nor is he alone in piling on this instance. I take plenty of nastiness from one of our resident jerkettes, articulett, and from time-to-time return the favor. Butt-in-skies who choose to stick their oar in those previously roiled waters may not appreciate the result.


Now, I don't expect every post to possess lengthy explanations, but something with this much ire should contain some justification. Otherwise it seems to come from pure emotion and devalues many of the interesting comments you've made up til now.
Thanks for sharing. :)

[kleinman]

Don’t confuse that I am not making any scientific claims about the origin of life with a claim that it occurs by magic.Why not? You refuse to state your hypothesis. If not by magic and not by evolution, then by what? Either life is a process of matter which occurs under suitable conditions or it's the product of some supernatural force.

And, if you have developed some third alternative, then tell us all what it is.Otherwise, I will assume that you are just dodging the issue, so you don't have to reveal that you do indeed believe in magic. Which is juvenile.
Now what are you whining about? I happen to have some interest in Dr Schneider’s ev program and what it shows when you put realistic parameters in the model. Just because his model shows that evolution by random point mutations and natural selection is mathematically impossible, somehow you figure it is my responsibility to give you a scientific explanation of how life appeared. I happen to believe that we were created, if you want to believe that life arose in a crock pot, that’s fine with me, just don’t try to pass off your beliefs as science.
Neither have I decried any scientific investigations we have been discussing. On numerous occasions I have applauded Dr Schneider’s work in developing ev. I am only critical of the superficial analysis he did with his model but I believe he did a good job applying the fundamental theories involved.You have yet to answer his three responses posted on his blog. You won't model anything further to see if it affects the outcome of EV. You're content to merely pound on your one point as if it is self evident that no selection mechanism, other than the artificial mechanism found in EV, has any effect on information gain.

Schneider doesn't think it's self evident. So if you actually respect him, then prove he's wrong. Until you do, you're just demanding that the evolutionary proponents exclude all possible alternatives to God, before you will concede that God is not the cause. Also juvenile.
You lazy Dilbert, you didn’t read the Evolutionisdead thread on this topic. If you had, you would have seen my responses to what Dr Schneider had posted on his blog. Since you are too lazy to read the thread, I’ll repost my responses to Dr Schneider’s points that he raised on his blog. These issues were raised on http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/blog-ev.html)

2006 Jun 27. Alan Kleinman started a discussion at Evolution Is Dead! (http://www.evolutionisdead.com/forum/viewtopic.php?t=348). He ran the Evj program with exponentially increasing genome size and proportionally increasing number of binding sites. He found that the time to evolution increases exponentially. From this he claims that although Ev is a good model for small genetic elements, it cannot be extended to large genomes. In particular, he is responding to this statement in the Ev paper (http://nar.oxfordjournals.org/cgi/content/full/28/14/2794) This is not an accurate representation of what I am contending about ev. At the time he posted this message, I had not varied the number of binding sites on any of the cases that I ran with ev. My initial cases presented in my initial post on this site simply consisted of doubling the genome length while keeping all other parameters fixed. In those cases, the generations for convergence quadrupled when the genome length was doubled. I believe ev is a plausible model for both small and large genomes.
Likewise, at this rate, roughly an entire human genome of ~4x109 bits (assuming an average of 1 bit/base, which is clearly an over­estimate) could evolve in a billion years, even without the advantages of large environmentally diverse world-wide populations, sexual recombination and interspecies genetic transfer. The reason Dr Schneider’s case accumulated 1 bit/base with the 256 base genome used in his ev paper is that a mutation rate of 1 mutation per generation for a genome this size is 10,000 times larger than would be seen in a real organism. Extending the genome length while keeping the mutation rate at 1 mutation per genome per generation starts to reflect the more realistic rate at which information would be accumulated.
There are a number of errors in Dr. Kleinman's argument:
1. The mutation rate was kept constant per genome. This is not what occurs in nature, where DNA polymerases make errors at a certain rate per base. I used a fixed mutation rate in Ev because that made the program simple and it was not the focus of the initial model. Paul Anagnostopoulos has modified Evj so that it can now have a constant error per base. The error rate for DNA polymerases in E coli has been measured at 1 in 10^6 to 10^7 nucleotides. That is one wrong nucleotide per organism per generation. I have no problem with Dr Schneider using a constant error rate per base but in order to represent reality, that number should be between 10^-6 and 10^-7, not 1 per 512 bases as Paul Anagnostopoulos was using in the cases he was presenting. A mutation rate that high could not be sustained by any living thing.
2. Large genomes are known to appear by many duplication mechanisms that are not in the Ev model. There are polymerase slippage, illegitimate recombination, transposons, insertion sequences, tetraploidization, and Robertsonain translations. These can all increase genome size rapidly. The mechanisms are currently not part of the Ev/Evj model.Ultimately, all these mechanisms of duplication and recombination errors must yield functional genes in order for evolution to proceed. Unless these genes are immediately functional, then more errors or mutations must occur to morph these pieces of genetic material into functional genes. You are now back to the ev model to accomplish this morphing process which as ev shows is profoundly slow for realistic sized genomes. Transposons and insertion sequences are seen in manufacture of antibodies. Dr Schneider, do you believe this same mechanism is involved in evolution? If so, how does this differ from crossing over recombination that is seen in meiosis? Dr Schneider works at the National Cancer Institute. He must be aware what genetic errors lead to.
3. Genes diverge after duplication. Once a genome has increased in size or a gene has duplicated, we know that genes diverge and take up similar but not identical function. An example is the vast family of ABC transporter genes (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=&rid=mono_001.TOC&depth=2). Kleinman objected to the idea of duplication because he could not see that there can be advantages eventually as the genes diverge. That is, he neglected the third point.Dr Schneider’s example of the ABC transporter genes is a good example of what happens when someone is heavily indoctrinated into the evolutionary way of thinking. If you look at the link to the ABC transporter genes, you will see a list of these genes and where they diverge and the diseases associated with each of these divergences. The following quote is taken from that web site:
A more detailed account of each of the human ABC genes (http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?chr=hum_chr.inf&query=ATP-binding+cassette&qchr=&advsrch=off) is given below. For each gene, a concise description is given on the known function and disease involvement,
Natural selection prevents divergence from taking the structure of each of these genes too far from their baseline structure. Too much divergence in a ABC gene causes disease.

I never objected to the idea of gene duplication. When Dr Schneider originally proposed this idea to me in our email communications, my argument to him was duplicating a gene introduces no new information. The gene still produces the same enzyme or protein. The duplicated gene must still be mutated to a new gene for new enzyme to be produced. If you are depending on point mutations and natural selection to convert the duplicated gene to a new gene, you are going to have a long, long, long wait according to ev.
When Paul Anagnostopoulos ran a model with 96 creatures, 16 sites, and 1 mutation per 256 bases, varying the genome size from 256 to 16,384 he got (generations to Rs >= Rf) = 3.37 (genome size)0.97 with r=.99. This is less than exponential.It surprises me that a PhD Molecular Biologist would use such a large mutation rate. Introductory Biochemistry texts give mutation rates for DNA polymerases at much smaller values. The mutation rate used in the above cases was more than 10,000 times greater than seen in reality. His selection process only kills off half the creatures per generation. A mutation rate this high would surely kill off every creature. The mutation is the questioning process and the weight matrix is the natural selection answering process. This is how information in the genome is accumulated. Unfortunately for evolutionists, mutation rates as high as Dr Schneider would like to use can not and do not exist in reality. When a realistic mutation rate is used, the exponential nature of the genome length/generations for convergence presents itself.
[quote="Dr Schneider"]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.)[quote="Kleinman"]I found it peculiar that a random seed would have such a large effect on the generations for convergence for ev. Perhaps this variance would not be as noticeable for large genomes. If Dr Schneider is convinced of the validity of his model, that is fine with me.
These responses were posted months ago on the Evolutionisdead forum and have been discussed on both the EID forum and this forum in more detail.
I haven’t lived in Clovis for years but now you can easily verify my medical credentials. With that piece of information and the title and publisher of my PhD thesis you can verify my engineering credentials. You are really trying to find the exit to your cubicle.I just needed to identify your county of residence. Thanks for making it so easy, by taking the bait and admitting you're licensed to practice in California. Doubtless your PO Box is located in the same county.

As for the exit to my cubical, I know where that is, too
This is all public information. You need the help; otherwise its going to take as long for you to present your marketing plan as it takes ev to converge with a realistic genome length and mutation rate.

How did you find the exit to your cubicle? Did you use the process of elimination?
Hammegk wasn’t the only one to interject God into a scientific discussion. You did this yourself...Your statement demonstrates your disingenuousness. You're smart enough to know that I only raised the God issue to question why someone else would raise it. So, what you're really doing is nothing more than juvenile baiting. Try to stick to what you know, and leave sarcasm to the professional comedians.
Stop bellyaching and prepare your marketing plan.
There also wasn’t a lack of evidence for the flat earth theory; however that evidence was overwhelmed by further discoveries.Actually, there wasn't a ton of evidence for flat earth. I do agree with the further discoveries point though. As we discover and know more we fit the data to the most logical models. But I'm still waiting for the evidence to be "stacked against" evolutionary theory. It needs work hammering out the details. (I think Paul's presentation of the cooperative effect represents this).

But saying, point mutation and natural selection isn't enough doesn't equate into evoution it wrong.
Random mutations and natural selection has always been the slogan for the theory of evolution. Random point mutations and natural selection has been the cornerstone for the theory. Ev demonstrates how profoundly slow this process is even with a very stringent selection process. I can not think of and have not heard a plausible explanation from evolutionists how other forms of mutations such as gene duplications, frame shifts, etc. would overcome this mathematical deficiency that ev demonstrates in the theory of evolution.
The field of immunology advances despite the theory of evolution, not because of the theory of evolution.Please explain this statement? Do you have some interesting examples where this is the case?
Consider the very example you raised of Flu vaccinations. The concept of immunization appeared before Darwin was born. Attempts at immunization for smallpox were done before 1800. The concept of immunization was not drawn from the theory of evolution.
It’s the mathematics joobz, the theory does not add up.You keep saying this, but the evidence has argued against it. All simulations that have been presented agree with Paul's analysis of the data. If you feel that the Rcapacity limitation in the model has a meaningful real world significance and is not a simulation oddity, that would be one thing. But as it stands, you are more interested in pretending to have found the proof against evolution than remaining within the bounds of reality. I would place more weight on your ideas/theories if you stopped contridicting hard data and stopped engaging in personal attacks.
What analysis of the data are you talking about? Why is Paul running a series with a wider binding site? The only thing Paul has been doing is retracting statements which support my contentions. I’m wondering when Paul is going to throw the entire ev model out.

I am considering co-opting Paul’s concept of Rcapacity. What is preventing me at this time is that I can’t tell whether this is a peculiar characteristic of Dr Schneider’s model or whether it represents something which would occur with a real genome. I suspect that in reality, natural selection doesn’t have the precision that Dr Schneider has given his model with his weight matrix and that Rcapacity is a reflection of this effect. What you have to consider is that Dr Schneider has designed a selection process that converges very quickly for short genomes but slows down very rapidly as you use larger genomes and slower mutation rates in the model. I don’t believe there is any selection process that would speed up convergence for longer genomes or correct the Rcapacity issue. This is the underlying mathematical conundrum that must be overcome for the theory of evolution to have real hard scientific validity. I don’t believe there is any known mechanism that overcomes this mathematical hurdle.

[kjkent1]

Now what are you whining about? I happen to have some interest in Dr Schneider’s ev program and what it shows when you put realistic parameters in the model. Just because his model shows that evolution by random point mutations and natural selection is mathematically impossible, somehow you figure it is my responsibility to give you a scientific explanation of how life appeared. I happen to believe that we were created, if you want to believe that life arose in a crock pot, that’s fine with me, just don’t try to pass off your beliefs as science.So, like I said, you believe in magic. The gods of Mt. Olympus are no less believable than the god of Moses. The stories are equally fanciful, and equally for children. If that's how you balance the left and right sides of your brain -- I'm fine with it. But, don't try to pan it off as anything other than exactly what it appears to be: nonsense.

You lazy Dilbert, you didn’t read the Evolutionisdead thread on this topic. If you had, you would have seen my responses to what Dr Schneider had posted on his blog. Since you are too lazy to read the thread, I’ll repost my responses to Dr Schneider’s points that he raised on his blog. These issues were raised on http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/blog-ev.html) See, it took a while for me to keep on poking you in the ribs, but you finally put up your argument in one place where everyone can see it. Congratulations on having your balls descend.

I'll leave it to the more scientifically knowledgeable here to argue your specific points. I'm just glad to be of service to the community.

This is all public information. You need the help; otherwise its going to take as long for you to present your marketing plan as it takes ev to converge with a realistic genome length and mutation rate.You are still blissfully ignorant of why I might want to know your county of residence. That's okay. As long as you remain civil with me, it will never be an issue.

How did you find the exit to your cubicle? Did you use the process of elimination?No, I use the toilet for elimination purposes. But, if you prefer to mark your territory the "old fashioned way," I can see why you'd live way out there by Yosemite.

Stop bellyaching and prepare your marketing plan.There's a world of difference between a marketing plan and a scientific research proposal. I'll handle the marketing plan, after you produce the research proposal.

[Paul C. Anagnostopoulos]

I am considering co-opting Paul’s concept of Rcapacity. What is preventing me at this time is that I can’t tell whether this is a peculiar characteristic of Dr Schneider’s model or whether it represents something which would occur with a real genome. I suspect that in reality, natural selection doesn’t have the precision that Dr Schneider has given his model with his weight matrix and that Rcapacity is a reflection of this effect.
I think you are correct. The binding site width isn't constrained in nature like it is in Ev. All I'm saying about Rcapacity is that you have to make sure it is large enough to accommodate the genomes sizes you're experimenting with, so you don't mistake an Rcapacity issue for some unknown dampening effect.

However, consider an existing binding site when a genome is enlarged by some sort of duplication or acquisition event. Then suddenly perhaps Rcapacity < Rfrequency. So it's not entirely irrelevant.


What analysis of the data are you talking about? Why is Paul running a series with a wider binding site?
See above.

~~ Paul

[Paul C. Anagnostopoulos]

Folks, it's getting a tad bickericious in here. Take it easy.

~~ Paul

[kleinman]

This is all public information. You need the help; otherwise its going to take as long for you to present your marketing plan as it takes ev to converge with a realistic genome length and mutation rate.You are still blissfully ignorant of why I might want to know your county of residence. That's okay. As long as you remain civil with me, it will never be an issue.
Let’s do a remake of the Scopes-monkey trial, you can play the monkey.

[joobz]

Random mutations and natural selection has always been the slogan for the theory of evolution. Random point mutations and natural selection has been the cornerstone for the theory.
This may at one time had been the case, but I don't know a single biologist who would hold to this.
Ev demonstrates how profoundly slow this process is even with a very stringent selection process. I can not think of and have not heard a plausible explanation from evolutionists how other forms of mutations such as gene duplications, frame shifts, etc. would overcome this mathematical deficiency that ev demonstrates in the theory of evolution.
Here is where we disagree. This model shows that point mutations alone within a ceratin functional window can form new binding sites. Any argument from a time line is erroneous. There exists too many different types of stimulii that can speed up the process.

Consider the very example you raised of Flu vaccinations. The concept of immunization appeared before Darwin was born. Attempts at immunization for smallpox were done before 1800. The concept of immunization was not drawn from the theory of evolution. look into the idea of original sin and immunizations. Flu shots can (and have been shown) known to enhance a person's likelyhood of contracting the disease. Genetic drift in the antigen sites reduce the effectiveness of the antibodies generated from a vaccine. If the drift is huge and the antibody raised is completely ineffective, the body can use a rapid antibody generation method to fend off the infection. If they drifted only slightly, the body trys to rework the existing antibodies to target the virus. this is a slower process and typically results in a enhanced likelyhood of catching the disease.

The game is, we can never really know which virus strain will propogate and how much genetic drift it will exhibit. Some change more than others. Our ability at understanding this viral evolution allows us to better select a range of viruses to immunize against. Also, it has suggested that a 4 strain (instead of the 3 used)selection spaced ideally across the epitope space would greatly minimize the likelyhood of "original sin" from occuring. This is directly a feature of evolution that has been modeled and effectively used in handling medical care.

What analysis of the data are you talking about? Why is Paul running a series with a wider binding site? The only thing Paul has been doing is retracting statements which support my contentions. I’m wondering when Paul is going to throw the entire ev model out.
I guess we've been reading different threads. I've seen ev work quite well within the Rcapacity bounds.

I am considering co-opting Paul’s concept of Rcapacity. What is preventing me at this time is that I can’t tell whether this is a peculiar characteristic of Dr Schneider’s model or whether it represents something which would occur with a real genome. I suspect that in reality, natural selection doesn’t have the precision that Dr Schneider has given his model with his weight matrix and that Rcapacity is a reflection of this effect.
I have a feeling you are right. But it also provides another look at an interesting fact. Binding sites don't evolve in a meaningless genome. In the model, every site can mutate and has no seperate positive negative effect. Such a system would be unlikely to evolve. However, the genomes didn't evolve that way. They seemed to have grown with time. At least current theory doesn't suggest it and this model agrees with that. We don't start with a informationless background genome.

[kleinman]

I am considering co-opting Paul’s concept of Rcapacity. What is preventing me at this time is that I can’t tell whether this is a peculiar characteristic of Dr Schneider’s model or whether it represents something which would occur with a real genome. I suspect that in reality, natural selection doesn’t have the precision that Dr Schneider has given his model with his weight matrix and that Rcapacity is a reflection of this effect.I think you are correct. The binding site width isn't constrained in nature like it is in Ev. All I'm saying about Rcapacity is that you have to make sure it is large enough to accommodate the genomes sizes you're experimenting with, so you don't mistake an Rcapacity issue for some unknown dampening effect.

However, consider an existing binding site when a genome is enlarged by some sort of duplication or acquisition event. Then suddenly perhaps Rcapacity < Rfrequency. So it's not entirely irrelevant.
I understand your hypothesis about Rcapacity. I view this as a side issue.
What analysis of the data are you talking about? Why is Paul running a series with a wider binding site?See above.
These questions were address to joobz. I know you understand why you are doing a series with a wider site width. I’ll stick my neck out here and guess that the wider site width will not give a significant reduction in the number of generations for convergence. The series you are doing now will show that your extrapolation of 200,000,000 generations for the 100k genome with a 10^-6 mutation rate and a population of 1meg was reasonably accurate.

I believe there is only one possible use for ev in support of the theory of evolution and that is for huge populations to accelerate evolution sufficiently. I can’t do any larger population series with my computer and you can only do one more data point than my machine. In order to do a population of 10^9 you would need a machine with 1000 gigabytes of memory and that would be for a genome length of 1k.
Folks, it's getting a tad bickericious in here. Take it easy.
Did I miss something?

[kjkent1]

Let’s do a remake of the Scopes-monkey trial, you can play the monkey.

That's fine. You can be...the defendant.

[John Hewitt]

If you want to engage in a scientific discussion on this topic, you have to come up with a workable definition that people can agree on. I think I see the distinction you are making between the words “data” and “information”. For example data could be the measured state of a system while the degree of order of the data would represent the information content.
Unfortunately, one would wait a long time for people to agree on definitions. The distinction I make between data and information is standard in school level IT but it tends to be ignored by experts in the same field. In the context of standard biochemistry, the genetic data would be the sequence of bases in a gene, while the biochemical activity of the gene's product (most often the enzymatic activity of a protein) would be information, the interpretation of that data.

If selection is as powerful as to be able to organize atoms and molecules to create the genetic molecules and proteins necessary for life and then evolve these complex molecules to the life forms we observe today you should be able to mathematically model such a profound force. Dr Schneider’s use of a binding protein (weight matrix) which imposes a very stringent selection process yet is still profoundly slow in evolving binding sites.Selection is quite logical but I do not think one can necessarily model it mathematically, one may be able to do so. Computer simulations are generally more powerful than mathematical modelling. My work is a metabolism first theory and my concern is with the selection of sun induced chemical oscillations to produce metabolic pathways. It may be techically possible to model that process but I think such simulations are beyond my capacities. I therefore confine myself to the general chemical picture.

[Paul C. Anagnostopoulos]

These questions were address to joobz. I know you understand why you are doing a series with a wider site width. I’ll stick my neck out here and guess that the wider site width will not give a significant reduction in the number of generations for convergence. The series you are doing now will show that your extrapolation of 200,000,000 generations for the 100k genome with a 10^-6 mutation rate and a population of 1meg was reasonably accurate.
Here is my data so far:

population 32
binding sites 8
weight width 9
site width 10
1 mutation / 512 bases

genome size, generations

1024, 8000
2048, 20000
4096, 34000
8192, 37000
16384, 76000
32768, 272000
65536, 392000
128000, 1000000 (est.)

(fits -15837 + 7.61G) So at 1 mutation per million bases, that's about 2 billion generations. If it varies as population^-.25, as our population experiments show, then at a tiny population of 1 million it would take about 63 million generations.

I'll post the final numbers when the 128K experiment finishes. This experiment will take about 150 hours of processor time, so I doubt I'll be running anything larger. Maybe while I'm on vacation in February.

~~ Paul

[RecoveringYuppy]

The distinction I make between data and information is standard in school level IT but it tends to be ignored by experts in the same field. In the context of standard biochemistry, the genetic data would be the sequence of bases in a gene, while the biochemical activity of the gene's product (most often the enzymatic activity of a protein) would be information, the interpretation of that data.
Since evolutionary theory is based on both genes their expression, what exactly did you mean earlier when you said that evolutionary theory should be based on information and not data?

And why not use the words "genes" and "expressions" rather than two terms that you got from some other field where you acknowledge that aren't even consistently used in your manner?? And not even to mean the same thing you are using them for here?

[Paul C. Anagnostopoulos]

In the context of standard biochemistry, the genetic data would be the sequence of bases in a gene, while the biochemical activity of the gene's product (most often the enzymatic activity of a protein) would be information, the interpretation of that data.
So there's no information in DNA? If not, then how does the information leak into the proteins?

Hey Kleinman, we can stop having this conversation. There's no information in DNA.

~~ Paul

[John Hewitt]

Since evolutionary theory is based on both genes their expression, what exactly did you mean earlier when you said that evolutionary theory should be based on information and not data?

And why not use the words "genes" and "expressions" rather than two terms that you got from some other field where you acknowledge that aren't even consistently used in your manner?? And not even to mean the same thing you are using them for here?
I believe I said that evolution should be based on data not genes.

I develop evolutionary theory that way because organisms seem to derive from, do contain and are involved in other manifestations of evolution besides biological evolution and genes. I have attempted to construct a generalised form of evolutionary theory capable of describing all manifestations of evolution in all milieu. "Genes" and "expressions" do not generalise in this way.

Certain concepts are necessarily present in all forms of evolution - data, interpretation, information, selection and knowledge - here defined as selected information. It is true that both data and information are necessarily common to all forms of evolution but the definition "information is interpreted data" clearly makes data the core concept and information into a derived concept.

I have no idea why luminaries of the IT field tend to ignore the distinction between data and information but experts in all fields seem to do similar things and ignore changes in nomenclature. Senior chemists, for example, sometimes still talk about "acetic acid." (IUPAC now ask us to call it ethanoic acid.)

[John Hewitt]

So there's no information in DNA? If not, then how does the information leak into the proteins?

Hey Kleinman, we can stop having this conversation. There's no information in DNA.

~~ Paul
This comment appears to be facetious.

I assure you that the distinction between data and information was not invented by me, it is taught in schools. It is given in Wikipedia and in the BBC's GCSE bitesize for school IT.

You might find the distinction between information and data easier if you think about a word processor file. You may write the same English text into a "word" document or into a wordperfect document. The data in the two files would be quite different but would be interpreted by English speaking readers in the same way. However, a non-English speaking readers might place a different interpretation. Information comes from data and from interpretation.

There is, in fact, very little information in DNA. The external shape and chemistry of the double helix is very uniform, regardless of its base sequence. Variability, and hence potential for biochemical interpretation, arise mainly after translation of base sequence data into protein.

[RecoveringYuppy]

I believe I said that evolution should be based on data not genes.
OK. But no matter what combination you use of the four words you are equivocating over you can find plenty of people studying evolution form that POV. So what exactly are you proposing?

[drkitten]

You might find the distinction between information and data easier if you think about a word processor file. You may write the same English text into a "word" document or into a wordperfect document. The data in the two files would be quite different but would be interpreted by English speaking readers in the same way. However, a non-English speaking readers might place a different interpretation. Information comes from data and from interpretation.

There is, in fact, very little information in DNA. The external shape and chemistry of the double helix is very uniform, regardless of its base sequence.

This is nonsensical. The shape and chemistry of the transistors comprising the memory image containing a "Word" document are also very uniform, but that doesn't prevent the document, or the computer's memory, from containing information. It merely means that you're looking in the wrong place for it and using the wrong tools. DNA contains a tremendous amount of information stored in the base pairs. In order to extract that information, the double helix is "unzipped" (which makes the base "pairs" much more chemically active, since they're now exposed to the rest of the world).

I may not be able to read a Word document by eyeball, but that doesn't mean that the document contains no information. It merely means that if I'm stupid enough to go looking for something with the wrong tool, I won't find it. I don't use microscopes as metal detectors, either.

[Paul C. Anagnostopoulos]

This comment appears to be facetious.

I assure you that the distinction between data and information was not invented by me, it is taught in schools. It is given in Wikipedia and in the BBC's GCSE bitesize for school IT.
It was facetious. If information is ever to be extracted from data, then the data contains an encoding of the information from the get-go.

Wikipedia does mention a distinction:

Information and Data

The words, information and data, are used interchangeably in many contexts. However, they are not synonyms. For example, according to Adam M. Gadomski's observation (1993), data are everything what is/can be processed and information are data which describe a physical or abstract domain.
As opposed to data which describe something that is neither physical nor abstract?

~~ Paul

[John Hewitt]

OK. But no matter what combination you use of the four words you are equivocating over you can find plenty of people studying evolution form that POV. So what exactly are you proposing?

Please give me the names of people basing their approach to evolution on data.

You can find exactly what I am proposing on my web site, http://www.sexandphilosophy.co.uk

[John Hewitt]

It was facetious. If information is ever to be extracted from data, then the data contains an encoding of the information from the get-go.

Wikipedia does mention a distinction:

As opposed to data which describe something that is neither physical nor abstract?

~~ Paul
Gadomski's defintion of information does not seem usable.

I took the following definition from wikipedia a couple of years ago.

"Meaning of data and information"
"Data on its own has no meaning, only when interpreted by some kind of data processing system does it take on meaning and become information."



You will find much that definition in other places. In any case, it is the definition I use. If you feel another is useful, use it.

[RecoveringYuppy]

Please give me the names of people basing their approach to evolution on data.

You can find exactly what I am proposing on my web site, http://www.sexandphilosophy.co.uk
By the definition you just posted in 1124, anyone who is counting the differences in DNA sequences is doing something based on data. Surely, I don't need to actually list the names of the people doing such research, do I? And to answer a similar question you might pose, anyone comparing the differences in protein shapes between species would be comparing information by your definition.

I'm not inclined to read your entire website. Please say something that succintly demonstrates you've got a novel and possibly useful approach. Based on your definition of "data", an approach to evolution based on "data" is certainly not novel.

[Yahzi]

I, like most people, believe that living things are subject to the laws of chemistry and physics but that does not mean or even imply that there is no difference between alive and dead.
Ok, I'll bite...

what's the difference?

(Keep in mind that the context of this discussion is about whether or not "information arising from simplicity due to energy" applies to living systems as well as non-living ones. I mention this because I fully expect Dr. Hewitt to respond with a classic definition of life, as if I were an idiot that did not already know it, thus having neatly redirected the conversation from the original point to a strawman.)

What is the difference between living and dead systems that allows complexity to arise from simplicity with the addition of energy in boxes of granola, but not in genetic populations?

[Yahzi]

There is, in fact, very little information in DNA. The external shape and chemistry of the double helix is very uniform, regardless of its base sequence.
Dude, I may be scientifically illiterate, but even I know that DNA doesn't get interesting until it gets unzipped.

If I am aware of such an elemental fact, and you are not, what does that say about your scientific literacy?

Like Dr Kitten said, using the wrong tool just implies you don't know what you are doing.

[John Hewitt]

By the definition you just posted in 1124, anyone who is counting the differences in DNA sequences is doing something based on data. Surely, I don't need to actually list the names of the people doing such research, do I? And to answer a similar question you might pose, anyone comparing the differences in protein shapes between species would be comparing information by your definition.

I'm not inclined to read your entire website. Please say something that succintly demonstrates you've got a novel and possibly useful approach. Based on your definition of "data", an approach to evolution based on "data" is certainly not novel.
As I previously pointed out, there is more data in living things than is to be found in their DNA sequence.
I see no point in regurgitating the entirety of my web site on this thread. I suggest you read the index page and then either read on by your own interests or stop if you have none.

[John Hewitt]

What is the difference between living and dead systems that allows complexity to arise from simplicity with the addition of energy in boxes of granola, but not in genetic populations?
I do not understand your question about breakfast cereals and do not have the impression that you want a sensible discussion.

[RecoveringYuppy]

As I previously pointed out, there is more data in living things than is to be found in their DNA sequence.

And which data is/are being ignored by other scientists?
I see no point in regurgitating the entirety of my web site on this thread.
Of course. Merely repeat enough to indicate you've got a novel idea worth further pursuit of your website and/or book.

[John Hewitt]

And which data is/are being ignored by other scientists?
I do not think the matter is being consciously ignored. My work, bioepistemic evolution, is an example of a multilevel selection theory. This study is unique in that it generalizes the levels using a base in the concept of data and distinguishes levels (I use the word ranks of evolution and levels of knowledge) according to the locus of selection.


Of course. Merely repeat enough to indicate you've got a novel idea worth further pursuit of your website and/or book.Evolutionary theory constructed this way is particularly applicable to humans in that they possess much more level3 knowledge than any other species. Hence, rank3 evolution should have a more pronounced effect on our species than upon any other species. The analysis of rank3 evolution and its expected impact at rank1 generates theories for the evolutionary origins of human sexuality and humour.
The study of evolution at rank0 leads to the theory of prebiotic oscillations, a theory of prebiosis, aka abiogenesis, which is much more parsimonious than any previous theory. It assumes only a data flow from the sun, namely the alternating zero-one, zero-one signal associated with the day night cycle, and the usual random primordial soup.
Other results also arise from bioepistemic evolution but those listed above are the most striking.

[Paul C. Anagnostopoulos]

"Data on its own has no meaning, only when interpreted by some kind of data processing system does it take on meaning and become information."

I don't like it. Sounds like an informal definition of information is being used. I wonder if the person was trying to make a distinction between uncertainty and information, but got confused.

Anyway, it doesn't matter too much.

~~ Paul

[RecoveringYuppy]

@1131 by John Hewitt

OK, that's helpful. If I recall your definition of "rank", a rank3 influence at rank1 sounds to me as being simply a nomenclature change. Intelligence being a sexual selection factor amongst humans is not a novel idea, for example. Could you point me at something in your website that might compare or contrast your approach to the more common treatments of similar ideas?

[articulett]

This is nonsensical. The shape and chemistry of the transistors comprising the memory image containing a "Word" document are also very uniform, but that doesn't prevent the document, or the computer's memory, from containing information. It merely means that you're looking in the wrong place for it and using the wrong tools. DNA contains a tremendous amount of information stored in the base pairs. In order to extract that information, the double helix is "unzipped" (which makes the base "pairs" much more chemically active, since they're now exposed to the rest of the world).

I may not be able to read a Word document by eyeball, but that doesn't mean that the document contains no information. It merely means that if I'm stupid enough to go looking for something with the wrong tool, I won't find it. I don't use microscopes as metal detectors, either.

Beautiful.

[articulett]

You finally typed something worthwhile. It's too bad you don't understand what it means.

From what I can tell no one has ever understood quite what you mean. I know you think it's due to your brilliance, but I have reached a very different conclusion as have others on this forum.

But I am always curious why you stick around. It's like your entire goal on this forum seems to convince others that materialism is illogical and that your "intelligent designer" is real.

I think I know what it is. It's like all those creationists who attempt to get an actual scientist to debate them so they can pretend that science takes their claims seriously -- or so they can say "science cant explain "x", therefore goddidit"...oh, and plus you think as long as we can't get you to understand materialsim, your "materialism makes no sense" theory is valid.

You seem to perceive yourself as a wise person interjecting witty banter which prods others to "see the light"--a warrior for your "intelligent designer"--but no-one else seems think of you quite that way. It's a little sad, really.

[articulett]

I opened the 8 December issue of Science and what did I find? An article by Martin Nowak titled "Five Rules for the Evolution of Cooperation." The final sentence:


~~ Paul

Ah yes...but you know that Confirmation Bias will immediately rise up to negate the implication of that article. There are none so blind...

[hammegk]

Beautiful.
Interesting, anyway.

If we have a printout of that Word file depicting only the underlying zeroes and ones, is that 'information'? I tend to say, no: that's 'data'.

[hammegk]

....as long as we can't get you to understand materialsim, your "materialism makes no sense" theory is valid.
You are a truly silly person. I could defend materialism better than most who post here.


You seem to perceive yourself as a wise person interjecting witty banter which prods others to "see the light"--a warrior for your "intelligent designer"--but no-one else seems think of you quite that way.
ROFL. If you say so, who could doubt such a cogent analysis? ;)


It's a little sad, really.
Not as sad as dupes like yourself regurgitating The Truth.

[articulett]

I note that you and Yahzi feel there is no difference between alive and not alive.

No, it's just that your biases have lead you to find that particular meaning in order to support the belief you want. Life is a continuum -- just like speciation On a macro level--we can readily distinguish alive things from dead/inanimate things--but there are things that don't fit neatly in either category. Just as we can see speciation readily from the perspective of time...from a DNA perspective the event is not instant...there is not a "moment" when an animal becomes a new species. The same is true for consciousness. It's your need to categorize that makes the concepts hard to grasp. It's the gray areas between your categories that gives us clues as to how systems, including life itself, evolves.

[kjkent1]

...

[articulett]

Interesting, anyway.

If we have a printout of that Word file depicting only the underlying zeroes and ones, is that 'information'? I tend to say, no: that's 'data'.

Whatever you call it, it's a "code"--just like DNA is a code. It contains information--even when there is no-one there to translate it...even if th computer is off--the code is there. DNA is similar to that code. Whether you print that code in it's raw form or in it's "more readable form"--it's still a code. It can be translated into useful or useless information just as DNA can--if it's useful information in has a better chance at getting passed on than if it's useless or harmful code.

[articulett]

As I previously pointed out, there is more data in living things than is to be found in their DNA sequence.
I see no point in regurgitating the entirety of my web site on this thread. I suggest you read the index page and then either read on by your own interests or stop if you have none.

Would you say that there is more data on a computer then can be found in the computer code on that computer? What you're saying is open to interpretation.

If you imagine some other kind of data, how exactly would you measure for it? What would happen if someone was missing this extra "data"? I think you've made a leap here that is incorrect, and you are using a semantic game to claim there is this "extra data" that can't be accounted for by our current understanding of DNA, energy input, and so forth.

[kleinman]

Random mutations and natural selection has always been the slogan for the theory of evolution. Random point mutations and natural selection has been the cornerstone for the theory.This may at one time had been the case, but I don't know a single biologist who would hold to this.
I am very interested in hearing how the other mechanisms of mutation, gene and/or chromosome duplication and recombination with/without error will replace random point mutations and natural selection as the driving force for evolution.

The way Dr Schneider has written about ev, he has given very high weight to random point mutations and natural selection as the driving force for evolution and he is a molecular biologist. The editors of Nucleic Acids Research published these results as well in 2001. So if biologists no longer think that random point mutations and natural selection is the cornerstone for the theory of evolution, this is a recent development.
Ev demonstrates how profoundly slow this process is even with a very stringent selection process. I can not think of and have not heard a plausible explanation from evolutionists how other forms of mutations such as gene duplications, frame shifts, etc. would overcome this mathematical deficiency that ev demonstrates in the theory of evolution.Here is where we disagree. This model shows that point mutations alone within a ceratin functional window can form new binding sites. Any argument from a time line is erroneous. There exists too many different types of stimulii that can speed up the process.
I have always been very careful to claim that ev shows that evolution is profoundly slow when realistic genome lengths and mutation rates are used. I understand that there are input parameters (short genomes with high mutation rates) that show that binding sites can evolve mathematically very rapidly. If that is the functional window you are going to choose, you will have to do this without any physical proof. It is not clear to me that there are other mechanisms that can speed up this process. Recombination without errors can give rapid divergence of a species such as what Darwin observed with finch beaks or what we see with dog breeding but there is no proof that this can lead to a new species.
Consider the very example you raised of Flu vaccinations. The concept of immunization appeared before Darwin was born. Attempts at immunization for smallpox were done before 1800. The concept of immunization was not drawn from the theory of evolution.look into the idea of original sin and immunizations. Flu shots can (and have been shown) known to enhance a person's likelyhood of contracting the disease. Genetic drift in the antigen sites reduce the effectiveness of the antibodies generated from a vaccine. If the drift is huge and the antibody raised is completely ineffective, the body can use a rapid antibody generation method to fend off the infection. If they drifted only slightly, the body trys to rework the existing antibodies to target the virus. this is a slower process and typically results in a enhanced likelyhood of catching the disease.
I don’t know what you are talking about with original sin and vaccinations. In addition, if flu shots enhance a person’s likelihood of contracting disease, the whole field of preventative medicine is turned on its head.

There are limitations on genetic drift. Changes in the sequence of a gene can not be so great that the protein coded for no longer functions properly. Natural selection will select out that organism. When the CDC and other organizations try to determine the particular flu vaccine that will be used in any given year, they try to anticipate the strain. They usually look to what strains are showing up in the orient and develop vaccines against these strains. You aren’t advocating against influenza immunization? In 1920 there was a world wide epidemic that killed 20,000,000 people. That is more than the number of people killed in WW1. The last time I checked the CDC data on influenza deaths was during the SARS scare. At that time, influenza was killing over 30,000 people/year in the U.S. alone when SARS was killing maybe a couple hundred.
The game is, we can never really know which virus strain will propogate and how much genetic drift it will exhibit. Some change more than others. Our ability at understanding this viral evolution allows us to better select a range of viruses to immunize against. Also, it has suggested that a 4 strain (instead of the 3 used)selection spaced ideally across the epitope space would greatly minimize the likelyhood of "original sin" from occuring. This is directly a feature of evolution that has been modeled and effectively used in handling medical care.
I believe the variation of strains of influenza viruses represents a microevolutionary process. I don’t believe there are an unlimited number of strains of influenza viruses.
What analysis of the data are you talking about? Why is Paul running a series with a wider binding site? The only thing Paul has been doing is retracting statements which support my contentions. I’m wondering when Paul is going to throw the entire ev model out. I guess we've been reading different threads. I've seen ev work quite well within the Rcapacity bounds.
You should know that one of the reasons I annoy Paul is that I like to quote him. When Paul runs his series with the wider site width (larger Rcapacity), I’m sure that he is going to have data that shows that the evolution of binding sites on a 100k genome with a mutation rate of 10^-6 is going to take around 200,000,000 generations as he previously extrapolated and has since retracted. I would agree that ev is working quite well—at proving evolution by random point mutations and natural selection is mathematically impossible, it is too slow. I’ll make sure I quote you when Paul generates the data.
I am considering co-opting Paul’s concept of Rcapacity. What is preventing me at this time is that I can’t tell whether this is a peculiar characteristic of Dr Schneider’s model or whether it represents something which would occur with a real genome. I suspect that in reality, natural selection doesn’t have the precision that Dr Schneider has given his model with his weight matrix and that Rcapacity is a reflection of this effect.I have a feeling you are right. But it also provides another look at an interesting fact. Binding sites don't evolve in a meaningless genome. In the model, every site can mutate and has no seperate positive negative effect. Such a system would be unlikely to evolve. However, the genomes didn't evolve that way. They seemed to have grown with time. At least current theory doesn't suggest it and this model agrees with that. We don't start with a informationless background genome.
I disagree, the first living things had to evolve from an information-less background genome but that is not the point of the ev model. Ev only simulates the evolution of binding sites, the rest of the genome only contributes if a binding site happens to be identified on this region and this is considered an error and selects against that particular organism.
Let’s do a remake of the Scopes-monkey trial, you can play the monkey.That's fine. You can be...the defendant.
This would give a lot more publicity to this issue than your dumb ass marketing plan. I think I would like this. What are you going to charge me with? Is it my calling you greedy, or is it the lazy part that you find so uncivil? Perhaps it is your inattentiveness? I take back the Dilbert part; at least Dilbert has some technical skills.

Maybe we can get this on Judge Judy.
If you want to engage in a scientific discussion on this topic, you have to come up with a workable definition that people can agree on. I think I see the distinction you are making between the words “data” and “information”. For example data could be the measured state of a system while the degree of order of the data would represent the information content.Unfortunately, one would wait a long time for people to agree on definitions. The distinction I make between data and information is standard in school level IT but it tends to be ignored by experts in the same field. In the context of standard biochemistry, the genetic data would be the sequence of bases in a gene, while the biochemical activity of the gene's product (most often the enzymatic activity of a protein) would be information, the interpretation of that data.
Have you looked at Dr Schneider’s ev program? Do you believe that Dr Schneider has applied IT in an appropriate manner?
If selection is as powerful as to be able to organize atoms and molecules to create the genetic molecules and proteins necessary for life and then evolve these complex molecules to the life forms we observe today you should be able to mathematically model such a profound force. Dr Schneider’s use of a binding protein (weight matrix) which imposes a very stringent selection process yet is still profoundly slow in evolving binding sites.Selection is quite logical but I do not think one can necessarily model it mathematically, one may be able to do so. Computer simulations are generally more powerful than mathematical modelling. My work is a metabolism first theory and my concern is with the selection of sun induced chemical oscillations to produce metabolic pathways. It may be techically possible to model that process but I think such simulations are beyond my capacities. I therefore confine myself to the general chemical picture.
I view computers as the tool which enables the computation of values in a mathematical model. Mathematical models which yield closed form algebraic solutions are usually so limited that it is very difficult to model a very realistic system. Unless the theory of evolution can be mathematically modeled to account for the needed genetic changes to evolve one species to the next, the theory will remain a soft science.

I don’t know how heating and cooling of the primordial soup would induce chemical oscillations to produce metabolic pathways. Ultimately, metabolic pathways are energy conversion processes, for example it can be photosynthesis for the production of glucose or the Krebs cycle for the breakdown of glucose for ATP. What type of energy conversion process to you see occurring in the primordial soup from these chemical oscillations?
These questions were address to joobz. I know you understand why you are doing a series with a wider site width. I’ll stick my neck out here and guess that the wider site width will not give a significant reduction in the number of generations for convergence. The series you are doing now will show that your extrapolation of 200,000,000 generations for the 100k genome with a 10^-6 mutation rate and a population of 1meg was reasonably accurate.Here is my data so far:

population 32
binding sites 8
weight width 9
site width 10
1 mutation / 512 bases

genome size, generations

1024, 8000
2048, 20000
4096, 34000
8192, 37000
16384, 76000
32768, 272000
65536, 392000
128000, 1000000 (est.)
If you take your estimated value of 1,000,000 generations and assume a mutation rate of 10^-6 which is about 2000 times slower than the mutation rate you are using for this series, you get 2 billion generations for convergence. Increasing the population to a million would reduce this number by an order of magnitude giving 200,000,000 generations. This is the same value that you extrapolated previously. One improvement for your argument is that you are evolving 160 loci instead of 96 loci in about the same number of generations.
In the context of standard biochemistry, the genetic data would be the sequence of bases in a gene, while the biochemical activity of the gene's product (most often the enzymatic activity of a protein) would be information, the interpretation of that data.So there's no information in DNA? If not, then how does the information leak into the proteins?

Hey Kleinman, we can stop having this conversation. There's no information in DNA.
And give up my status as the annoying creationist, forget it. You aren’t getting out of this that easily.

[joobz]

I apologize I don't have time to address all your comments. I'm swamped with work.

I have always been very careful to claim that ev shows that evolution is profoundly slow when realistic genome lengths and mutation rates are used. this is not true. Paul, Dr. Adequate, and others have demonstrated why your values are not "realistic".

I (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?I) don’t know what you are talking about with original sin and vaccinations.
Deem, MW, Lee, HY, "Sequence space localization in the immune system response to vaccination and disease" Phys Rev Letter, 2003, 8, 91:068101


In addition, if flu shots enhance a person’s likelihood of contracting disease, the whole field of preventative medicine is turned on its head.


Not at all. Although, it does demonstrate that healthy individuals shouldn't get the flu vaccine. Plain and simple.

[kjkent1]

This would give a lot more publicity to this issue than your dumb ass marketing plan. I think I would like this. What are you going to charge me with? Is it my calling you greedy, or is it the lazy part that you find so uncivil? Perhaps it is your inattentiveness? I take back the Dilbert part; at least Dilbert has some technical skills.

Maybe we can get this on Judge Judy.

<shrug> in response to your lame attempts at juvenile baiting.

On the substantive issue, I find your attempts to discredit various other selection methods as not capable of increasing the speed of evolution unpersuasive. But, that's the beauty of the Internet. Critics never actually have to prove an affirmative case. They can survive by simply criticizing.

The blunt fact, which you cannot avoid is that there are a myriad of life forms in existence, and if they are not the product of some natural process, then they are the product of magic, because there is no third alternative.

So, it's really up to you, whether you continue to bait others while wearing a cape and wand, or whether you actually contribute to the advancement of science.

Frankly, I couldn't care less.

[John Hewitt]

@1131 by John Hewitt
OK, that's helpful. If I recall your definition of "rank", a rank3 influence at rank1 sounds to me as being simply a nomenclature change. Intelligence being a sexual selection factor amongst humans is not a novel idea, for example.

I am not quite sure what you mean by nomenclature change. Rank1 evolution is essentially biological evolution, though some data omitted from genetics is included, such as the data that defines the sequence of genes on a chromosome. Yes, sexual selection is Darwin, The Descent of Man, and he does argue that the brain is a consequence of sexual selection - and I agree. Coevolution between biological and social evolution should transfer traits from social to biological by the Baldwin effect.

Could you point me at something in your website that might compare or contrast your approach to the more common treatments of similar ideas?Multilevel selection is Sloan Wilson, Jablonska is another, but apart from myself I know of nobody who analyses the different levels from a foundation in data.

Edit: Oh, and you should consider Plotkin's book, "the nature of knowledge" and Popper's "three worlds" interpretation.

[John Hewitt]

"Data on its own has no meaning, only when interpreted by some kind of data processing system does it take on meaning and become information."

I don't like it. Sounds like an informal definition of information is being used. I wonder if the person was trying to make a distinction between uncertainty and information, but got confused.

Anyway, it doesn't matter too much.

~~ Paul
You are free to dislike it but it is the position taken by a good number of people in IT. That being so, it does matter.

Consider, for example, a number sequence 0120145673

You might interpret that data as you social security number or as my phone number or as any of several other interpretations. Knowledge would arise from the selection of one of those interpretations.

[Paul C. Anagnostopoulos]

If you take your estimated value of 1,000,000 generations and assume a mutation rate of 10^-6 which is about 2000 times slower than the mutation rate you are using for this series, you get 2 billion generations for convergence. Increasing the population to a million would reduce this number by an order of magnitude giving 200,000,000 generations. This is the same value that you extrapolated previously. One improvement for your argument is that you are evolving 160 loci instead of 96 loci in about the same number of generations.
Why do you think increasing the population from 32 to 1 million would reduce the generations by an order of magnitude? Our population experiments show that it varies as p^-.25.

~~ Paul

[Paul C. Anagnostopoulos]

You are free to dislike it but it is the position taken by a good number of people in IT. That being so, it does matter.

Consider, for example, a number sequence 0120145673

You might interpret that data as you social security number or as my phone number or as any of several other interpretations. Knowledge would arise from the selection of one of those interpretations.
Certainly we can interpret that digit sequence in any number of ways. Perhaps what you're getting at is that, if we don't know anything about the origin of the digit sequence, then speaking of information is misleading. Then certainly we should just refer to it as data.

Still, if we have a set of digit sequences such as the one above, we can calculate the information measure of the set according to Shannon. If that measure is positive, doesn't it make sense to talk of the information in the set? If it does not, then you need another name for the information measure.

And here's an interesting thing: If that digit sequence is entirely random, but we interpret it as a social security number, then we have gone from data to knowledge without information. I guess that's how belief systems work. :D

~~ Paul

[Paul C. Anagnostopoulos]

Now that the 128K run is finished, I'll republish the results:

Here is my data so far:

population 32
binding sites 8
weight width 9
site width 10
1 mutation / 512 bases

genome size, generations

1024, 8000
2048, 20000
4096, 34000
8192, 37000
16384, 76000
32768, 272000
65536, 392000
128000, 991000

(fits -14946 + 7.55G) So at 1 mutation per million bases, that's about 2 billion generations. If it varies as population^-.25, as our population experiments show, then at a tiny population of 1 million it would take about 63 million generations.

~~ Paul

[John Hewitt]

Certainly we can interpret that digit sequence in any number of ways. Perhaps what you're getting at is that, if we don't know anything about the origin of the digit sequence, then speaking of information is misleading. Then certainly we should just refer to it as data.

Still, if we have a set of digit sequences such as the one above, we can calculate the information measure of the set according to Shannon. If that measure is positive, doesn't it make sense to talk of the information in the set? If it does not, then you need another name for the information measure.

And here's an interesting thing: If that digit sequence is entirely random, but we interpret it as a social security number, then we have gone from data to knowledge without information. I guess that's how belief systems work. :D

~~ Paul
Yes, knowing the origin of a data string is one of the things that would give you and interpretative context for it. In general, information is data to given interpretative context or subject to an interpretative process.

It is worth remembering that, in Shannon's time, the words information and data were treated synonymously. Hence, he wasn't attaching any significance to his choice of "information" rather than "data." It is only the subsequent change in usage that causes this problem.

"If that digit sequence is entirely random, but we interpret it as a social security number," then I think we would be applying a wrong interpetation. We would then be in danger of following an incorrect knowledge system and, possibly, even of having trouble with the tax man.

[Paul C. Anagnostopoulos]

It is worth remembering that, in Shannon's time, the words information and data were treated synonymously. Hence, he wasn't attaching any significance to his choice of "information" rather than "data." It is only the subsequent change in usage that causes this problem.
But this shows that the change in usage is window dressing. Shannon used the primary term uncertainty. Perhaps we would have spoken of "data measure" instead of "information measure," but what difference does it make? There is still information in the data! It makes no sense to say that there is data in the data.


"If that digit sequence is entirely random, but we interpret it as a social security number," then I think we would be applying a wrong interpetation. We would then be in danger of following an incorrect knowledge system and, possibly, even of having trouble with the tax man.
Let's say I have some mysterious data sitting in front of me and I embark on a forensic analysis to determine what the data represents. I start with no a priori interpretation. How do I get anywhere, if there is no information in the data?

I think the distinction between information and knowledge may make some sense, but the distinction between data and information is funky. The distinction appears to be the result of a bunch of IT professionals needing a separation between data and the processing of data.

~~ Paul

[John Hewitt]

But this shows that the change in usage is window dressing. Shannon used the primary term uncertainty. Perhaps we would have spoken of "data measure" instead of "information measure," but what difference does it make? There is still information in the data! It makes no sense to say that there is data in the data.

Let's say I have some mysterious data sitting in front of me and I embark on a forensic analysis to determine what the data represents. I start with no a priori interpretation. How do I get anywhere, if there is no information in the data?

I think the distinction between information and knowledge may make some sense, but the distinction between data and information is funky. The distinction appears to be the result of a bunch of IT professionals needing a separation between data and the processing of data.
~~ Paul
I am sure that the distinction between information and data does arise from a professional need, but that does not make it invalid, just the reverse in fact. Moreover, it is not true, by this definition, that the information is in the data. Data is a matter of pattern and the statistical likelihood of the pattern existing by chance. Information is the resultant of data and some interpretative context of process.
As I said before, the same data can, when acted upon by different interpretative modes, give rise to different of information - telephone number or social security number. Conversely, different pieces of data can give rise to the same interpretation, "The sky is blue" or "le ciel est bleu." The same meaning arises from different interpretative modes.
The same situation arises in biology. As is widely reported, a DNA sequence in phage phiX174 codes for three different proteins in three different reading frames. Thus we have the same data producing three different interpetations. Conversely, in many species, we have two or more different variants of genes that produce proteins with the same enzymatic activity. Two pieces of data producing the same interpetation.

[RecoveringYuppy]

...but apart from myself I know of nobody who analyses the different levels from a foundation in data.

Can you point me at some part of your website, hopefully the most direct example you can think of, that will demonstrate this difference?

By "nomenclature change" I mean a change of terms used to identify things. Such as you using "rank1" to refer to something that most other people would refer to as "biological evolution", at least according to what you just wrote to me.

[kleinman]

In addition, if flu shots enhance a person’s likelihood of contracting disease, the whole field of preventative medicine is turned on its head.Not at all. Although, it does demonstrate that healthy individuals shouldn't get the flu vaccine. Plain and simple.
Perhaps you believe that healthy individuals shouldn’t get the polio, measles, mumps, rubella, tetanus, chicken pox, diphtheria, whooping cough, tetanus, etc. vaccines as well.
If you take your estimated value of 1,000,000 generations and assume a mutation rate of 10^-6 which is about 2000 times slower than the mutation rate you are using for this series, you get 2 billion generations for convergence. Increasing the population to a million would reduce this number by an order of magnitude giving 200,000,000 generations. This is the same value that you extrapolated previously. One improvement for your argument is that you are evolving 160 loci instead of 96 loci in about the same number of generations.Why do you think increasing the population from 32 to 1 million would reduce the generations by an order of magnitude? Our population experiments show that it varies as p^-.25.
Every population series we have run shows a very rapid drop off in the rate of decline of generations of convergence as population is increased. This is one of the many extrapolations you make that I will not argue with you when you retract it.
Now that the 128K run is finished, I'll republish the results:

Here is my data so far:

population 32
binding sites 8
weight width 9
site width 10
1 mutation / 512 bases

genome size, generations

1024, 8000
2048, 20000
4096, 34000
8192, 37000
16384, 76000
32768, 272000
65536, 392000
128000, 991000

(fits -14946 + 7.55G) So at 1 mutation per million bases, that's about 2 billion generations. If it varies as population^-.25, as our population experiments show, then at a tiny population of 1 million it would take about 63 million generations.
We are in agreement with the extrapolation for 2 billion generations however; I think your extrapolation of 63 million generations is probably a little low. I think the number is probably closer to 200 million generations. Still, your numbers are not that far different than mine.

Your previous extrapolation of 200 million generations to evolve 16 binding sites, each 6 bases wide with a mutation rate of 10^-6 and a population of 1 million does not look so idiotic.

Ev reveals a mathematical problem in your theory of evolution.

[fishbob]

Perhaps you believe that healthy individuals shouldn’t get the polio, measles, mumps, rubella, tetanus, chicken pox, diphtheria, whooping cough, tetanus, etc. vaccines as well.

Comments such as this are very useful to readers of this discussion in clarifying your reasoning and logic capabilities. In case there was any doubt. Thanks.

[John Hewitt]

Can you point me at some part of your website, hopefully the most direct example you can think of, that will demonstrate this difference?

By "nomenclature change" I mean a change of terms used to identify things. Such as you using "rank1" to refer to something that most other people would refer to as "biological evolution", at least according to what you just wrote to me.

This is discussed in the bioepistemic evolution page.
The correspondences are
Rank0 evolution = prebiotic evolution
Rank1 evolution = biological evolution
Rank2 evolution = evolution within organs of the body using input from externally derived data and selected within the receiver. Example, evolution within the brain (see Edelman and other studies into the brain as a Darwinian machine)
Rank3 evolution = Evolution of social knowledge
Rank4 evolution = One example is professional knowledge. (Compare with structure of Popper's logic and the evolution of scientific knowledge.)

[kleinman]

Perhaps you believe that healthy individuals shouldn’t get the polio, measles, mumps, rubella, tetanus, chicken pox, diphtheria, whooping cough, tetanus, etc. vaccines as well.Comments such as this are very useful to readers of this discussion in clarifying your reasoning and logic capabilities. In case there was any doubt. Thanks.
I can’t tell whether this is a sarcastic remark or not. Immunization is probably the most cost effective part of the medical system. When joobz suggests that healthy individuals don’t need flu vaccination, I doubt he makes this recommendation with any experience caring for someone with influenza. This is a very debilitating disease. I have seen a patient suffocate to death from influenza induced adult respiratory distress syndrome. There is a small risk and cost with obtaining an influenza vaccination but this is a gamble I tell people is worth taking.

[Paul C. Anagnostopoulos]

As I said before, the same data can, when acted upon by different interpretative modes, give rise to different of information - telephone number or social security number. Conversely, different pieces of data can give rise to the same interpretation, "The sky is blue" or "le ciel est bleu." The same meaning arises from different interpretative modes.
We have two different definitions of information here. If IT professionals want to use information to mean "knowledge that arises when we select a way to interpret data," then they need to come up with another term for "Shannon information, "Kolmogorov information," etc. Perhaps they have to use "information measure" or something.

~~ Paul

[Paul C. Anagnostopoulos]

Your previous extrapolation of 200 million generations to evolve 16 binding sites, each 6 bases wide with a mutation rate of 10^-6 and a population of 1 million does not look so idiotic.
Yes, it still does, because that model will not converge at the 100K genome you were talking about. If you're going to object to extrapolation in general, surely you should object to extrapolation in an impossible scenario, right?


Ev reveals a mathematical problem in your theory of evolution.
Not due to that particular experiment, it doesn't. The question now is: How do the generations vary with population in my latest model? I've selected the 4K genome size and I'm running experiments with increasing populations. Then I'll do the same with the 8K genome so we can see the difference.

~~ Paul

[John Hewitt]

We have two different definitions of information here. If IT professionals want to use information to mean "knowledge that arises when we select a way to interpret data," then they need to come up with another term for "Shannon information, "Kolmogorov information," etc. Perhaps they have to use "information measure" or something.
~~ Paul
Yes, there are two definitions there but lets come back to "knowledge." If information is taken as synonymous with data and as also meaning interpreted data that is two meanings of the word information. I am just following the "interpreted data" meaning.
Knowledge comes in later and, in respect of that word, I follow the evolutionary definition of it. "Knowledge" as a word is much less well defined. IT people do various things but I wanted a link to evolutionary theory so I follow the definition that comes from evolutionary epistemology, namely that knowledge is "selected information." One then uses that framework in generalizing evolutionary theory by fitting that sequence, as far as possible to the various evolutionary ranks.

[Paul C. Anagnostopoulos]

Yes, there are two definitions there but lets come back to "knowledge." If information is taken as synonymous with data and as also meaning interpreted data that is two meanings of the word information.
I wouldn't take information as synonymous with data. Data are numbers. Information is some measure of the content of the numbers, so to speak. It's just not necessarily dependent on the interpretation of the data, since I can come up with an information measure without knowing anything about the data. And I can analyze the Golmogorov content without knowing anything about the data, as compression algorithms do.

Of course, in the experimental sciences, the word data already implies an interpretation. No one collects data without knowing what it is.

I agree the whole thing is a bit slippery.

~~ Paul

[Yahzi]

I do not understand your question about breakfast cereals and do not have the impression that you want a sensible discussion.
Nice dodge!

When asked a question too difficult to answer, just pretend it's irrelevant. And toss out another insult.

The coolest part is that immediately before this post, you told someone else to read your entire web page before asking questions.

Which makes my telling you to read this entire thread superbly ironic!

But since I know reading is hard for you, I'll help you out.

You assert the precursor to genes are created by chance (ignoring the question of what this has to do with genetic evolution, of course):
http://forums.randi.org/showpost.php?p=2182801&postcount=1069

I introduce granola, showing that order arising from simplicity is not merely "chance:"
http://forums.randi.org/showpost.php?p=2182952&postcount=1072

You dodge this by nattering on about the difference between live and dead:
http://forums.randi.org/showpost.php?p=2183386&postcount=1075

I call your bluff and ask you to explain the difference:
http://forums.randi.org/showpost.php?p=2189750&postcount=1126

And now you've magically forgotten what the question was! (The question you introduced!)
http://forums.randi.org/showpost.php?p=2189870&postcount=1129

I begin to understand. Your misdirection, red herrings, and obfuscations are not for us; they are for you. Your goal is not to confuse us, but to keep yourself confused, so that you don't have to actually consider the issue logically and rationally.

[joobz]

I can’t tell whether this is a sarcastic remark or not. Immunization is probably the most cost effective part of the medical system. When joobz suggests that healthy individuals don’t need flu vaccination, I doubt he makes this recommendation with any experience caring for someone with influenza. This is a very debilitating disease. I have seen a patient suffocate to death from influenza induced adult respiratory distress syndrome. There is a small risk and cost with obtaining an influenza vaccination but this is a gamble I tell people is worth taking.
You're comment on equivicating flu vaccine and other immunizations demonstrates the rudimentary level of knowledge you hold in this area. Read up on the literature. There is evidence for heightened risks for healthy individuals to contract flu by being immunized with a poorly season matched vaccination.
People in the "at risk" populations still gain a benefit that supercedes this effect.

I know full well the problems from ARDS and ALI, I worked in a hyperbaric lung institute but did not do direct patient care. I do not take lightly my statements. It is for this reason that I say healthy normal adults can increase the risk of catching the flu by taking the vaccine. This isn't the case for immune compromised indivuals.

[John Hewitt]

Nice dodge!

When asked a question too difficult to answer, just pretend it's irrelevant. And toss out another insult.

The coolest part is that immediately before this post, you told someone else to read your entire web page before asking questions.

Which makes my telling you to read this entire thread superbly ironic!

But since I know reading is hard for you, I'll help you out.

You assert the precursor to genes are created by chance (ignoring the question of what this has to do with genetic evolution, of course):
http://forums.randi.org/showpost.php?p=2182801&postcount=1069

I introduce granola, showing that order arising from simplicity is not merely "chance:"
http://forums.randi.org/showpost.php?p=2182952&postcount=1072

You dodge this by nattering on about the difference between live and dead:
http://forums.randi.org/showpost.php?p=2183386&postcount=1075

I call your bluff and ask you to explain the difference:
http://forums.randi.org/showpost.php?p=2189750&postcount=1126

And now you've magically forgotten what the question was! (The question you introduced!)
http://forums.randi.org/showpost.php?p=2189870&postcount=1129

I begin to understand. Your misdirection, red herrings, and obfuscations are not for us; they are for you. Your goal is not to confuse us, but to keep yourself confused, so that you don't have to actually consider the issue logically and rationally.
No, I don't recall telling anyone to read the whole of my web site. I hope I do not insult people (too often). On the other hand, I cannot pretend that I have found much of merit in your commentaries; it seems to me that they are often merely empty.

I have never asserted that the precursors to genes were created by chance. Just the reverse, I have asserted that the chance creation of genes from a primordial soup is infeasible and deplored this widespread assertion.

I really, genuinely and sincerely have not the slightest idea what point you are making about breakfast cereals or your beliefs about life and death. These are things you will have to explain and I will, or will not, reply depending upon whether I feel able to do so usefully.

As for my forgetting your question - if that is so I am sorry you feel so cross. Perhaps you should phrase your question more clearly or ask other people for their opinions.

[fishbob]

I can’t tell whether this is a sarcastic remark or not.

You can't? Really?

[kleinman]

Your previous extrapolation of 200 million generations to evolve 16 binding sites, each 6 bases wide with a mutation rate of 10^-6 and a population of 1 million does not look so idiotic. Yes, it still does, because that model will not converge at the 100K genome you were talking about. If you're going to object to extrapolation in general, surely you should object to extrapolation in an impossible scenario, right?
You have a point on this Rcapacity issue however both series are showing essentially the same mathematical trends. I have never objected to extrapolation in general. However it seems that any extrapolations you make that I agree with, you soon retract.
Ev reveals a mathematical problem in your theory of evolution.Not due to that particular experiment, it doesn't. The question now is: How do the generations vary with population in my latest model? I've selected the 4K genome size and I'm running experiments with increasing populations. Then I'll do the same with the 8K genome so we can see the difference.
This series from ev again shows that you can evolve nothing on a realistic length genome by random point mutations and natural selection, this process is far too slow.

For the 4k genome you will be able to do up to a 500k population and 8k genome up to a 250k population. It will be interesting to see if this shows anything different from the other population series we have done so far, I doubt it.
I can’t tell whether this is a sarcastic remark or not. Immunization is probably the most cost effective part of the medical system. When joobz suggests that healthy individuals don’t need flu vaccination, I doubt he makes this recommendation with any experience caring for someone with influenza. This is a very debilitating disease. I have seen a patient suffocate to death from influenza induced adult respiratory distress syndrome. There is a small risk and cost with obtaining an influenza vaccination but this is a gamble I tell people is worth taking.You're comment on equivicating flu vaccine and other immunizations demonstrates the rudimentary level of knowledge you hold in this area. Read up on the literature. There is evidence for heightened risks for healthy individuals to contract flu by being immunized with a poorly season matched vaccination.
People in the "at risk" populations still gain a benefit that supercedes this effect.

I know full well the problems from ARDS and ALI, I worked in a hyperbaric lung institute but did not do direct patient care. I do not take lightly my statements. It is for this reason that I say healthy normal adults can increase the risk of catching the flu by taking the vaccine. This isn't the case for immune compromised indivuals.
Why don’t you explain to us how a healthy person taking a poorly seasoned matched flu vaccine increases the risk of catching a different strain of influenza? Then you can explain how people in the “at risk” population still gain a benefit from taking a poorly seasoned matched flu vaccine.
I can’t tell whether this is a sarcastic remark or not.You can't? Really?
It doesn’t really matter. The point is that joobz made a broad statement about influenza vaccination that suggests that healthy people should not get this vaccination. I have a friend who is a Professor of Neurology and we have discussed the sequela to influenza. He said that there is a theory that the 1920 influenza epidemic led to a large increase in the incidence of Parkinson’s disease in the 1930’s. I haven’t checked out his statement but my view is it is much better to get immunized than get the disease. If joobz has a point to make, he needs to do a much better job in making it.

[joobz]

Why don’t you explain to us how a healthy person taking a poorly seasoned matched flu vaccine increases the risk of catching a different strain of influenza? Then you can explain how people in the “at risk” population still gain a benefit from taking a poorly seasoned matched flu vaccine.

It doesn’t really matter. The point is that joobz made a broad statement about influenza vaccination that suggests that healthy people should not get this vaccination. I have a friend who is a Professor of Neurology and we have discussed the sequela to influenza. He said that there is a theory that the 1920 influenza epidemic led to a large increase in the incidence of Parkinson’s disease in the 1930’s. I haven’t checked out his statement but my view is it is much better to get immunized than get the disease. If joobz has a point to make, he needs to do a much better job in making it.


I am not an expert in immunology, but I'll give my rather lay understanding of this issue.
There is a Fast B-Cell response and a slow response in the generation of antibodies. This fast response typically generates functioning antibodies which can recognize an antigen. there is a delay in their production, but they can be formed after several days. After this formation, memory cells can be generated to stably produce a antibody against that antigen.

From then on, when a second exposure occurs, these cells will shuffle the antibody binding site a bit to improve recognition. However, this shuffling is quite slow compared to the first time exposure system.

Anyway, once you have antibodies raised against a certain flu strain, there is a limited window of efficacy which is decided by how well the antibody can recognize this virus. If the virus mutated sufficently enough (or that the flu vaccine given was chosen poorly), the antibody won't recognize the virus well. Yet, the body doesn't consider it a seperate strain (I do not knwo what mechanism decides this), so a fast antibody response won't be enacted. Which means, it will take more time to generate an effective antibody against the virus than had you not had a flu vaccine to begin with.

Why do I say this is only true for healthy adults?
healthy adults have a rapidly/effectively functioning fast b-cell response. So they can become compromised due to original antigenic sin.

However, for elderly or children or people with poorly functioning immunes, this fast response isn't soo fast anymore. So, it is still better to get memory cells generated and allow for some antibody functioning to occur. They will always benefit from the flu shot.

With all of this said. my key point is that the work used to model evolutionary trends in viruses allows for improved methods in selecting a Flu vaccine cocktail that wouldn't have been considered without the notion of evolutionary theory. it is very possible that if flu vaccines cocktails are designed better, everyone can benefit, not just the elderly...

[Paul C. Anagnostopoulos]

I have never objected to extrapolation in general.
Sure seems like you do. You would never let me extrapolate population past the experiments I actually ran.


For the 4k genome you will be able to do up to a 500k population and 8k genome up to a 250k population. It will be interesting to see if this shows anything different from the other population series we have done so far, I doubt it.
Which population series? The one we have shows generations varying as p^-.25. Yet you keep saying:

Every population series we have run shows a very rapid drop off in the rate of decline of generations of convergence as population is increased. This is one of the many extrapolations you make that I will not argue with you when you retract it.
Could you present the data from the series that shows this very rapid drop off past a population of, say, 64? I refer you to this post:

http://forums.randi.org/showthread.php?postid=2174709#post2174709

~~ Paul

[kleinman]

Why don’t you explain to us how a healthy person taking a poorly seasoned matched flu vaccine increases the risk of catching a different strain of influenza? Then you can explain how people in the “at risk” population still gain a benefit from taking a poorly seasoned matched flu vaccine.

It doesn’t really matter. The point is that joobz made a broad statement about influenza vaccination that suggests that healthy people should not get this vaccination. I have a friend who is a Professor of Neurology and we have discussed the sequela to influenza. He said that there is a theory that the 1920 influenza epidemic led to a large increase in the incidence of Parkinson’s disease in the 1930’s. I haven’t checked out his statement but my view is it is much better to get immunized than get the disease. If joobz has a point to make, he needs to do a much better job in making it.I am not an expert in immunology, but I'll give my rather lay understanding of this issue.
It has been a while since I took a course in immunology so I can’t really comment on your fast and slow B cell responses. My understanding in that IgM is formed rapidly and then drops off rapidly to the initial exposure to an antigen and then IgG is formed more slowly but remains at higher titers for a longer period of time.

I’ll try to explain my view on this a little more completely. No one wants to inoculate anyone with an antigen that would not give the desired immunity. However, influenza strains can reappear every few years. So even if you get immunized with a poorly matched vaccine, it may serve as a booster if that strain does reappear at a later date. If you get flu vaccinations on a yearly basis, over a period of years you will have exposed your immune system to so many different strains of the influenza virus antigens that you may confer partial immunity even if you get a poorly matched vaccine in any given year. When I recommend influenza immunization to a patient, I tell them of the possibility of a poorly matched vaccine as well as the possibility of adverse reactions to the flu shot, including flu like symptoms or worse. In all the years I have practiced medicine I have never had anyone have an adverse reaction worse than running a fever and having some body aches and these have been very rare and quickly passed.

A healthy well fed population can better withstand an influenza epidemic but a non-immune population that is debilitated which could happen in this country if something interrupted the food supply would be very vulnerable to an influenza epidemic.

This is far from the topic of ev and macroevolution. I classify this discussion of influenza strains as one of a microevolutionary process. This is one of the very few components of the theory of evolution that has any truth in it.
I have never objected to extrapolation in general.Sure seems like you do. You would never let me extrapolate population past the experiments I actually ran.For the 4k genome you will be able to do up to a 500k population and 8k genome up to a 250k population. It will be interesting to see if this shows anything different from the other population series we have done so far, I doubt it.
What I have objected to is your use of curve fits to extrapolate many orders of magnitude beyond the range of the data used to generate the curve. Every time you have done this, the data generated by ev has been well off the curve fit predictions.

You know I like some of your extrapolations but then you retract them.
Which population series? The one we have shows generations varying as p^-.25. Yet you keep saying: Every population series we have run shows a very rapid drop off in the rate of decline of generations of convergence as population is increased. This is one of the many extrapolations you make that I will not argue with you when you retract it.

http://forums.randi.org/showthread.p...09#post2174709 (http://forums.randi.org/showthread.php?postid=2174709#post2174709)
I’ll repost the data if you want but you know where the debate is. Is the population data approaching an asymptote or does the generations for convergence continue to make a slow descent to Adequate’s estimate of 1 generation at infinite population? This is the only issue left where ev may possibly give some support to the theory of evolution. If you remain true to form, you will do a curve fit on a population range of say 64 to 1 meg and then extrapolate multiple orders of magnitude beyond the range of the data. This won’t settle this issue; you have to run the numbers.

I know the data very well that is posted on the URL you give. I generated the data. I sent you the pascal version of ev to run the 2 meg population case which you have yet to run. If you examine that data, you will see that the decrease in the generations for convergence between a population of 64 and 1 meg is less than 2 orders of magnitude. The first order of magnitude drop occurs between a population of 64 and 2048. You are going to need much larger drops in the generations for convergence to support your theory.

[joobz]

It has been a while since I took a course in immunology so I can’t really comment on your fast and slow B cell responses. My understanding in that IgM is formed rapidly and then drops off rapidly to the initial exposure to an antigen and then IgG is formed more slowly but remains at higher titers for a longer period of time.
I do believe this is the heart of the fast slow responses. I do find it interesting that to make up for the lack of specificity of the single fab fragment by increasing the number of fabs on a single molecule. We use same binding enhancement in multimerization for drug targeting of nanoparticles.

I’ll try to explain my view on this a little more completely. No one wants to inoculate anyone with an antigen that would not give the desired immunity. However, influenza strains can reappear every few years. So even if you get immunized with a poorly matched vaccine, it may serve as a booster if that strain does reappear at a later date.
That's not a bad thought. But some strains mutate more than others. There's some influenza strains that don't vary much, and a vaccine against them will work this way. Although for the more aggresively mutating varieties, a 3 year old vaccine might not help.

If you get flu vaccinations on a yearly basis, over a period of years you will have exposed your immune system to so many different strains of the influenza virus antigens that you may confer partial immunity even if you get a poorly matched vaccine in any given year. This isn't so true. 3 strains per year(per cocktail) for 20 years, is only 60 different strains. If you consider 20+peptides and a antigen epitope domain of even just 8 amino acids... well you get the picture. On the other hand, I do not know off the top of my head how many different antibodies are raised against a single strain, which may counteract this problem. I'm assuming we generate polyclonals from a vaccination, but I really don't know.

When I recommend influenza immunization to a patient, I tell them of the possibility of a poorly matched vaccine as well as the possibility of adverse reactions to the flu shot, including flu like symptoms or worse. In all the years I have practiced medicine I have never had anyone have an adverse reaction worse than running a fever and having some body aches and these have been very rare and quickly passed.

A healthy well fed population can better withstand an influenza epidemic but a non-immune population that is debilitated which could happen in this country if something interrupted the food supply would be very vulnerable to an influenza epidemic.
This is an interesting point. I hadn't considered the food supply side of the game.

[Mr. Scott]

...which is ironic because another forum Kleinman participated robustly in is the one dishonestly named "evolutionisdead"


This is far from the topic of ev and macroevolution. I classify this discussion of influenza strains as one of a microevolutionary process. This is one of the very few components of the theory of evolution that has any truth in it

Dr. Kleinman has refrained to rigorously defined the difference between micro and macro evolution, but only says one is small and the other is big.

The purpose of this posting is to jump-start a discussion to help nail down the distinction.

I'll take it that Dr. Kleinman believes in evolution, but not to the point that it results in new species. Still, where to draw the line is open to debate.

Ordinarily, we say two species are distinct if they cannot mate to produce fertile offspring. Are creationists using science to help identify species separately created by The Creator? Some examples come to mind:

We have lions and tigers. Did God create them separately? According to my googling, hybird ligers and tigons have been known to be fertile. This suggests that God created some ancestral big cat which micro-evolved, or branched on an evolutionary tree, into lions and tigers. So, Dr. Kleinman, would you agree that the divergence of lions from tigers was an example of microevolution? If so, would Ev, if it's as accurate a model of evolution as you claim, confirm that there was sufficient time to result in that divergence?

I looked up the possibility of the human/chimp (said to be our closest non-human relative) hybridization and learned that the chimps beat us with 24 chromosome pairs over our 23 pairs (link (http://www.gate.net/~rwms/hum_ape_chrom.html)). Difference in chromosome count suggests infertile hybridization but does not guarantee it, and the close count suggests it is not impossible that a chimp/human hybrid could be fertile. If it was, would creationists acknowledge microevolution between chimps and humans? It seems that different species of bears can hybridize. Did they diverge through microevolution from the original creatures created by God?

I'd also like to use humans alone as evolutionary examples, going by the creationist assumption that we are all descended from a single mating pair (Adam and Eve). We nevertheless have a branching tree of "races" that resemble trees of macroevolution. Dr. Kleinman, do you attribute the difference between, say, asians, blacks, and whites to microevolution? How about neanderthals and modern humans, who may have hybridized? (link (http://cogweb.ucla.edu/ep/Neanderthal.html)) Were Adam and Eve white? Or perhaps of an original race that is presently extinct, leaving only its micro-evolutionarily diverged descendents?

Similar types, like the zebra and the horse, often have different chromosome counts. On the other hand, animals of differing chromosome counts can have fertile offspring:

The Przewalski [Eurasian Wild Horse] has notable biological differences from the domestic horse: unlike domesticated horses, which have 64 chromosomes, the wild horse has 66 chromosomes. However, the offspring of Przewalski and domestic horses are fertile, possessing 65 chromosomes

(link (http://en.wikipedia.org/wiki/Wild_Horse))

This makes me wonder if the critical event causing a cleaving of one species into two could often be a reproductive error that causes a gene pair to be duplicated or missed. I assume the Ev program does not model this. My conclusion is that this is but one example of how Ev is not a complete model of evolution, and therefore its failure to demonstrate macro evolution that diverges species does not disprove darwinian evolution nor prove intelligent design.

[Paul C. Anagnostopoulos]

What I have objected to is your use of curve fits to extrapolate many orders of magnitude beyond the range of the data used to generate the curve. Every time you have done this, the data generated by ev has been well off the curve fit predictions.
Huh? If I've extrapolated orders of magnitude beyond the range of the data, then certainly we have never run the extrapolated experiments. Your second sentence doesn't make sense.


I’ll repost the data if you want but you know where the debate is. Is the population data approaching an asymptote or does the generations for convergence continue to make a slow descent to Adequate’s estimate of 1 generation at infinite population?
If you frame it as a question, I'll certainly agree that it's an interesting one. However, you made a dogmatic statement:

This series from ev again shows that you can evolve nothing on a realistic length genome by random point mutations and natural selection, this process is far too slow.
Could you please either stick with the dogma or back off to question mode? You're giving me whiplash.


I know the data very well that is posted on the URL you give. I generated the data.
Are we talking about the same data? Only the last three points are yours.


If you examine that data, you will see that the decrease in the generations for convergence between a population of 64 and 1 meg is less than 2 orders of magnitude. The first order of magnitude drop occurs between a population of 64 and 2048.
So what? As I've said countless times, the data fits p^-.25. You need to explain why you think this is going to change for higher populations. You might also explain why you're so excited about the 2 million population run, when you claim to object only to extrapolations of "many orders of magnitude."

~~ Paul

[Paul C. Anagnostopoulos]

Okay, so I took the 4K genome from my latest experiments (http://forums.randi.org/showthread.php?postid=2191375#post2191375) and varied the population.

genome size 4096
binding sites 8
weight width 9
site width 10
1 mutation / 512 bases

population, generations

64, 18000
128, 19000
256, 7000
512, 3000
1024, 2200
2048, 2100
4096, 1700
8192, 1000
16384, 1000
32768, 600

This fits $g=153403p^{-.55}$.

Now I will run a series with genome size 2K and one with size 8K. I'm interested to see how the curve fit varies.

~~ Paul

[kleinman]

I’ll try to explain my view on this a little more completely. No one wants to inoculate anyone with an antigen that would not give the desired immunity. However, influenza strains can reappear every few years. So even if you get immunized with a poorly matched vaccine, it may serve as a booster if that strain does reappear at a later date.That's not a bad thought. But some strains mutate more than others. There's some influenza strains that don't vary much, and a vaccine against them will work this way. Although for the more aggresively mutating varieties, a 3 year old vaccine might not help.
I’m not suggesting that a 3 year old vaccine be used. I think the CDC’s strategy of looking for strains of influenza in the orient or other parts of the world and preparing for these strains is a rational approach.
If you get flu vaccinations on a yearly basis, over a period of years you will have exposed your immune system to so many different strains of the influenza virus antigens that you may confer partial immunity even if you get a poorly matched vaccine in any given year.This isn't so true. 3 strains per year(per cocktail) for 20 years, is only 60 different strains. If you consider 20+peptides and a antigen epitope domain of even just 8 amino acids... well you get the picture. On the other hand, I do not know off the top of my head how many different antibodies are raised against a single strain, which may counteract this problem. I'm assuming we generate polyclonals from a vaccination, but I really don't know.
Getting zero influenza vaccinations per year guarantees zero immunity. I understand that even if you get influenza vaccinations it does not guarantee immunity. Unless a better strategy comes along, I recommend the one we got.
A healthy well fed population can better withstand an influenza epidemic but a non-immune population that is debilitated which could happen in this country if something interrupted the food supply would be very vulnerable to an influenza epidemic.This is an interesting point. I hadn't considered the food supply side of the game.
The immune system is a big energy consumer. It becomes obvious when you have a patient fighting an infection who is at complete bed rest and still rapidly loses weight (not due to dehydration).
Dr. Kleinman Believes in Evolution......which is ironic because another forum Kleinman participated robustly in is the one dishonestly named "evolutionisdead"
I have consistently acknowledged that microevolutionary processes can and do occur. Evolutionarians have taken these processes and extrapolated these occurrences to explain much larger changes in genomes. There is no scientific basis for these types of extrapolations and this is what I have argued on the Evolutionisdead forum and this forum as well. If there was no truth at all in the theory of evolution, I don’t think the theory would have any staying power. It’s like my arguments about ev. If there were no truth in my arguments, this thread would have died long ago.
This is far from the topic of ev and macroevolution. I classify this discussion of influenza strains as one of a microevolutionary process. This is one of the very few components of the theory of evolution that has any truth in it.Dr. Kleinman has refrained to rigorously defined the difference between micro and macro evolution, but only says one is small and the other is big.

The purpose of this posting is to jump-start a discussion to help nail down the distinction.

I'll take it that Dr. Kleinman believes in evolution, but not to the point that it results in new species. Still, where to draw the line is open to debate.
Paul and others want me to nail down this distinction. I have argued that the evolution of binding sites is a macroevolutionary process. Any de novo creation of a gene or fundamental genetic control system represents a macroevolutionary process. I have even said that once you get past 2 or 3 point mutations in a single creature, in a single generation that are subject to natural selection that you are starting to cross the line between macro and microevolutionary process. I don’t have a definition for the difference between macro and microevolution that will give you a warm, tingly feeling. It is like evolutionarian don’t give a good definition for natural selection. I have suggested that it is a restatement of the 1st law of thermodynamics but no one seems to have a better suggestion.
I'd also like to use humans alone as evolutionary examples, going by the creationist assumption that we are all descended from a single mating pair (Adam and Eve). We nevertheless have a branching tree of "races" that resemble trees of macroevolution. Dr. Kleinman, do you attribute the difference between, say, asians, blacks, and whites to microevolution? How about neanderthals and modern humans, who may have hybridized? (link (http://cogweb.ucla.edu/ep/Neanderthal.html)) Were Adam and Eve white? Or perhaps of an original race that is presently extinct, leaving only its micro-evolutionarily diverged descendents?
Don’t mistake the diversity you can obtain from recombination and natural selection as a macroevolutionary process. I prefer to keep this discussion on the hard scientific mathematical level because once you leave the mathematical arena, anyone can speculate anything. If you want to speculate that humans and chimpanzee evolved from a common ancestor, show the arithmetic that accounts for the genetic differences. Ev (an evolutionist developed, peer reviewed and published model for random point mutations and natural selection) show that you have a mathematical problem in accounting for these differences.
What I have objected to is your use of curve fits to extrapolate many orders of magnitude beyond the range of the data used to generate the curve. Every time you have done this, the data generated by ev has been well off the curve fit predictions.Huh? If I've extrapolated orders of magnitude beyond the range of the data, then certainly we have never run the extrapolated experiments. Your second sentence doesn't make sense.
I have been unfair to you here. It is Dr Schneider who extrapolated from the results of a 256 base genome to the evolution of a 3 billion base genome (with conditions). Your extrapolations have not been so extreme. You have done curve fits previously that have not been accurate in predicting the next point in a series. Your latest curve fit for the population series is p^-.25. Why don’t you do the 2 meg population case and see how closely it fits your curve?
I’ll repost the data if you want but you know where the debate is. Is the population data approaching an asymptote or does the generations for convergence continue to make a slow descent to Adequate’s estimate of 1 generation at infinite population?If you frame it as a question, I'll certainly agree that it's an interesting one. However, you made a dogmatic statement:This series from ev again shows that you can evolve nothing on a realistic length genome by random point mutations and natural selection, this process is far too slow.Could you please either stick with the dogma or back off to question mode? You're giving me whiplash.
This discussion about the population effects in ev has been going on for a while. I don’t believe that I have been dogmatic about this issue. When talking about population sizes that would have been available at the time of primate ancestor->human evolution, ev shows that with the available time and population sizes, you can not evolve anything by random point mutations and natural selection.
I know the data very well that is posted on the URL you give. I generated the data.Are we talking about the same data? Only the last three points are yours.
If I remember correctly, you started a population series with a mutation rate of 10^-6. I did the last point in that series and it was clear that further data points in that series would be taking weeks if not months/years to generate. I thought I started the other series with a higher mutation rate to try to do larger populations. I can’t remember for sure so you can have the credit for running the smaller population cases in this series.
If you examine that data, you will see that the decrease in the generations for convergence between a population of 64 and 1 meg is less than 2 orders of magnitude. The first order of magnitude drop occurs between a population of 64 and 2048. So what? As I've said countless times, the data fits p^-.25. You need to explain why you think this is going to change for higher populations. You might also explain why you're so excited about the 2 million population run, when you claim to object only to extrapolations of "many orders of magnitude."
So run the population=2 meg case and show us how accurate your curve fit is when you simply double the population.
64, 18000
128, 19000
256, 7000
512, 3000
1024, 2200
2048, 2100
4096, 1700
8192, 1000
16384, 1000
32768, 600
You still haven’t shown a two order of magnitude decrease in the generations of convergence and you need much more than that to support your theory. Every population series done so far shows the same trends as you have posted here. As Myriad has shown, increasing population obeys less than an additive effect on the probabilities of getting a good mutation at a proper locus. You can approximate this effect as additive with small populations but with increasing population, the improvement in the probabilities become less and less.

[articulett]

Kleinman,
You are dodging and repeating the same error in argument. You won't define macroevolution on a genetic level and then you are saying that to prove it, you'd need to show mathamatically how it could happen via point mutations. But there are relatively few if any point mutations between humans and chimps. The major differences in the genomes involve translocations, inversions, and differences in promoter regions (different proteins are turned on and off at different time in the development of the organism.) Humans do not have "more" DNA than chimps--and they have one less pairs of chromosomes. That which we'd call higher function (such as intelligence) does has no direct correlation to amount of DNA (base pairs) or number of genes or number of point mutations between us and a common ancestor. You insist on this point muatation paradigm because it disproves evolution (in your mind), but evolution is not merely a point mutation process! Entire chromosomes can be duplicated and or deleted--old genes in junk DNA can be turned on via translocations and newer genes can be turned off by the same process.

There is no peer reviewed articles on how point mutations in the common ancestor of humans and chimps resulted in the variations we we see today because we can LOOK AT THE DNA and see that the differences have very little to do with point mutations! Why are you not hearing this? Mathematical models are irrelevant if they are missing important data. Your entire goal is to prove that evolution cannot be true (without an intelligent designer) and so you only let yourself plug in math facts that allow you to reach that conclusion. But the very DNA itself shows us that your mathematical model for how species diverge is utterly insufficient--it's wrong. We look at the DNA and note the differences and similarities--we can presume the similarities came from the common ancestor--we can look at the differences and deduce what sort of mutation accounts for the differences (of which there are few)--we can actually see if it was a point muatation in a gene or a frameshift mutation or a translocation etc. And that is what is going on in current peer reviewed journals on the topic today.

You asked for something which you know does not exist so that you can continue to believe that evolution can't be true because your point mutation analysis proves it. If you want the truth, you need to get over your fixation with point mutations. If you want use your befuddlement to make yourself believe that evolution requires and intelligent designer, then proceed as you are doing, but don't expect to convince anyone without the "need" to believe that a certain book is true to ensure their salvation. You are aiming to prove a conclusion that is invalid in the first place and ignoring all attempts at showing you why it is invalid. When the questions threaten your beliefs you change the questions or the topic or the standard of proof.

[Paul C. Anagnostopoulos]

Why don’t you do the 2 meg population case and see how closely it fits your curve?
When I have weeks of time, I will. I'll also do the 256K, 512K, and 1024K genome sizes for my latest experiments. I estimate the 256K genome size will take about a month. I'd sure appreciate it if you could run the 2 million population, just so I don't have to do all the work.


You still haven’t shown a two order of magnitude decrease in the generations of convergence and you need much more than that to support your theory.
Alan, it's your theory, not mine. It's called the Theory of Point Mutation and Natural Selection, remember?

~~ Paul

[kleinman]

Why don’t you do the 2 meg population case and see how closely it fits your curve?When I have weeks of time, I will. I'll also do the 256K, 512K, and 1024K genome sizes for my latest experiments. I estimate the 256K genome size will take about a month. I'd sure appreciate it if you could run the 2 million population, just so I don't have to do all the work.
Paul, you know I would do this case if I could. This is an issue of memory capacity on our computers. I have 512mbytes and you have 1 gig of memory which allows you to do one more data point.
You still haven’t shown a two order of magnitude decrease in the generations of convergence and you need much more than that to support your theory.Alan, it's your theory, not mine. It's called the Theory of Point Mutation and Natural Selection, remember?
Not quite. This is the much repeated quote from Dr Schneider’s paper:
Likewise, at this rate, roughly an entire human genome of ~4x10^9 bits (assuming an average of 1 bit/base, which is clearly an overestimate) could evolve in a billion years, even without the advantages of large environmentally diverse worldwide populations, sexual recombination and interspecies genetic transfer.
I added the bold face in the quote. Running the numbers in ev appears to be showing that large populations do not give that much of an advantage in increasing the rate of evolution (when being driven by random point mutations and natural selection).

I am open to you showing mathematically how large population will accelerate evolution sufficiently by any mechanism you can think of for it to be a viable theory.

[Mr. Scott]

If there were no truth in my arguments, this thread would have died long ago.

Your narcissism is in full display there. Truth is not a prerequisite for argumentative staying power. In case you haven't noticed, the law of Internet forums is the last person who posts wins, so a thread can go on forever with no truth on either side.

I don’t have a definition for the difference between macro and microevolution that will give you a warm, tingly feeling.

What an obnoxious remark. I'm not looking for a warm, tingly, feeling there. I'm looking for a rigorous definition we can apply mathematics to. Your admission reveals why you feel you can deny moving goal posts. You use fuzzy goal posts so you can deny they move. Not specifying exactly where your goal posts reside allows you to dismiss new evidence of macro evolution by claiming it missed goals you only vaguely defined. Nice try.

What gives me a warm, tingly feeling is locating the holes in your arguments, and I'm getting a fine dose from your remarks. Thanks!

[I less than three logic]

If there were no truth in my arguments, this thread would have died long ago.
Your narcissism is in full display there. Truth is not a prerequisite for argumentative staying power. In case you haven't noticed, the law of Internet forums is the last person who posts wins, so a thread can go on forever with no truth on either side.
You know, I've heard this claim before. The Light created Life (http://forums.randi.org/showthread.php?t=63587) thread is close to twice the size of this thread and still going strong it seems. As long as the thread doesn't die, Kleinman (and LCL) must be on to something.... right? :rolleyes:

Maybe we need a new fallacy term. Appeal to forum longevity? :)

[Yahzi]

No, I don't recall telling anyone to read the whole of my web site.
I'm sorry, but it's not worth my time anymore to link to the posts where you contradict yourself.

I hope I do not insult people (too often). On the other hand, I cannot pretend that I have found much of merit in your commentaries; it seems to me that they are often merely empty.
Irony much?

I have never asserted that the precursors to genes were created by chance. Just the reverse, I have asserted that the chance creation of genes from a primordial soup is infeasible and deplored this widespread assertion.
I'm sorry, but it's not worth my time anymore to link to the posts where you contradict yourself.

I really, genuinely and sincerely have not the slightest idea what point you are making about breakfast cereals or your beliefs about life and death.
Thast's quite evident. As is your obduracy.

Perhaps you would care to explain what part of this sentence is too difficult for you to comprehend:

Order can arise from simple mechancial laws and the interjection of energy.

Perhaps you could respond to how this statement allows for evolution without dragging in your concepts of the difference between alive and dead.

These are things you will have to explain and I will, or will not, reply depending upon whether I feel able to do so usefully.
You won't find any useful way to keep dodging the issue you brought up.

As for my forgetting your question - if that is so I am sorry you feel so cross. Perhaps you should phrase your question more clearly or ask other people for their opinions.
You didn't actually read the links I provided, did you. And you wonder why I am cross? You can't be bothered to read the posts - even when you wrote half of them. Yet you insist on declaring my posts empty and insulting. How would you even know? It's not like you actually read them...

You introduced the topic of vitalism. You suggested that information theory was different for living systems as opposed to non-living ones. And now you're trying to pretend you never typed those words.

This is your great argument? To deny your own words three times before the cock crows?

When faced with an incontrovertible example that you are wrong (the granola example), you pretend you don't understand the question anymore.

There is something else you are wrong about. I am not cross; I am amused. As is anyone else watching you play Judas to your own arguments.

[articulett]

You know, I've heard this claim before. The Light created Life (http://forums.randi.org/showthread.php?t=63587) thread is close to twice the size of this thread and still going strong it seems. As long as the thread doesn't die, Kleinman (and LCL) must be on to something.... right? :rolleyes:

Maybe we need a new fallacy term. Appeal to forum longevity? :)

Yes! I like it. Appeal to fl for short. It's the notion that because people are still engaging in conversation with you that your idea contains truth.

I don't think anyone who understands the basics of evolution find any truth in Kleinman's point mutation theory. But I find it fascinating how he keeps ignoring the very pertinent information that, now that we can physically see and decode the genome--we can also see that point mutations may be the least means of mutation whereby different species emerge. It's like point mutations are to evolution what a tax rebate is to income. It is seldom something that moves someone into a different income bracket. It's contribution to income in minor. Kleinman is trying to prove that the rebate can't account for the income levels we see in people. We agree. We know that there are much larger sources of income than tax rebates.

We also know that there are much more significant mutations than point mutations in speciation (or macro evolution).

[Paul C. Anagnostopoulos]

I added the bold face in the quote. Running the numbers in ev appears to be showing that large populations do not give that much of an advantage in increasing the rate of evolution (when being driven by random point mutations and natural selection).
Where "large" is defined as 1 million or less and "not give that much of an advantage" is entirely undefined.

~~ Paul

[dv82matt]

When faced with an incontrovertible example that you are wrong (the granola example), you pretend you don't understand the question anymore.
Yahzi, it's pretty obvious that you simply misunderstood some of John's posts. I looked at the ones you linked to in your earlier post and they don't say what you seem to think they say.

[Paul C. Anagnostopoulos]

You still haven’t shown a two order of magnitude decrease in the generations of convergence...
Really?

genome size 1024
sites 16
widths 5/6
1 mu / genome

Population, Generations

4, 64697
8, 34337
16, 19531
32, 16994
64, 13491
128, 5202
256, 5724
512, 3900
1024, 2700
2048, 1800
4096, 1770
8192, 1641
16384, 1253
23100, 1275
32768, 1288
46200, 1709
65536, 922
92680, 718
110000, 776
262000, 702
524000, 642
1048000, 438


~~ Paul

[kjkent1]

You realize, of course, that until you modify ev to evolve the genome of some known living organism within the time that said organism would be reasonably estimated to have evolved in, that kleinman will simply waive you off as having failed to prove your theory.

Meanwhile, kleinman will never do any affirmative modification to the software, himself, because he might just defeat his entire belief system.

So, it's really up to you, and your fellow researchers, to work out models for the other various selection methods, until you have an ev version that reproduces a living organism. Immediately thereafter, kleinman, or someone like him, will declare this not good enough and demand that you produce a giraffe.

Cest' la vie!

[articulett]

Yahzi, it's pretty obvious that you simply misunderstood some of John's posts. I looked at the ones you linked to in your earlier post and they don't say what you seem to think they say.

Can you be more specific. While I agree that John Hewitt doesn't see how the cereal example shows that order can come by purely natural processes, I think Yahtzi was correct in his understanding of what John said and how he's dodged defining living objects from non-living. There are man things in between...just like there are many microevolutionary changes that account for macroevolution (speciation); it's not a single "event". There is no single generation when a tiger became a tiger and a lion became a lion--just a continual divergence from a common ancestor one through a series of small changes (of which point mutation is only one.) Granted, John is no Kleinmann (and it would be interesting to hear them debate with eachother)--but, like Kleinman, he has a belief that order cannot arise by purely natural means--and because he believes this (or can't recognize evidence which shows that it can and does) he posits a "supernatural" explanation (god) must have had a hand in the formation of life.

[Yahzi]

Yahzi, it's pretty obvious that you simply misunderstood some of John's posts. I looked at the ones you linked to in your earlier post and they don't say what you seem to think they say.
This certainly could be possible; I have confused Klienman and Hewitt at least once before, so I am prepared to learn I have done it again.

Thus, could you please be more specific? Didn't Hewitt assert that evolutionists claim ribozymes arose through "chance?" Didn't I point out that granola shows that order can arise from simple mechanics, and didn't he respond to that by saying there was a difference between living and dead?

What part of this did I get confused on?

[dv82matt]

Can you be more specific. While I agree that John Hewitt doesn't see how the cereal example shows that order can come by purely natural processes, I think Yahtzi was correct in his understanding of what John saidWell if you look at John's initial post http://forums.randi.org/showthread.php?p=2182801#post2182801 he says,
And, just by CHANCE, this self-propagating chemistry (the details of which I look forward to reading) happens to produce a ribozyme, a piece of RNA which has the amazing property of being able to copy itself, from precursors that had the equally amazing properties of being present in the first place and of not diffusing off into the prebiotic soup.
He is arguing against chance as being a mechanism behind the genesis of genes.

Yahzi responded with this:
I know that evolution doesn't happen by chance. I learned this from granola.
This misses the point since John was speaking in context of abiogenesis rather than evolution proper. And in any case John was arguing against chance.

Yahzi continues:
Shake a box of granola gently, and what happens? The the little flakes sink to the bottom, and the big pieces float to the top where you can eat them by hand. Some time ago I noticed this sorting effect happens every single time. And, not being scientifically illiterate, I realized it wasn't because of chance.
Yahzi seems to be trying to make the point that order arising spontaneously from non-order is not dependent on chance. Which is fine, but it actually puts him in agreement with John on this point.
and how he's dodged defining living objects from non-living.
Well he initially spoke of biological complexity and inanimate order. It was Yahzi who brought up live and dead. But the respective concepts are not synonomous.
There are man things in between...just like there are many microevolutionary changes that account for macroevolution (speciation); it's not a single "event". There is no single generation when a tiger became a tiger and a lion became a lion--just a continual divergence from a common ancestor one through a series of small changes (of which point mutation is only one.)
I agree. Is this something John disagrees with? I have not gotten that impression.
Granted, John is no Kleinmann (and it would be interesting to hear them debate with eachother)--but, like Kleinman, he has a belief that order cannot arise by purely natural means--and because he believes this (or can't recognize evidence which shows that it can and does) he posits a "supernatural" explanation (god) must have had a hand in the formation of life.Hmmm... fair enough. I suppose there's a bit of history here that I am not aware of.

[dv82matt]

This certainly could be possible; I have confused Klienman and Hewitt at least once before, so I am prepared to learn I have done it again.

Thus, could you please be more specific? Didn't Hewitt assert that evolutionists claim ribozymes arose through "chance?"Hewitt experessed incredulity that ribozymes could arise by chance.
Didn't I point out that granola shows that order can arise from simple mechanics,Indeed you did. I question the relevance of the analogy.
and didn't he respond to that by saying there was a difference between living and dead?Not exactly. He said there was a difference between biological complexity and inanimate order.

[John Hewitt]

Hewitt experessed incredulity that ribozymes could arise by chance.
Indeed you did. I question the relevance of the analogy.
Not exactly. He said there was a difference between biological complexity and inanimate order.

Thank you dv82matt, you said those things very well.

[kleinman]

Paul, I’ve been doing a little thinking about your concept of Rcapacity and why it prevents ev from converging. It seems that when you increase the genome length in ev, it requires more than a proportional increase in the generations for convergence when all other parameters are held constant. When you increase the genome length sufficiently such that Rfrequency exceeds Rcapacity, ev behaves as if you turned off selection. I don’t believe that increasing genome length prevents the weight matrix from identifying a binding site. What I believe is happening is that as you increase the length of the genome, mistakes in the non-binding site region of the genome have increasing influence on the selection process. When the non-binding site region is made large enough, mistakes in this portion of the genome dominate the selection process preventing binding sites from evolving in the binding site portion of the genome.

If there were no truth in my arguments, this thread would have died long ago. Your narcissism is in full display there. Truth is not a prerequisite for argumentative staying power. In case you haven't noticed, the law of Internet forums is the last person who posts wins, so a thread can go on forever with no truth on either side.
That sounds really boring.
I don’t have a definition for the difference between macro and microevolution that will give you a warm, tingly feeling.What an obnoxious remark. I'm not looking for a warm, tingly, feeling there. I'm looking for a rigorous definition we can apply mathematics to. Your admission reveals why you feel you can deny moving goal posts. You use fuzzy goal posts so you can deny they move. Not specifying exactly where your goal posts reside allows you to dismiss new evidence of macro evolution by claiming it missed goals you only vaguely defined. Nice try.
You evolutionarians are the ones who say that science explains everything.
If there were no truth in my arguments, this thread would have died long ago. Your narcissism is in full display there. Truth is not a prerequisite for argumentative staying power. In case you haven't noticed, the law of Internet forums is the last person who posts wins, so a thread can go on forever with no truth on either side.You know, I've heard this claim before. The Light created Life (http://forums.randi.org/showthread.php?t=63587) thread is close to twice the size of this thread and still going strong it seems. As long as the thread doesn't die, Kleinman (and LCL) must be on to something.... right?
Less_than_three, do you mind if I use your logic to describe Darwinism and the theory of evolution?
I added the bold face in the quote. Running the numbers in ev appears to be showing that large populations do not give that much of an advantage in increasing the rate of evolution (when being driven by random point mutations and natural selection).Where "large" is defined as 1 million or less and "not give that much of an advantage" is entirely undefined.
This is why I think that larger populations have to be run in ev.
You still haven’t shown a two order of magnitude decrease in the generations of convergence... Really?

genome size 1024
sites 16
widths 5/6
1 mu / genome

Population, Generations

4, 64697
8, 34337
16, 19531
32, 16994
64, 13491
128, 5202
256, 5724
512, 3900
1024, 2700
2048, 1800
4096, 1770
8192, 1641
16384, 1253
23100, 1275
32768, 1288
46200, 1709
65536, 922
92680, 718
110000, 776
262000, 702
524000, 642
1048000, 438
Why didn’t you include the population=2 case in that series? That case doesn’t converge at all. From a population of 10^1 to a population of 10^6 you still don’t get a 10^2 drop in the generations for convergence and most of that drop in the generations for convergence occurs with the first 10^5 population. You are really struggling to make a point.
You realize, of course, that until you modify ev to evolve the genome of some known living organism within the time that said organism would be reasonably estimated to have evolved in, that kleinman will simply waive you off as having failed to prove your theory.

Meanwhile, kleinman will never do any affirmative modification to the software, himself, because he might just defeat his entire belief system.

So, it's really up to you, and your fellow researchers, to work out models for the other various selection methods, until you have an ev version that reproduces a living organism. Immediately thereafter, kleinman, or someone like him, will declare this not good enough and demand that you produce a giraffe.
Kjkent1, you do not understand this debate. As I have written numerous times in this thread previously, the only reason I get traction in this discussion is that I am using an evolutionarian written, peer reviewed and published model of random point mutations and natural selection.

Evolutionarians have questioned the results I have obtained with their own sanctioned model. Why would evolutionarians believe any modification I do to their model? If I thought there was a selection method or mechanism for mutation other than random point mutations that would make your theory work, I would tell you, but I don’t believe there are any such selection methods or mechanisms for mutation that would overcome this mathematical hurdle.

I encourage evolutionarians to include other selection methods and mechanisms of mutations to their mathematical models, so that they convince themselves of the mathematical impossibility of their theory.

[I less than three logic]

Less_than_three, do you mind if I use your logic to describe Darwinism and the theory of evolution?
I suppose that depends on how you'd like to use it. If you can find any one that makes the claim that evolution is true for no other reason than people are still talking about it, then by all means use it. However, I suspect that you're only interested in it because you've already completed the design phase and are all ready to begin construction of your straw man.

[kleinman]

Less_than_three, do you mind if I use your logic to describe Darwinism and the theory of evolution?I suppose that depends on how you'd like to use it. If you can find any one that makes the claim that evolution is true for no other reason than people are still talking about it, then by all means use it. However, I suspect that you're only interested in it because you've already completed the design phase and are all ready to begin construction of your straw man.
Dr Schneider said the following on his ev blog web site located at http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html)
I went to Pubmed Central (http://www.pubmedcentral.nih.gov/) and searched for 'evolution'. I found 19250 papers all of which you can read!
It looks like Dr Schneider is arguing that evolution is true since so many people are talking about it. I set up no straw man on this forum. I took an evolutionarian written, peer reviewed and published model of random point mutation and natural selection and post the data that shows how slow this process is when realistic parameters are used in the program. Run the program yourself and see whether what I say is true or not. What has happened is exactly as I told Dr Schneider months ago which was evolutionarians would question the validity of the ev model.

The theory of evolution started without a mathematical basis and remains that way.

[Paul C. Anagnostopoulos]

Paul, I’ve been doing a little thinking about your concept of Rcapacity and why it prevents ev from converging. It seems that when you increase the genome length in ev, it requires more than a proportional increase in the generations for convergence when all other parameters are held constant. When you increase the genome length sufficiently such that Rfrequency exceeds Rcapacity, ev behaves as if you turned off selection. I don’t believe that increasing genome length prevents the weight matrix from identifying a binding site. What I believe is happening is that as you increase the length of the genome, mistakes in the non-binding site region of the genome have increasing influence on the selection process. When the non-binding site region is made large enough, mistakes in this portion of the genome dominate the selection process preventing binding sites from evolving in the binding site portion of the genome.
What evolves is a code or tag that identifies binding sites while not appearing anywhere else on the chromosome. This code is pictured in the sequence logo and consists of Rsequence bits of information. You'll notice that the total number of bits in the sequence logo equals Rsequence.

If Rcapacity < Rfrequency, then there are not enough bases in the binding sites to contain a code unique to the sites (more or less). Another way to think of it is that the threshold can't get high enough to exclude sufficient combinations of bases, so that a distinction between binding sites and other sites is impossible.

So your last two sentences are somewhat accurate. However, if you watch a simulation of this situation, you will see the best creature quickly has exactly 16 mistakes, a high age (I'm looking at a mean age of 1,920 right now), but just can't get anywhere. I wouldn't say that non-binding mistakes dominate. I'd say that the weight matrix just can't discriminate.

~~ Paul

[kleinman]

Paul, I’ve been doing a little thinking about your concept of Rcapacity and why it prevents ev from converging. It seems that when you increase the genome length in ev, it requires more than a proportional increase in the generations for convergence when all other parameters are held constant. When you increase the genome length sufficiently such that Rfrequency exceeds Rcapacity, ev behaves as if you turned off selection. I don’t believe that increasing genome length prevents the weight matrix from identifying a binding site. What I believe is happening is that as you increase the length of the genome, mistakes in the non-binding site region of the genome have increasing influence on the selection process. When the non-binding site region is made large enough, mistakes in this portion of the genome dominate the selection process preventing binding sites from evolving in the binding site portion of the genome.What evolves is a code or tag that identifies binding sites while not appearing anywhere else on the chromosome. This code is pictured in the sequence logo and consists of Rsequence bits of information. You'll notice that the total number of bits in the sequence logo equals Rsequence.

If Rcapacity < Rfrequency, then there are not enough bases in the binding sites to contain a code unique to the sites (more or less). Another way to think of it is that the threshold can't get high enough to exclude sufficient combinations of bases, so that a distinction between binding sites and other sites is impossible.

So your last two sentences are somewhat accurate. However, if you watch a simulation of this situation, you will see the best creature quickly has exactly 16 mistakes, a high age (I'm looking at a mean age of 1,920 right now), but just can't get anywhere. I wouldn't say that non-binding mistakes dominate. I'd say that the weight matrix just can't discriminate.
What is it about a genome length that prevents the weight matrix from identifying (discriminating) a binding site? If you use a mutation rate that is fixed to a specific number of bases, the only thing that changes in the model is the number of mistakes which can occur on the non-binding site region of the genome. If it is the mistakes in the non-binding site region that is driving selection, this would explain why the binding site region is not evolving. You can easily check this out by keeping track of mistakes in both the binding site region and non-binding site region and counting which mistakes are driving the selection process.

[I less than three logic]

Dr Schneider said the following on his ev blog web site located at http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html)

It looks like Dr Schneider is arguing that evolution is true since so many people are talking about it. I set up no straw man on this forum. I took an evolutionarian written, peer reviewed and published model of random point mutation and natural selection and post the data that shows how slow this process is when realistic parameters are used in the program. Run the program yourself and see whether what I say is true or not. What has happened is exactly as I told Dr Schneider months ago which was evolutionarians would question the validity of the ev model.

The theory of evolution started without a mathematical basis and remains that way.
You haven't set up any straw men? Not even the one in this post here? On that page you linked to, Dr. Schneider does appear to use a fallacious appeal to popularity, claiming people should believe him because of how many papers on evolution exist, but no where, not even your quoted text, does he claim that evolution is true for no other reason than people are talking about it. Your arguing against a position that doesn't appear to exist in order to claim your easy victory, that is a straw man whether you think so or not.

[Paul C. Anagnostopoulos]

Why didn’t you include the population=2 case in that series? That case doesn’t converge at all. From a population of 10^1 to a population of 10^6 you still don’t get a 10^2 drop in the generations for convergence and most of that drop in the generations for convergence occurs with the first 10^5 population. You are really struggling to make a point.
Oh, I have to get a factor of 100 drop beginning with a population of 10. I did not know that was a requirement.

Does this count?

genome size 1024
sites 8
width 9/10 (Rcapacity 20)
1 mutation / 512 bases

population, generations

10, 24000
32, 9900
64, 5000
128, 3000
256, 4600
512, 1600
2048, 1600
65536, 175


~~ Paul

[Paul C. Anagnostopoulos]

What is it about a genome length that prevents the weight matrix from identifying (discriminating) a binding site? If you use a mutation rate that is fixed to a specific number of bases, the only thing that changes in the model is the number of mistakes which can occur on the non-binding site region of the genome. If it is the mistakes in the non-binding site region that is driving selection, this would explain why the binding site region is not evolving. You can easily check this out by keeping track of mistakes in both the binding site region and non-binding site region and counting which mistakes are driving the selection process.
The other thing that changes is that the binding site weightings cannot exceed the threshold.

~~ Paul

[kleinman]

You haven't set up any straw men? Not even the one in this post here?
You evolutionarians need a new play book. If the only argument you can make is this silly straw man argument, you don’t make much of a case. At least Paul is trying to make a mathematical case with ev, weak as it is.
Why didn’t you include the population=2 case in that series? That case doesn’t converge at all. From a population of 10^1 to a population of 10^6 you still don’t get a 10^2 drop in the generations for convergence and most of that drop in the generations for convergence occurs with the first 10^5 population. You are really struggling to make a point.Oh, I have to get a factor of 100 drop beginning with a population of 10. I did not know that was a requirement.

Does this count?

genome size 1024
sites 8
width 9/10 (Rcapacity 20)
1 mutation / 512 bases

population, generations

10, 24000
32, 9900
64, 5000
128, 3000
256, 4600
512, 1600
2048, 1600
65536, 175
Of course that is a requirement; the point of increasing population is to show that you get sufficient reduction in the generations for convergence to support your theory.

You are still struggling to make a point, but perhaps you are finding the right combination of genome length, population, binding site number, binding site width, and mutation rate that may give some support to your theory. Why didn’t you post any points between 2048 and 65536? Why don’t you extend this series to a population of 1 meg and see whether you can get down close to Adequate’s value of 1 generation for an infinite population?

I also note something peculiar in your data. You posted the following series recently:
population 32
binding sites 8
weight width 9
site width 10
1 mutation / 512 bases

genome size, generations

1024, 8000
2048, 20000
4096, 34000
8192, 37000
16384, 76000
32768, 272000
65536, 392000
128000, 991000
In one series you have a generations of convergence of 9900 generations in the first series (the second data point) and 8000 generations for the second series (the first data point) when both cases should give identical results. Are you using identical random seeds?

Your latest un-retracted extrapolation for the evolution of 8 binding sites, population 32, weight width 9, site width 10, 1 mutation / 512 bases would require 2 billion generations to evolve for a mutation rate of 10^-6 and 63 million generations to evolve with a population of 1 meg. Are you going to modify your extrapolation based on your most recent data posted above?

[Yahzi]

He is arguing against chance as being a mechanism behind the genesis of genes.
I know that. That was perfectly clear to anyone following the conversation. Hewitt claimed that evolutionists claim that it was "chance." When I referred to him claiming it was us claiming it was chance, everyone but you understood what I meant.

This misses the point since John was speaking in context of abiogenesis rather than evolution proper. And in any case John was arguing against chance.
And again. Hewitt decided to switch topics in the middle of the conversation, but we all knew exactly what he meant. Except, apparently, you.

Yahzi seems to be trying to make the point that order arising spontaneously from non-order is not dependent on chance. Which is fine, but it actually puts him in agreement with John on this point.
And once again, you state the obvious.

What you seem to be unaware of is that Hewitt disagrees when it comes to living systems.

Well he initially spoke of biological complexity and inanimate order. It was Yahzi who brought up live and dead. But the respective concepts are not synonomous.
What is the difference between biological order and inanimate order?

How would you characterize "living" other than referring to its complex order?

Why am I still arguing against vitalism?

Indeed you did. I question the relevance of the analogy.
The relevance is that biological systems are subject to the same rules as inanimate systems.

Which part of that do you disagree with?

The relevance is that if inanimate systems can generate order from mechanics and energy, then so can animate systems.

Which part of that do you disagree with?

He said there was a difference between biological complexity and inanimate order.
And that difference would be... what, exactly?

Order is order. It doesn't matter whether it is biological or inanimate; the laws of information theory apply to order, regardless of its origin.

Which part of that do you disagree with?

[Yahzi]

Thank you dv82matt, you said those things very well.
No, he didn't.

But I'm glad you found his diversion adequate excuse to avoid answering the question. I'm happy for you.

Now perhaps you would care to explain what your point is. I made the point that order can arise from simplicity in inanimate systems. So why do you think it can't do the same in animate systems?

In other words (for anyone who may have become confused by your misdirection), ribozymes did not arise from chance, and no one - least of all evolutionists - are saying they did. Ribozymes arose from the same process that sorts granola into large and small chunks.

Your position is that this is impossible - that even while you agree with the granola example, you feel it doesn't apply to ribozymes. Because you seem to think there is a difference between granola and "living systems."

What you have not done - or even come close to doing - is explaining what that difference is with respect to order. Obviously there are many differences between animate and inanimate systems. But there are also many similarities. I have asserted that they are similar in the application of information theory. You have asserted they are not. Please explain.

[Paul C. Anagnostopoulos]

Of course that is a requirement; the point of increasing population is to show that you get sufficient reduction in the generations for convergence to support your theory.
What I said was that I didn't know I had to start at a population of 10.


You are still struggling to make a point, but perhaps you are finding the right combination of genome length, population, binding site number, binding site width, and mutation rate that may give some support to your theory. Why didn’t you post any points between 2048 and 65536?
I didn't run those populations yet.


Why don’t you extend this series to a population of 1 meg and see whether you can get down close to Adequate’s value of 1 generation for an infinite population?
1 million should get me "down close" to the theoretical limit at an infinite population? Wow.


In one series you have a generations of convergence of 9900 generations in the first series (the second data point) and 8000 generations for the second series (the first data point) when both cases should give identical results. Are you using identical random seeds?
Yes, I vary the random seed all the time. It's interesting to see the variance when you do.


Your latest un-retracted extrapolation for the evolution of 8 binding sites, population 32, weight width 9, site width 10, 1 mutation / 512 bases would require 2 billion generations to evolve for a mutation rate of 10^-6 and 63 million generations to evolve with a population of 1 meg. Are you going to modify your extrapolation based on your most recent data posted above?
No. Now I'm running experiments with fixed genome sizes and varying populations to see if I can find a pattern.

Please note that I don't give a damn about that extrapolation, because I am not an afficionado of the Theory of Point Mutations and Natural Selection.

~~ Paul

[kleinman]

Of course that is a requirement; the point of increasing population is to show that you get sufficient reduction in the generations for convergence to support your theory.What I said was that I didn't know I had to start at a population of 10.
I had been looking at population trends starting with populations of 64 since that was the baseline population that Dr Schneider used. What minimum population do you want to use when looking at population trends. We can use whatever value you want to use.
Why don’t you extend this series to a population of 1 meg and see whether you can get down close to Adequate’s value of 1 generation for an infinite population?1 million should get me "down close" to the theoretical limit at an infinite population? Wow.
Isn’t that the question? If Adequate is correct in his estimate, how large a population do you need in order approach that estimate?
In one series you have a generations of convergence of 9900 generations in the first series (the second data point) and 8000 generations for the second series (the first data point) when both cases should give identical results. Are you using identical random seeds?Yes, I vary the random seed all the time. It's interesting to see the variance when you do.
We are already dealing with noisy data and varying the random seed introduces more variation into the data. You know that when you post a series like you just did with a peculiar data point that I am going to call you on this issue. You need to start posting the random seed number you are using.
Your latest un-retracted extrapolation for the evolution of 8 binding sites, population 32, weight width 9, site width 10, 1 mutation / 512 bases would require 2 billion generations to evolve for a mutation rate of 10^-6 and 63 million generations to evolve with a population of 1 meg. Are you going to modify your extrapolation based on your most recent data posted above?No. Now I'm running experiments with fixed genome sizes and varying populations to see if I can find a pattern.
Good idea!
Please note that I don't give a damn about that extrapolation, because I am not an afficionado of the Theory of Point Mutations and Natural Selection.
Hey, it’s ok to change your mind. Do you think that random point mutations and natural selection have any role in the theory of evolution?

You all have a Merry Christmas.

[Paul C. Anagnostopoulos]

I had been looking at population trends starting with populations of 64 since that was the baseline population that Dr Schneider used. What minimum population do you want to use when looking at population trends. We can use whatever value you want to use.
It doesn't really matter. The problem with 64 is that we probably can't run large enough populations to see a factor of 100 drop in generations. Then again, I have no idea why a factor of 100 is magical, except possibly to set the goalpost beyond what we can simulate.


Isn’t that the question? If Adequate is correct in his estimate, how large a population do you need in order approach that estimate?
No idea, since his asymptote was for an infinite population.


We are already dealing with noisy data and varying the random seed introduces more variation into the data. You know that when you post a series like you just did with a peculiar data point that I am going to call you on this issue. You need to start posting the random seed number you are using.
Why would you call me on it? Some weeks ago you said you were okay if I used the lowest number of generations I got for any given data point. Lots of my generation counts are the average of three or four runs.


Hey, it’s ok to change your mind. Do you think that random point mutations and natural selection have any role in the theory of evolution?
Are you suggesting that I was once an afficionado of the TPMNS? Cuz, like, if you are, then you're lying. Of course point mutations have a role; consider the latest finding on eye color. Can you distinguish between a supporting role and a one-woman show?

~~ Paul

[hammegk]

Hey, it’s ok to change your mind. Do you think that random point mutations and natural selection have any role in the theory of evolution?
Er, at least as much as does Yahzi shaking his box of corn flakes?


BTW, Yahzi, when something alive crawls out of the box I suspect very very strongly it will be a 'bio-contaminant'. Also, I believe I should advise you "Don't play in traffic!".

[Paul C. Anagnostopoulos]

Just to demonstrate how variable the experiments are, I ran my current experiment 10 times on a population of 128:

generations

5101
2879
2534
2019
4645
1742
3137
2465
3121
4516

Range: 3359
Mean: 3216
Standard deviation: 1157

~~ Paul

[kjkent1]

Kjkent1, you do not understand this debate. As I have written numerous times in this thread previously, the only reason I get traction in this discussion is that I am using an evolutionarian written, peer reviewed and published model of random point mutations and natural selection.

Evolutionarians have questioned the results I have obtained with their own sanctioned model. Why would evolutionarians believe any modification I do to their model? If I thought there was a selection method or mechanism for mutation other than random point mutations that would make your theory work, I would tell you, but I don’t believe there are any such selection methods or mechanisms for mutation that would overcome this mathematical hurdle.

I encourage evolutionarians to include other selection methods and mechanisms of mutations to their mathematical models, so that they convince themselves of the mathematical impossibility of their theory.

LOL! I tell Paul that you won't do any of the work, and that you will waive off any possible explanation which might defeat your belief system, and how do you respond? Why, by confirming that you won't do any work, and by waiving me off by telling me that I don't understand the debate.

The debate, which you claim I do not understand, is trivially simple, and it will continue, unabated, as long as humans exist in their present form. I.E., (1) a creator has existed eternally and has designed the universe to function in a specified manner, such that human life now exists, (2) matter contained in the universe is naturally capable of self organization, such that human life now exists, or (3) some combination of #1 and/or #2.

At the more mundane level, if you want to soundly defeat the theory that no accurate selection model will improve ev's performance, and you consider yourself to be a scientist, then you should put aside your preconceptions/beliefs, and conduct some research, by modeling selection mechanisms inside of ev and presenting your findings for peer-reviewed publication.

You're obviously a very capable scientist, and you should be able to aid in speeding up the research process. The fact that you refuse to undertake the investigation clearly demonstrates that you view the risk of your discovering that your belief is in error, as insufficient to outweigh the benefit obtained by successfully modeling the evolutionary selection mechanism.

It's certainly easier to believe that evolution is mathematically impossible. However, as you've pointed out yourself in this thread, doing real science is hard work.

[kleinman]

Kjkent1, you do not understand this debate. As I have written numerous times in this thread previously, the only reason I get traction in this discussion is that I am using an evolutionarian written, peer reviewed and published model of random point mutations and natural selection.

Evolutionarians have questioned the results I have obtained with their own sanctioned model. Why would evolutionarians believe any modification I do to their model? If I thought there was a selection method or mechanism for mutation other than random point mutations that would make your theory work, I would tell you, but I don’t believe there are any such selection methods or mechanisms for mutation that would overcome this mathematical hurdle.

I encourage evolutionarians to include other selection methods and mechanisms of mutations to their mathematical models, so that they convince themselves of the mathematical impossibility of their theory.LOL! I tell Paul that you won't do any of the work, and that you will waive off any possible explanation which might defeat your belief system, and how do you respond? Why, by confirming that you won't do any work, and by waiving me off by telling me that I don't understand the debate.
You won’t even read these threads, let alone Dr Schneider’s web pages and publications on ev. Why should I take anything you say seriously?
The debate, which you claim I do not understand, is trivially simple, and it will continue, unabated, as long as humans exist in their present form. I.E., (1) a creator has existed eternally and has designed the universe to function in a specified manner, such that human life now exists, (2) matter contained in the universe is naturally capable of self organization, such that human life now exists, or (3) some combination of #1 and/or #2.
Too bad #2 has no mathematical basis.
At the more mundane level, if you want to soundly defeat the theory that no accurate selection model will improve ev's performance, and you consider yourself to be a scientist, then you should put aside your preconceptions/beliefs, and conduct some research, by modeling selection mechanisms inside of ev and presenting your findings for peer-reviewed publication.
Here is where your lack of understanding of ev is revealing itself. Dr Schneider has devised a selection mechanism that is very precise and stringent. It works very rapidly on small genomes with large mutation rates. The only way I can see devising a selection mechanism that works more rapidly than this is that every mutation is selected for or against on a mutation by mutation basis. Dr Schneider’s weight matrix is already very close to this and it still becomes profoundly slow when you apply this process to a realistic length genome. Don’t you think Dr Schneider, Paul or Myriad would redefine the selection process if they could? The reason they don’t is there is no known selection mechanism that could speed up the evolutionary process. This is an accounting problem and I know of no accounting rules that fix this mathematical fact that contradicts the theory of evolution.
You're obviously a very capable scientist, and you should be able to aid in speeding up the research process. The fact that you refuse to undertake the investigation clearly demonstrates that you view the risk of your discovering that your belief is in error, as insufficient to outweigh the benefit obtained by successfully modeling the evolutionary selection mechanism.
I know of no way to speed up the research process. The only parameter in ev that has even the slightest possibility of giving results that support the theory of evolution is huge populations. Running these types of cases requires hardware with much larger memory and processor speeds than our desktop machines have and I doubt your marketing people would want to get involved in such a controversial issue.
It's certainly easier to believe that evolution is mathematically impossible. However, as you've pointed out yourself in this thread, doing real science is hard work.
About 25-30 years ago there was an attempt to screen women for breast cancer by using thermography. The problem with this screening test was there were 50% false positives. I looked at the thermodynamics of this problem for my PhD. Once you did the mathematics for this situation, it became clear why there were so many false positives. I could see no way to overcome the physics and mathematics of this situation. The mathematics of the theory of evolution is presenting itself in the same way. There are no known selection processes or mutation mechanisms that would allow you to evolve a megabase genome in the time available, let alone a gigabase genome. This is a mathematical fact of life.

[Paul C. Anagnostopoulos]

There are no known selection processes or mutation mechanisms that would allow you to evolve a megabase genome in the time available, let alone a gigabase genome. This is a mathematical fact of life.
Whiplash! Now we're back to the mathematical proof that you refuse to present.

~~ Paul

[kjkent1]

There are no known selection processes or mutation mechanisms that would allow you to evolve a megabase genome in the time available, let alone a gigabase genome. This is a mathematical fact of life.

And yet, we are here, either as an amazing mathematical fact of nature, which has yet to be completely understood, or as the result of the application of the magical will of an all powerful entity who is definitionally beyond the limits of any possible mathematical proof.

Since proof of the latter is impossible, the only alternative is to research the former. Otherwise, all of your scientific skills are wasted. I doubt that God would have granted you such mental capacity for the purpose of not using it.

[kleinman]

I had been looking at population trends starting with populations of 64 since that was the baseline population that Dr Schneider used. What minimum population do you want to use when looking at population trends. We can use whatever value you want to use.It doesn't really matter. The problem with 64 is that we probably can't run large enough populations to see a factor of 100 drop in generations. Then again, I have no idea why a factor of 100 is magical, except possibly to set the goalpost beyond what we can simulate.
There is nothing magical about the factor of 100. You need a greater reduction in the generations for convergence than this for creatures with large genomes and generation times measured in years for random point mutations and natural selection to contribute to the evolutionary process. I think the only unsettled question about ev is whether populations of 10^28 will speed up the evolutionary process sufficiently for a 1 meg genome.
Isn’t that the question? If Adequate is correct in his estimate, how large a population do you need in order approach that estimate?No idea, since his asymptote was for an infinite population.
A population of 1,000,000 doesn’t get you there with a 1k genome. Do you think it will get better with larger genomes?
We are already dealing with noisy data and varying the random seed introduces more variation into the data. You know that when you post a series like you just did with a peculiar data point that I am going to call you on this issue. You need to start posting the random seed number you are using.Why would you call me on it? Some weeks ago you said you were okay if I used the lowest number of generations I got for any given data point. Lots of my generation counts are the average of three or four runs.
As long as you are consistent with your data collection I have no problem with this. However you ran the same case in two different series with two different random seeds. This can obscure the trends.
Hey, it’s ok to change your mind. Do you think that random point mutations and natural selection have any role in the theory of evolution?Are you suggesting that I was once an afficionado of the TPMNS? Cuz, like, if you are, then you're lying. Of course point mutations have a role; consider the latest finding on eye color. Can you distinguish between a supporting role and a one-woman show?
I have no idea what your view toward ev is or was. You have back peddled so much on this topic since it has started, I don’t even know if you believe that random point mutation and natural selection contributes to macroevolution at all unless you consider a single point mutation affecting eye color as a macroevolutionary process. Maybe you would like to explain the selection process that would select for that mutation that effects eye color.
Just to demonstrate how variable the experiments are, I ran my current experiment 10 times on a population of 128:

generations

5101
2879
2534
2019
4645
1742
3137
2465
3121
4516

Range: 3359
Mean: 3216
Standard deviation: 1157
How do you want to address this issue so that we can get data that we can agree on?
There are no known selection processes or mutation mechanisms that would allow you to evolve a megabase genome in the time available, let alone a gigabase genome. This is a mathematical fact of life.Whiplash! Now we're back to the mathematical proof that you refuse to present.
Feel free to prove my statement wrong. If you know of a selection process or mutation mechanism that proves your theory, present it. The results from Dr Schneider’s model using realistic genome lengths and mutation rates are my mathematical proof. I do appreciate you writing the java version of ev. It made it so much easier to come up to speed on this problem.

[John Hewitt]

No, he didn't.

But I'm glad you found his diversion adequate excuse to avoid answering the question. I'm happy for you.

Now perhaps you would care to explain what your point is. I made the point that order can arise from simplicity in inanimate systems. So why do you think it can't do the same in animate systems?

In other words (for anyone who may have become confused by your misdirection), ribozymes did not arise from chance, and no one - least of all evolutionists - are saying they did. Ribozymes arose from the same process that sorts granola into large and small chunks.

Your position is that this is impossible - that even while you agree with the granola example, you feel it doesn't apply to ribozymes. Because you seem to think there is a difference between granola and "living systems."

What you have not done - or even come close to doing - is explaining what that difference is with respect to order. Obviously there are many differences between animate and inanimate systems. But there are also many similarities. I have asserted that they are similar in the application of information theory. You have asserted they are not. Please explain.

I do accept that order can arise from physical processes but, in my view and I believe of most people, living things are not ordered in the same way that order exists in crytals or in the layering that arises from differential sedimentation in breakfast cereals. Such arrangements, that arise from physical processes, have about the them a simplicity which is not present in living things. Living things are complex and, on casual inspection, might even appear disordered, though that is an illusion. The debate on this thread has, to a large extent, concerned how the complexity of living things might have arisen.

It has been suggested by some observers that some self-replicating ribozyme, made from RNA or from some similar, precursor material. My point about such ribozymes is that they too would be complex and would be very unlikely to arise by chance. Some observers, Crick for example, calculate that such an entity could not arise within the lifetime of the universe. Even if it did arise by chance, it would not be adapted to survive within the primordial soup and would not have supplies of the activated precursors needed to make copies of itself. Hence my dismissal of such ideas.

For the same reason, I do not think that any self-replicating entity would arise as a result of your shaking your corn-flake packet.

I short animate and inanimate objects are different. There difference in respect of information theory is probably best given by the people who try to define the term "complexity." I would not claim to be an expert on this matter, Paul could undoubtedly give a better explanation, but the essence of the argument is that the data pattern that describes an ordered structure is highly compressible. Thus, for example, if you wished to describe the structure of a crytal of salt, you could describe the position of every atom of sodium and chlorine in the crystal lattice, which would be a very large data file, or you could describe one unit cell and then indicate the number of repeats in each axis needed to describe the whole crystal. This would be a very much smaller data file. The same would apply to you breakfast cereal.

So, the data files needed to describe inanimate structures can be compressed. By comparison, the data files needed to describe complex structurees, such as living things cannot be compressed nearly so easily. Hence, in respect of this aspect of information theory, animate and inanimate things are different.

[dv82matt]

I know that. That was perfectly clear to anyone following the conversation. Hewitt claimed that evolutionists claim that it was "chance."
This is somewhat tortured. If you were taking issue with a claim about a claim that evolutionists make about abiogenesis then at the very least it seems you failed to make your point. In any case there is this:

John: I have never asserted that the precursors to genes were created by chance. Just the reverse, I have asserted that the chance creation of genes from a primordial soup is infeasible and deplored this widespread assertion.
Yahzi: I'm sorry, but it's not worth my time anymore to link to the posts where you contradict yourself.

If you wish to move the goalposts do so explicitly.

When I referred to him claiming it was us claiming it was chance, everyone but you understood what I meant.:rolleyes:
And again. Hewitt decided to switch topics in the middle of the conversation,
That is your own speculation. It is not born out by the evidence.
...but we all knew exactly what he meant. Except, apparently, you.Do you have evidence to support this appeal to popularity?
And once again, you state the obvious.
Indeed, I am glad that you agree that I have correctly summarized your analogy.
What you seem to be unaware of is that Hewitt disagrees when it comes to living systems.
It's just not particularily relevant. You are conflating complexity and order. Your analogy is only applicable to order. You may as well have pointed out that gravity applies to living systems.
What is the difference between biological order and inanimate order?Don't arbitrarily switch out words like that. It appears dishonest. It's biological complexity and inanimate order.
How would you characterize "living" other than referring to its complex order?There are many ways to characterize "living". And biological complexity does not nessessarily mean life.
Why am I still arguing against vitalism?
Perhaps because you misinterpreted John's posts as being an argument in favor of vitalism.
The relevance is that biological systems are subject to the same rules as inanimate systems.

Which part of that do you disagree with?

The relevance is that if inanimate systems can generate order from mechanics and energy, then so can animate systems.

Which part of that do you disagree with?
No one has disagreed with this (except for the part about it being relevant). You are essentially arguing against your own misconceptions about what others believe.
He said there was a difference between biological complexity and inanimate order.
And that difference would be... what, exactly?
The words complexity and order, self-replication there may be more.
Order is order. It doesn't matter whether it is biological or inanimate; the laws of information theory apply to order, regardless of its origin.

Which part of that do you disagree with?I don't disagree. The essential point you have been missing is that order and complexity are not synonomous.

[Yahzi]

You are essentially arguing against your own misconceptions about what others believe.
Did you read Hewitt's response to me?

You know, the part where he explicitly states:

I[n] short animate and inanimate objects are different
From this we can conclude that Hewitt is arguing that order in inanimate things is different than order in animate things. We can conclude this because it is exactly what he says.

My entire argument has been that he is making a distinction between order in inaminate things and order in animate things.

The essential point you have been missing is that order and complexity are not synonomous.
From the above quote of Hewitt's, it would appear that the essential point you have been missing is that Hewitt is arguing that order in inaminate things is different than order in animate things.

I am sorry that you are no more equipped to understand Hewitt's posts than you are mine, but unless you can demonstrate you actually know what either of us is talking about, I'm going to stop reading your posts.

[Yahzi]

I do accept that order can arise from physical processes but, in my view and I believe of most people, living things are not ordered in the same way that order exists in crytals or in the layering that arises from differential sedimentation in breakfast cereals.
Order is order. Period. There is not a special kind of order for living things, or complex things. It's just more of the same.

The debate on this thread has, to a large extent, concerned how the complexity of living things might have arisen.
And I have conclusively shown that order can arise from simple mechanics and energy.

You have agreed with this, but argued that a lot of order cannot arise in this way. You have offered no reason why the ability to stack order on order suddenly breaks down; no evidence that simple mechanics cannot - with appropriate selective mechanisms - continue to accrue order.

You have simply stated that you personally find it unbeleivable that a lot of order can arise from simple beginnings, even while you freely admit that some order can.

My point about such ribozymes is that they too would be complex and would be very unlikely to arise by chance.
Who said they arose from chance?

When did anyone, anywhere, ever say they arose from chance?

Why do you keep bringing up chance?

The granola did not sort itself by chance. Ribozymes did not arise by chance. Why do you keep bringing up the word chance? It has no place in this conversation, ever. Period.

For the same reason, I do not think that any self-replicating entity would arise as a result of your shaking your corn-flake packet.
But my granola-shaking example is not an example of chance.

You have dismissed "ribozymes arising from chance" by dismissing "order arising through mechanics." How, exactly, does that work?

I short animate and inanimate objects are different. There difference in respect of information theory is probably best given by the people who try to define the term "complexity." I would not claim to be an expert on this matter, Paul could undoubtedly give a better explanation, but the essence of the argument is that the data pattern that describes an ordered structure is highly compressible. Thus, for example, if you wished to describe the structure of a crytal of salt, you could describe the position of every atom of sodium and chlorine in the crystal lattice, which would be a very large data file, or you could describe one unit cell and then indicate the number of repeats in each axis needed to describe the whole crystal. This would be a very much smaller data file. The same would apply to you breakfast cereal.
The fact that you can compress simple order into a simple package does not make it non-order. As for an example of supremely complex order that can be reduced to a simple equation: Fractals (http://math.rice.edu/~lanius/frac/)

We can - theoretically - reduce almost any complex system to a relatively short fractal equation.

So, the data files needed to describe inanimate structures can be compressed. By comparison, the data files needed to describe complex structurees, such as living things cannot be compressed nearly so easily. Hence, in respect of this aspect of information theory, animate and inanimate things are different.
Your argument is: "compressing simple systems is easier than compressing complex systems. Therefore, simple systems can evolve from mechanics, but complex ones can't."

What has compression got to do how they arise? Why do you assume there is some magic cut-off level of compressibility, which on one side you can arise from simple mechanics and on the other you can't? Can you express this compressiblity limit as a number?

You have not shown any essential link between the compressibility of a system and its ability to be generated by simple mechanics and accrual. You have simply asserted such a link. As a professional programmer, I am intimately aware of how simple objects can be combined to produce complex behavours, and I am totally unimpressed with your assertion.

[John Hewitt]

I have conclusively shown that order can arise from simple mechanics and energy.
You have agreed with this, but argued that a lot of order cannot arise in this way. You have offered no reason why the ability to stack order on order suddenly breaks down; no evidence that simple mechanics cannot - with appropriate selective mechanisms - continue to accrue order.

You have simply stated that you personally find it unbeleivable that a lot of order can arise from simple beginnings, even while you freely admit that some order can.

I have stated previously that the informational difference between animate and inanimate is not order, it is complexity.


Who said they arose from chance?

When did anyone, anywhere, ever say they arose from chance?
Dawkins, in the Selfish gene. This proposal is quite widely considered.


Why do you keep bringing up chance?

The granola did not sort itself by chance. Ribozymes did not arise by chance. Why do you keep bringing up the word chance? It has no place in this conversation, ever. Period.
Read Chance and necessity, by Monod


We can - theoretically - reduce almost any complex system to a relatively short fractal equation.

Your argument is: "compressing simple systems is easier than compressing complex systems. Therefore, simple systems can evolve from mechanics, but complex ones can't."No you can't reduce complex systems to fractals in that way. When I talked about compression, I was talking about data compression, not about compressing physical objects. The compressibility of the data file needed to describe a system is one way of assessing the complexity of that system. I am not sufficiently au fait with this topic to go into details. You will have to ask someone else for that.

I would add that dv82matt seems to me a thoughtful and intelligent person. You should consider his comments carefully.

[articulett]

And you should consider Yahtzi's comments carefully. Dawkins selfish gene is not about chance--mutation might be random--but selection is not...and it's the ratcheting that brings complexity. Earth is complex--but we can deduce much about how it came to be and natural forces explain it very well--some even liken the earth itself to a living organism. And life, too, is a ratcheting...change occurs through regular physical processes (like water forming crystal structure when it freezes...like ionic bonds...like granola sorting)--and some of these changes have a selective advantage over others
So, no matter how you define life--even if you say it's "x" degree of complexity or "order" or has these qualities--there is something that you think is life that won't fit in your category and something that you think isn't life that will. If you give examples of what you think is necessary for something to be alive, I'd be glad to show you the in between things (I've listed some before)--so which of those things are alive and which are not? At what point does a ribosomic molecule become life? If it participates in life--does it stop being alive when it's no longer in a living organism? There just isn't the clear cut difference between life and non-life that you imagine. There are things that could fall in either category depending on your definition. A body can be dead yet the insects and larva and bacteria and fungi on it can be alive. Living sperm can be on a dead body. Embryos can be frozen and after some time the slowly lose their ability to become someone. Are they dead? Alive?
And at what point are they alive and at what point are they dead. Are viruses alive?--prions?--if life evolved from viruses http://www.discover.com/issues/mar-06/cover/ at what point would you consider them alive? Are mitochondria alive? Yeast? Fungi spores? Pollen? Are people kept alive by artificial means alive? Spermatazoa? Babies with anencephaly? parasitic twins? There is no clear dividing line between life and death--not even on the complexity scale. Some viruses are bigger and more complex than simple bacteria. What Yatzi is saying is that there is no line or definition that divides life and non life in any simple way. Life is an emerging process--just like consciousness--just like speciation--a continuum. There are many things that don't necessarily fall neatly into the category "alive" or "not alive". And the complexity of such things varies.

[Paul C. Anagnostopoulos]

I think the only unsettled question about ev is whether populations of 10^28 will speed up the evolutionary process sufficiently for a 1 meg genome.
Using only point mutations? Who knows? Who gives a crap?

A population of 1,000,000 doesn’t get you there with a 1k genome. Do you think it will get better with larger genomes?
Huh?

I have no idea what your view toward ev is or was. You have back peddled so much on this topic since it has started, I don’t even know if you believe that random point mutation and natural selection contributes to macroevolution at all unless you consider a single point mutation affecting eye color as a macroevolutionary process.
I haven't backpeddled at all. Never did I state that we were dealing with the Theory of Point Mutation and Natural Selection. I don't know whether point mutation contributes to macroevolution, because you've never defined macroevolution. What difference does it make, exactly? Is there a world somewhere that employs only point mutations?


Feel free to prove my statement wrong.
Not my job, mon.


The results from Dr Schneider’s model using realistic genome lengths and mutation rates are my mathematical proof.
First of all, you have no idea what realistic genome lengths and mutations rates are. Second, you haven't used realistic populations, so your proof is defective. Third, even if this were all true, what have you proven? You've proven that the Kleinman Theory of Point Mutations and Natural Selection is flawed. We know that. We agree.

~~ Paul

[joobz]

I don't get it, Kleinman. You only acknowledge evolution when you care for your patients. You use science and fact in doing so. But, when you look at the overall picture, you claim that it doesn't exist. And you use illogic and lies to do so.

So far, I can say that I respect Kleinman the Dr, but have severe doubts about Kleinman the scientist.

[cyborg]

1) Believe in GOD
2) Abuse mathematics
3) ???
4) Profit!

[articulett]

1) Believe in GOD
2) Abuse mathematics
3) ???
4) Profit!

There may be a Templeton prize in that.

[fishbob]

Originally Posted by kjkent1
The debate, which you claim I do not understand, is trivially simple, and it will continue, unabated, as long as humans exist in their present form. I.E., (1) a creator has existed eternally and has designed the universe to function in a specified manner, such that human life now exists, (2) matter contained in the universe is naturally capable of self organization, such that human life now exists, or (3) some combination of #1 and/or #2.

Too bad #2 has no mathematical basis.

Neither does #1.

[fishbob]

Here is where your lack of understanding of ev is revealing itself. Dr Schneider has devised a selection mechanism that is very precise and stringent. It works very rapidly on small genomes with large mutation rates. The only way I can see devising a selection mechanism that works more rapidly than this is that every mutation is selected for or against on a mutation by mutation basis. Dr Schneider’s weight matrix is already very close to this and it still becomes profoundly slow when you apply this process to a realistic length genome. Don’t you think Dr Schneider, Paul or Myriad would redefine the selection process if they could? The reason they don’t is there is no known selection mechanism that could speed up the evolutionary process. This is an accounting problem and I know of no accounting rules that fix this mathematical fact that contradicts the theory of evolution.

About 25-30 years ago there was an attempt to screen women for breast cancer by using thermography. The problem with this screening test was there were 50% false positives. I looked at the thermodynamics of this problem for my PhD. Once you did the mathematics for this situation, it became clear why there were so many false positives. I could see no way to overcome the physics and mathematics of this situation. The mathematics of the theory of evolution is presenting itself in the same way. There are no known selection processes or mutation mechanisms that would allow you to evolve a megabase genome in the time available, let alone a gigabase genome. This is a mathematical fact of life.

Apparently you drive nails with a screwdriver.
I imagine a collection in your garage of abused tools in broken piles on the workbench. The mathematics of drilling holes with sandpaper is indeed difficult to overcome.

[kleinman]

I think the only unsettled question about ev is whether populations of 10^28 will speed up the evolutionary process sufficiently for a 1 meg genome.Using only point mutations? Who knows? Who gives a crap?
That’s a strange thing for you to say. Just a few short months ago you thought that ev represented the holy grail for the theory of evolution and you even wrote the online version of this model. Now you are professing ignorance and are even indignant that I should raise such a point. Do I detect some annoyance?
A population of 1,000,000 doesn’t get you there with a 1k genome. Do you think it will get better with larger genomes?Huh?
None of the population series we have done show a rapid convergence to Adequate’s proposed value of 1 generation for convergence with an infinite population. Do you think larger genomes will show a more rapid approach to this value of 1 generation? I believe that larger genomes will show lower rates of reduction in the generations for convergence as population is increased.
I have no idea what your view toward ev is or was. You have back peddled so much on this topic since it has started, I don’t even know if you believe that random point mutation and natural selection contributes to macroevolution at all unless you consider a single point mutation affecting eye color as a macroevolutionary process.I haven't backpeddled at all. Never did I state that we were dealing with the Theory of Point Mutation and Natural Selection. I don't know whether point mutation contributes to macroevolution, because you've never defined macroevolution. What difference does it make, exactly? Is there a world somewhere that employs only point mutations?
You are so cute when you squirm.
Feel free to prove my statement wrong.Not my job, mon.
That’s ok; you have already given me more than enough red meat to keep this barbeque going for months.
The results from Dr Schneider’s model using realistic genome lengths and mutation rates are my mathematical proof.First of all, you have no idea what realistic genome lengths and mutations rates are. Second, you haven't used realistic populations, so your proof is defective. Third, even if this were all true, what have you proven? You've proven that the Kleinman Theory of Point Mutations and Natural Selection is flawed. We know that. We agree.
Why don’t you tell us what your idea of a realistic genome lengths and mutation rates are? With respects to realistic populations, 1 meg is a realistic estimate for the population of our supposed primate ancestor. If you are supporter of Gould’s hypothesis of punctuated equilibrium, populations would even be smaller. The only portion of my proof with ev on the effects of population size which has not been completed (not defective) is the effects of population on the microorganism population scale. The initial data from ev on this issue does not look good for the evolutionarian viewpoint.

The only things that we have agreed on in this discussion you have retracted-whoops, squirmed on. Does random point mutation and natural selection have any role in your theory of evolution?
I don't get it, Kleinman. You only acknowledge evolution when you care for your patients. You use science and fact in doing so. But, when you look at the overall picture, you claim that it doesn't exist. And you use illogic and lies to do so.

So far, I can say that I respect Kleinman the Dr, but have severe doubts about Kleinman the scientist.
It has been a while since I posted my view of abiogenesis and the theory of evolution. I do not believe there is any scientific or mathematical basis for the concept of abiogenesis. I look at the theory of evolution as composed of two parts. The first part consists of microevolutionary processes which have a mathematical and scientific basis and the second part consists of macroevolutionary processes which do not have a mathematical and scientific basis.

I understand that evolutionarians do not draw this kind of distinction and view microevolution and macroevolution as part of a continuum. This is why I like using ev in this debate. It shows how little can be accomplished by random point mutations and natural selection in billions of generations. Hard science comes down to applying known physical laws in as precise a mathematical model as possible in order to predict the behavior of a system.

Most evolutionarians who have studied the mathematics of the theory of evolution know that chance alone can not explain their theory so they introduce the concept of a selection process in order to overcome these virtually impossible probabilities. The problem with the concept of a selection process is that none is known that overcome these virtually impossible probabilities, either to evolve one species to another or to generate the initial ribozymes needed in the primordial soup to generate the first life forms.

Hard science ultimately comes down to bookkeeping. The bookkeeping of the theory of evolution does not balance. This will become more and more clear as the human/chimpanzee genomes are compared in more detail as well as the genomes of other living things become better described. There are no known mechanisms to transform the genomes of one species to another species in the time available. Ev demonstrates this with random point mutations and natural selection.
The debate, which you claim I do not understand, is trivially simple, and it will continue, unabated, as long as humans exist in their present form. I.E., (1) a creator has existed eternally and has designed the universe to function in a specified manner, such that human life now exists, (2) matter contained in the universe is naturally capable of self organization, such that human life now exists, or (3) some combination of #1 and/or #2.Too bad #2 has no mathematical basis.Neither does #1.
#2 can be disproved mathematically, that is what I am doing with ev. Are you saying you can disprove #1 mathematically? I would really like to see this.

Here is where your lack of understanding of ev is revealing itself. Dr Schneider has devised a selection mechanism that is very precise and stringent. It works very rapidly on small genomes with large mutation rates. The only way I can see devising a selection mechanism that works more rapidly than this is that every mutation is selected for or against on a mutation by mutation basis. Dr Schneider’s weight matrix is already very close to this and it still becomes profoundly slow when you apply this process to a realistic length genome. Don’t you think Dr Schneider, Paul or Myriad would redefine the selection process if they could? The reason they don’t is there is no known selection mechanism that could speed up the evolutionary process. This is an accounting problem and I know of no accounting rules that fix this mathematical fact that contradicts the theory of evolution.

About 25-30 years ago there was an attempt to screen women for breast cancer by using thermography. The problem with this screening test was there were 50% false positives. I looked at the thermodynamics of this problem for my PhD. Once you did the mathematics for this situation, it became clear why there were so many false positives. I could see no way to overcome the physics and mathematics of this situation. The mathematics of the theory of evolution is presenting itself in the same way. There are no known selection processes or mutation mechanisms that would allow you to evolve a megabase genome in the time available, let alone a gigabase genome. This is a mathematical fact of life.Apparently you drive nails with a screwdriver.
I imagine a collection in your garage of abused tools in broken piles on the workbench. The mathematics of drilling holes with sandpaper is indeed difficult to overcome.
You evolutionarians continue to accuse me of abusing your mathematics. It is easy enough to demonstrate this if it were true but you fail to do this. Where is the problem? Is it in using known genome lengths and mutation rates in ev? Ev is forcing evolutionarians to speculate that there were life forms that had much shorter genome lengths than any free living organism known today and that these life forms could endure much higher mutation rates than any living thing known today. In addition, ev is showing that no gene or fundamental genetic control system can evolve on a megabase genome by random point mutation and natural selection. It is mathematically impossible as so well demonstrated by the ev computer model.

[dv82matt]

Did you read Hewitt's response to me?
I did yes.
You know, the part where he explicitly states:
I[n] short animate and inanimate objects are different
From this we can conclude that Hewitt is arguing that order in inanimate things is different than order in animate things. We can conclude this because it is exactly what he says.

My entire argument has been that he is making a distinction between order in inaminate things and order in animate things.Sigh, it's as if you didn't read my prior post? Why do you still insist on redefining complexity as order? Do you understand the concept of complexity? Do you understand that you are not substituting an equivalent term when you use the word "order"?
The essential point you have been missing is that order and complexity are not synonomous.
From the above quote of Hewitt's, it would appear that the essential point you have been missing is that Hewitt is arguing that order in inaminate things is different than order in animate things.
You appear to have quoted me here not for the purpose of responding to the point but merely to mimic the word pattern. re: "the essential point you have been missing". Do you have anything to say to the point?
I am sorry that you are no more equipped to understand Hewitt's posts than you are mine, but unless you can demonstrate you actually know what either of us is talking about, I'm going to stop reading your posts.
Shrug. I can't say that I'm particularily surprised to see you retreat to a bunker mentality.

[joobz]

It has been a while since I posted my view of abiogenesis and the theory of evolution. I do not believe there is any scientific or mathematical basis for the concept of abiogenesis. I look at the theory of evolution as composed of two parts. The first part consists of microevolutionary processes which have a mathematical and scientific basis and the second part consists of macroevolutionary processes which do not have a mathematical and scientific basis.

I understand that evolutionarians do not draw this kind of distinction and view microevolution and macroevolution as part of a continuum. This is why I like using ev in this debate. It shows how little can be accomplished by random point mutations and natural selection in billions of generations. Hard science comes down to applying known physical laws in as precise a mathematical model as possible in order to predict the behavior of a system.

Most evolutionarians who have studied the mathematics of the theory of evolution know that chance alone can not explain their theory so they introduce the concept of a selection process in order to overcome these virtually impossible probabilities. The problem with the concept of a selection process is that none is known that overcome these virtually impossible probabilities, either to evolve one species to another or to generate the initial ribozymes needed in the primordial soup to generate the first life forms.



but this is the heart of it. No one has claimed chance alone.
No one has claimed point mutation alone. No one has claimed we know all mechanisms. Yet,you continue to beat the straw man and no one understands your efforts. When these facts are pointed out to you, you ignore it. That makes your methods dishonest, which can never exist in science.

Maybe you have legitimate complaints about a minority of investigators who hold to the things you argue against. But these people aren't here on this forum. And, your methods make your actions worse then these ficticious foes. How can we take your arguements seriously when you continue to chant the same mistaken views, mistaken conclusions and mistaken assumptions?

[dv82matt]

Dawkins selfish gene is not about chance--mutation might be random--but selection is not...and it's the ratcheting that brings complexity.When it comes to abiogenesis we don't yet know enough to say to what roles chance and selection play. It may be continuous as you say but it may in fact be discontinuous in which case chance likely plays a larger role. In short, given our ignorace of abiogenesis, I think it is premature to dismiss chance.

Also, if John were to attempt to get ID or God in through the backdoor so to speak, then I would object to that, but I haven't seen him do that.

[kleinman]

It has been a while since I posted my view of abiogenesis and the theory of evolution. I do not believe there is any scientific or mathematical basis for the concept of abiogenesis. I look at the theory of evolution as composed of two parts. The first part consists of microevolutionary processes which have a mathematical and scientific basis and the second part consists of macroevolutionary processes which do not have a mathematical and scientific basis.

I understand that evolutionarians do not draw this kind of distinction and view microevolution and macroevolution as part of a continuum. This is why I like using ev in this debate. It shows how little can be accomplished by random point mutations and natural selection in billions of generations. Hard science comes down to applying known physical laws in as precise a mathematical model as possible in order to predict the behavior of a system.

Most evolutionarians who have studied the mathematics of the theory of evolution know that chance alone can not explain their theory so they introduce the concept of a selection process in order to overcome these virtually impossible probabilities. The problem with the concept of a selection process is that none is known that overcome these virtually impossible probabilities, either to evolve one species to another or to generate the initial ribozymes needed in the primordial soup to generate the first life forms.but this is the heart of it. No one has claimed chance alone.
No one has claimed point mutation alone. No one has claimed we know all mechanisms. Yet,you continue to beat the straw man and no one understands your efforts. When these facts are pointed out to you, you ignore it. That makes your methods dishonest, which can never exist in science.

Maybe you have legitimate complaints about a minority of investigators who hold to the things you argue against. But these people aren't here on this forum. And, your methods make your actions worse then these ficticious foes. How can we take your arguements seriously when you continue to chant the same mistaken views, mistaken conclusions and mistaken assumptions?
This discussion about ev is forcing evolutionarians to take positions on their views that are subject to the rules of mathematical logic and analysis. You no longer say that that abiogenesis and theory of evolution are based on chance alone because analysis of this concept shows the virtual mathematical impossibility of this concept. So you introduce selection into these concepts but can not demonstrate what this selection process is for abiogenesis and how it could work and ev demonstrates how slow selection is for random point mutations and natural selection when using known measured genome lengths and mutation rates. So now you retreat to the position that there are other selection mechanisms and mechanisms of mutations and rearrangements of genomes that can rescue your theories but you don’t present the mathematical models that demonstrate your theories.

The only fact you can present for the theory of evolution is that there are some similarities between genomes of living things. I acknowledge this fact. What you won’t acknowledge is there are no mechanisms that explain how you can transform these genomes from one to another in the time available. Random point mutations and natural selection does not provide the mechanism for these transformations, ev shows this mathematical impossibility. If you believe that other mechanisms will accomplish this transformation, produce your mathematical model and prove your theory. Otherwise, your theory started without a mathematical basis and remains that way. Your pronouncements about other mechanisms will serve as sufficient proof only for devout evolutionarians. Hard science requires you run the numbers. The theories of evolution and abiogenesis can not withstand this type of scrutiny.

[articulett]

When it comes to abiogenesis we don't yet know enough to say to what roles chance and selection play. It may be continuous as you say but it may in fact be discontinuous in which case chance likely plays a larger role. In short, given our ignorace of abiogenesis, I think it is premature to dismiss chance.

Also, if John were to attempt to get ID or God in through the backdoor so to speak, then I would object to that, but I haven't seen him do that.

No, he's just trying to insert god into the gaps between knowledge. I am pointing out that no matter how you define life--via complexity or anything else--there is no easy dividing line--there is much that doesn't fit neatly in one side or the other no matter what definition you give. For example, are tumors "alive"? Are the bacteria that help you digest food? At what point is a virus alive (they give "live" polio vaccinations and "killed" ones).

One thing creationists do is to talk about "increasing complexity" in the genome--but they never say exactly what they mean. More DNA? More genes? More chromosomes? More order? A more masterful symphony between the interacting components? Higher functioning? To say "life is more complex" than "non-life" is an argument that can't be proven false or even tested until you say what it is about life that makes it "more complex" than non-life. If you're looking to insert God--you have to have a clue as to where he would need to be inserted. And so far, god just seems to be the answer for stuff we don't have a complete grasp on yet--just as he always has been. Remember when humans had weather gods? --When mental illness was thought to be possession? We know humans like explanations, and when they don't have explanations they make up supernatural explanations. But we don't know that anything supernatural has ever existed. Saying "golly gee--what a puzzle--it must be god" might make people feel might--but it sure isn't science.

Proving there are gaps in knowledge doesn't prove anything supernatural--just as proving that there are missing elements does not prove god is keeping them under wraps. Gaps in knowledge are great places for exploration--and we humans have been steadying filling in more and more precise and detailed answers. It never has been a means of proving anybody's god...in the same way it's doesn't prove space aliens are doing an experiment with life on our planet.

So what is the complexity that makes life different than non-life?--or are you talking more about consciousness?--which also exists on a continuum. Never defining the terms or what this god or whomever is supposed to have done is just useless (though I bet you could get a Templeton prize if you do it well.)

No one is dismissing chance. There's trillions of chance events--but some lead to something else slightly more complex--slightly more "life-like"--slightly more likely to survive and evolve into something else rather than break down and let the molecules of existence be incorporated elsewhere. If a chance event (from meteors to blind luck) even enhances some group of molecules chance of surviving on earth--that group of molecules can evolve--living or not. Just like molecules in a snowball can evolve into a bigger snowball-- or melt and join other molecules as a puddle--or evaporate into water vapor (which still as mass and molecules)--the molecules can also freeze in a lattice structure making ice. You'll agree that water is necessary to life on this planet...but it is not life itself. At what point do water molecules become a part of life?

As for life being discontinuous--what do you mean? Do you mean that it could just poof into existence (with whatever complexity you define life to be). Wouldn't that be on par with a Mountain poofing into existence? Why would you presume that anything "poofs" into existence when we know that our earth evolved, trees come from seeds, forests come from plants, solar systems evolve--cancers evolve, bacteria evolves--all complexity known to humans evolved from something less complex, didn't it? Why would you even presume life (however you define it or wherever you put the divinding line) is different. And if it is different--what the heck are you imagining? A god that evolved from nothing inserting this thing called life upon a protolife to see what happens--like kids releasing computer viruses onto the internet to see what happens? Why not look for aliens who inserted life? We have some pretty great models and understanding about how life most likely evolved...and consciousness too-- how can pointing to the gaps prove anything at all? Much less anything supernatural or "beyond human understanding", etc.

So, what is the complexity factor that separates life from non-life. And what makes you think it was discontinuous? Do you also think speciation is discontinuous? When are the sperm and eggs officially "alive"? (or pollen and other plant gametes or spores?) At what point does the alive thing cease being alive?

[dv82matt]

No, he's just trying to insert god into the gaps between knowledge.
I will reserve judgement on that.
I am pointing out that no matter how you define life--via complexity or anything else--there is no easy dividing line--there is much that doesn't fit neatly in one side or the other no matter what definition you give. For example, are tumors "alive"? Are the bacteria that help you digest food? At what point is a virus alive (they give "live" polio vaccinations and "killed" ones).
I agree that defining life is problematic. I guess I don't see why this is such an issue for you though. The lack of a rigorous definition across all disciplines does not imply that shaking up a box of granola is equivalent to life except simpler.
One thing creationists do is to talk about "increasing complexity" in the genome--but they never say exactly what they mean. More DNA? More genes? More chromosomes? More order? A more masterful symphony between the interacting components? Higher functioning?
Well you didn't really expect a valid argument from creationists did you? ;)
So what is the complexity that makes life different than non-life?--or are you talking more about consciousness?--which also exists on a continuum.
No, I don't mean consciousness.
Never defining the terms or what this god or whomever is supposed to have done is just useless (though I bet you could get a Templeton prize if you do it well.)It is true that I cannot give you a precise definition of "complex". I can provide you with several informal descriptions of complex systems if that would be helpful. From wikipedia:
A complex system is a highly structured system, which shows structure with variations (Goldenfeld and Kadanoff)

A complex system is one whose evolution is very sensitive to initial conditions or to small perturbations, one in which the number of independent interacting components is large, or one in which there are multiple pathways by which the system can evolve (Whitesides and Ismagilov)

A complex system is one that by design or function or both is difficult to understand and verify (Weng, Bhalla and Iyengar)

A complex system is one in which there are multiple interactions between many different components (D. Rind)

Complex systems are systems in process that constantly evolve and unfold over time (W. Brian Arthur).
No one is dismissing chance. There's trillions of chance events--but some lead to something else slightly more complex--slightly more "life-like"--slightly more likely to survive and evolve into something else rather than break down and let the molecules of existence be incorporated elsewhere. If a chance event (from meteors to blind luck) even enhances some group of molecules chance of surviving on earth--that group of molecules can evolve--living or not. Just like molecules in a snowball can evolve into a bigger snowball-- or melt and join other molecules as a puddle--or evaporate into water vapor (which still as mass and molecules)--the molecules can also freeze in a lattice structure making ice.Without self-replication evolution won't happen. Most non-living systems cannot replicate themselves.
You'll agree that water is necessary to life on this planet...but it is not life itself. At what point do water molecules become a part of life?
Certainly I agree. Why does it matter?
As for life being discontinuous--what do you mean?
I mean that it might have required a large degree of luck to get started.
Why would you even presume life (however you define it or wherever you put the divinding line) is different.
Maybe I'm missing what your getting at. Despite a fuzzy middle ground, life is clearly different from non-life.
So, what is the complexity factor that separates life from non-life.
See above.
And what makes you think it was discontinuous?I don't think that. I said it may be.
Do you also think speciation is discontinuous?
No.
When are the sperm and eggs officially "alive"? (or pollen and other plant gametes or spores?) At what point does the alive thing cease being alive?It's a big fuzzy middle ground. ;)

[cyborg]

You no longer say that that abiogenesis and theory of evolution are based on chance alone because analysis of this concept shows the virtual mathematical impossibility of this concept.

You dumb ****.

Natural Selection is not chance.

But do keep banging that drum about how YOU'VE changed us from believing in a chance theory based on your amazing insights with ev. ****, you might even eventually persuade us that probabilities can go all the way to 11.

Hard science requires you run the numbers.

NO, YOU RUN THE NUMBERS YOU LAZY ASS. YOU FALSIFY.

Dumbass.

[hammegk]

Natural Selection is not chance.
Hmm. Who schedules the asteroid strikes, volcanoes, plate movements, smoker vent availability, etc? :)


NO, YOU RUN THE NUMBERS YOU LAZY ASS. YOU FALSIFY.

Er, no. It works the other way, although point mutation seems to be taking a beating as having potential effectiveness outside the microev scale.

[kleinman]

You no longer say that that abiogenesis and theory of evolution are based on chance alone because analysis of this concept shows the virtual mathematical impossibility of this concept.You dumb ****.

Natural Selection is not chance.

But do keep banging that drum about how YOU'VE changed us from believing in a chance theory based on your amazing insights with ev. ****, you might even eventually persuade us that probabilities can go all the way to 11.
Cyborg, your attention span is limited to one sentence because if you had read the sentence after the one you quoted you would have seen:
You no longer say that that abiogenesis and theory of evolution are based on chance alone because analysis of this concept shows the virtual mathematical impossibility of this concept. So you introduce selection into these concepts but can not demonstrate what this selection process is for abiogenesis and how it could work and ev demonstrates how slow selection is for random point mutations and natural selection when using known measured genome lengths and mutation rates.
Hard science requires you run the numbers.NO, YOU RUN THE NUMBERS YOU LAZY ASS. YOU FALSIFY.
Why don’t you post the numbers that you say I am too lazy to run and then I falsify?

What has happen to you? Did someone put coal in your stocking? There is more truth in the story of Santa Claus than there is in the theory of evolution.

Merry Christmas to you all.

[joobz]

This discussion about ev is forcing evolutionarians to take positions on their views that are subject to the rules of mathematical logic and analysis. You no longer say that that abiogenesis and theory of evolution are based on chance alone because analysis of this concept shows the virtual mathematical impossibility of this concept. So you introduce selection into these concepts but can not demonstrate what this selection process is for abiogenesis and how it could work and ev demonstrates how slow selection is for random point mutations and natural selection when using known measured genome lengths and mutation rates. So now you retreat to the position that there are other selection mechanisms and mechanisms of mutations and rearrangements of genomes that can rescue your theories but you don’t present the mathematical models that demonstrate your theories.
See, this is what I'm talking about. Your continuous lies.

The only retreat that has existed here has been your position. You stated that evolution can't be real cause ev says so.(it's mathematical.)

but then after giving an example of the use of evolutionary theory in immunizations, you counter with a statement that you don't believe in "macroevolution", oh but evolution does occur. Yet you cannot draw a line to explain where one ends and the other begins.

ev has clearly demonstrated that binding site evolution can occur. It occurs within a window of functioning. But why would that be considered a proof that it's impossible? There is a window of opportunity where laminar flow is posisble (dependant upon kenimatic viscosity and speed of flow), but does that mean laminar flow is impossible because it is bounded? The logic makes no sense.

The fact that you continually beat a strawman argument is proof that you have nothing new to add or give. I had hope for you, but it seems to be wasted.

[John Hewitt]

No, he (Hewitt) is just trying to insert god into the gaps between knowledge. I am pointing out that no matter how you define life--via complexity or anything else--there is no easy dividing line--there is much that doesn't fit neatly in one side or the other no matter what definition you give. <snip>

One thing creationists do is to talk about "increasing complexity" in the genome--but they never say exactly what they mean. <snip>
If you're looking to insert God--you have to have a clue as to where he would need to be inserted. And so far, god just seems to be the answer for stuff we don't have a complete grasp on yet--just as he always has been. <snip>

Proving there are gaps in knowledge doesn't prove anything supernatural--just as proving that there are missing elements does not prove god is keeping them under wraps. Gaps in knowledge are great places for exploration--and we humans have been steadying filling in more and more precise and detailed answers. It never has been a means of proving anybody's god...in the same way it's doesn't prove space aliens are doing an experiment with life on our planet.

So what is the complexity that makes life different than non-life?--or are you talking more about consciousness?--which also exists on a continuum. Never defining the terms or what this god or whomever is supposed to have done is just useless (though I bet you could get a Templeton prize if you do it well.)

<snip>Just like molecules in a snowball can evolve into a bigger snowball-- or melt and join other molecules as a puddle--or evaporate into water vapor (which still as mass and molecules)--the molecules can also freeze in a lattice structure making ice. You'll agree that water is necessary to life on this planet...but it is not life itself. At what point do water molecules become a part of life?

<snip>

So, what is the complexity factor that separates life from non-life. And what makes you think it was discontinuous? Do you also think speciation is discontinuous? When are the sperm and eggs officially "alive"? (or pollen and other plant gametes or spores?) At what point does the alive thing cease being alive?

I think it is true that there are many gaps in our understanding of evolution but I do not recall trying to fill one of them with God. Could you please explain why you keep introducing supernatural entities into discussion concerning me?
For some purposes, the precise distinction between alive and not alive and the definition of complexity is immaterial. Most people agree that complexity increases as evolution progresses.

[fishbob]

Why don’t you post the numbers that you say I am too lazy to run . . . . .

I guess that writing the words does not in any way imply understanding what the words mean.

[cyborg]

Hmm. Who schedules the asteroid strikes, volcanoes, plate movements, smoker vent availability, etc? :)

The Stonecutters.

[cyborg]

Why don’t you post the numbers that you say I am too lazy to run and then I falsify?

Because it is your proof dumb-ass. I am fed up with your lazy ****. Your continual bitching here is tiresome. It's only so long you can watch someone like yourself jerk themselves off in public before the disgust is too much.

Go away and publish your goddamn proof. Moaning about science being against you will not be accepted - that is just is a lazy man talking who doesn't want to fight. If it is true go and fight for it. If you only care about jerking yourself off then continue masturbating here.

What has happen to you? Did someone put coal in your stocking?

Just about had enough of your **** is all.

There is more truth in the story of Santa Claus than there is in the theory of evolution.

There is more truth in the story of Thor than there is in the story of the birth of Christ.

Merry Christmas to you all.

Screw you Bible-freak.

[Dr Adequate]

Isn’t that the question? If Adequate is correct in his estimate, It's not an estimate.

how large a population do you need in order approach that estimate? The generation size approaches the asymptote as the population size approaches infinity.

The curve is always approaching the asymptote.

Do you know what these words mean?

[Paul C. Anagnostopoulos]

That’s a strange thing for you to say. Just a few short months ago you thought that ev represented the holy grail for the theory of evolution and you even wrote the online version of this model. Now you are professing ignorance and are even indignant that I should raise such a point. Do I detect some annoyance?
Yes, you detect my standard annoyance about your lies. Perhaps you could quote me where I said that Ev simulates the totality of the evolutionary landscape?


None of the population series we have done show a rapid convergence to Adequate’s proposed value of 1 generation for convergence with an infinite population. Do you think larger genomes will show a more rapid approach to this value of 1 generation? I believe that larger genomes will show lower rates of reduction in the generations for convergence as population is increased.
Dr. A. proposed that the asymptote for an infinite population was 1 generation. He said nothing about the rate at which the asymptote would be approached for finite populations.


You are so cute when you squirm.
Excellent answer. Thorough evasion noted.


Why don’t you tell us what your idea of a realistic genome lengths and mutation rates are? With respects to realistic populations, 1 meg is a realistic estimate for the population of our supposed primate ancestor.
So Ev simulates the evolution of a binding site in our primate ancestor? I did not realize that.


If you are supporter of Gould’s hypothesis of punctuated equilibrium, populations would even be smaller.
This statement is utterly nonsensical.


Does random point mutation and natural selection have any role in your theory of evolution?
Yes.

~~ Paul

[Paul C. Anagnostopoulos]

Hmm. Who schedules the asteroid strikes, volcanoes, plate movements, smoker vent availability, etc?
Oh please, could we stop with this cutesy observation? "Natural selection is not chance" is short for "Natural selection is not chance with respect to the environment."


Er, no. It works the other way, although point mutation seems to be taking a beating as having potential effectiveness outside the microev scale.
It doesn't work the other way when Kleinman says "Macroevolution is mathematically impossible," which he says at least twice a day. That statement implies that he has a proof. Where is the proof?

~~ Paul

[Paul C. Anagnostopoulos]

Interesting essay on the emergence of cells:

http://www.sciencemag.org/cgi/content/full/314/5805/1558

~~ Paul

[hammegk]

Oh please, could we stop with this cutesy observation? "Natural selection is not chance" is short for "Natural selection is not chance with respect to the environment."
Evolutionarians only wish the problem was a 'cutesy statement'. Even at the most basic level "Random" remains the problem.


It doesn't work the other way when Kleinman says "Macroevolution is mathematically impossible," which he says at least twice a day. That statement implies that he has a proof. Where is the proof?

~~ Paul
I think he looks your point mutation results, and deems 'true speciation' mathematically impossible on that basis. He then comments, yup, there are certainly other factors besides point mutations ... evolutionarians need to identify and mathematize them, and let's see how that model looks. We all know how the fossil record looks. "Model it" is the challenge.

[Paul C. Anagnostopoulos]

Evolutionarians only wish the problem was a 'cutesy statement'. Even at the most basic level "Random" remains the problem.
Only if you insist that life is some sort of super special thing unlike anything else whatsoever, instead of simply an island of organization in the midst of, and relative to, the surrounding environment.


I think he looks your point mutation results, and deems 'true speciation' mathematically impossible on that basis. He then comments, yup, there are certainly other factors besides point mutations ... evolutionarians need to identify and mathematize them, and let's see how that model looks. We all know how the fossil record looks. "Model it" is the challenge.
Mathematical modeling is not a required bit of evidence for evolution. And if it is, then it's a required bit of evidence for every other theory of the origin of species, too.

In any event, the idea that point mutations alone could not result in speciation is open to question. What if point mutations changed the sex organs of a critter sufficiently to make mating physically difficult?

~~ Paul

[hammegk]

Only if you insist that life is some sort of super special thing unlike anything else whatsoever, instead of simply an island of organization in the midst of, and relative to, the surrounding environment.
Actually, I insist just the opposite.


Mathematical modeling is not a required bit of evidence for evolution.
You may continue to wave your arms all you wish. Others may continue to point out that's what you're doing.

And if it is, then it's a required bit of evidence for every other theory of the origin of species, too.
If ever to be rigorous, yup.


In any event, the idea that point mutations alone could not result in speciation is open to question. What if point mutations changed the sex organs of a critter sufficiently to make mating physically difficult?

~~ Paul
"What if", indeed? You encapsulated everything in two words. :)

[Paul C. Anagnostopoulos]

Actually, I insist just the opposite.
You insist that life isn't special at all? Then what's the issue with it being just an island of organization in the midst of the surrounding environment? Why did you say "Even at the most basic level "Random" remains the problem"? If random is a problem, then "special" sounds just like what you're arguing for.


You may continue to wave your arms all you wish. Others may continue to point out that's what you're doing.
Is mathematical modeling a required piece of the puzzle for, say, history?


"What if", indeed? You encapsulated everything in two words.
Fine, as long as you agree it's a legitimate question, then Kleinman's dogmatic rejection of point mutation as a source of speciation can be rejected. For his dogmatic rejection to work, he has to show that point mutations cannot result in speciation even in principle.

~~ Paul

[articulett]

The creationists purposely ask for something ridiculous so they can say that evolution isn't proven. We don't need a mathematical model though we have a pretty good idea of mutation rates and which mutations happened where and when--because we have DNA. We can SEE the changes. We can see old genes turned off and alterations in genes and the proteins they make. We can see translocations, duplications, and point mutations. We can see all of it--and what sort of mathematical model would there need to be for something that only needed to happen once--because all life is built upon some mutation or change that only happened once--out of infinite chance and possibililities (and the more life there is and the more genetic copying and dividing there is--the more chances there are for "beneficial" mutations.)

We don't need a mathematical formula to show how forests came to be or a mountain came to be though we have a pretty good understanding. We don't have a mathematical model about how our oceans came to be--because we don't need one. We don't need a mathematical model to show how evolution came to be either. It's apparent--in the genes. You can make all the mathematical models you want about how a mountain contains x number of granuals and couldn't build up in the time given--and it doesn't change the fact that it did--and it did through natural processes. You just need to change your formula so that it factors in things like tectonic plate movement, earth quakes, volcanic explosions, meteors, etc. Because mountains exist via natural processes even if it wasn't grain by grain construction. That is true of life also.

Asking Paul or any serious scientist to show the forumula for mutations that lead to life and species divergence is like asking a geologist for the formula for mountain formation.

Or the formula for how language evolved to the languages we have today via symbolic sound.

These formulas are just digressions meant to confuse the issue so you can say, "humans can't explain it, therefore god did it."

It's dishonest. And even if someone showed you THE mathematical formula, you'd still find fault in it--you'd say, "well, by my calculations that would take a trillion years and the odds are very much against it happening in the millions of years it happened in." The bottom line is, humans have no idea of even figuring out the odds--we have no idea how many planets have evolved life forms of some kind in their history--we have no idea how many natural events are happening that can line the circumstances up right for life. We have no idea how many replication "experiments" there are in every cell and possibly outside of cells every day from the beginning of the first replicator. Or even if the first replicator is a single "thing" or on a continuum.

But we know for sure it happened because we can see it in the DNA. And we know it's very unlikely to have a supernatural explanation behind it--because none of the stuff we've come to know ever has--even though humans once thought it did. None of this stuff was written about by any omniscient entities so we have to slowly figure it out for ourselves. Because the deeper our understanding gets--the less likely any supernatural creator seems to be at the heart of it.

To say, you can't give me the math formula for life, therefore god did it--makes as much sense as claiming our failure to have a mathematic model for the evolution of language means the tower of Babel has a chance of being true.

[RecoveringYuppy]

I haven't read this whole thread but the ~3% difference between humans and chimps would be equivalent to a 3 in 100 million base pair difference between generations. How can anyone claim that rate is any kind of obstacle?

[dv82matt]

You no longer say that that abiogenesis and theory of evolution are based on chance alone...
So many misconceptions.

Apparently you think that:
1. at one time the theory of evolution was based on chance alone.
2. selection is just a recent "add on" to the theory.
3. anything which has not been mathematically explained is impossible.
4. if a model is at odds with reality then reality is wrong.
5. being annoying is a sign that you're onto something.

Your only trick is to repeatedly point out a possible limitation of ev and try to dress it up as a disproof of evolution.