Annoying creationists

[Paul C. Anagnostopoulos]

Note that mutations are a result of external events and cellular chemistry. A complete model of mutation would require a complete model of chemistry. It ain't gonna happen, so if that's what Creationists insist on, they've got a perfect long-term godgap.

Here's a paper to get them started:

http://www.nature.com/hdy/journal/v96/n3/full/6800771a.html

And here's an order, the sturgeon, that won't cooperate at all. Bad sturgeon!

http://www.genetics.org/cgi/content/full/158/3/1203

~~ Paul

[hammegk]

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?
Since, as you well know, in my view 'what-is' is life (rather than not-life=matter) I have no problem with that statement, as long as terran rna/dna bio-life is what you intend 'life' to mean.


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.
Nah, that's your argument. What else does a materialist have?


Is mathematical modeling a required piece of the puzzle for, say, history?
No, but I thought you were purporting Modern Ev Theory to be "science".


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.
Perhaps he has, perhaps he hasn't. My reading so far says the jury is still out. As the expalnation for microev, even he agrees it has merit.


As I said before: You have the fossil record; tie that to your argument rather than just pointing at it. We all agree that whatever macroev is, fossils actually demonstrate that it occured.

[articulett]

Interesting essay on the emergence of cells:

http://www.sciencemag.org/cgi/content/full/314/5805/1558

~~ Paul

That was a good link! I wonder what John Hewitt will say about it.

http://www.the-scientist.com/news/home/38145/

The above link talks about the bacterial biodiversity in the air we breathe.

and this is about bacterial cell signaling to form colonies....

http://www.the-scientist.com/article/display/23546/

I think these both offer interesting clues about the emergence of life from single cell life forms, but I wonder if those who can't let go of the idea of a creator can enjoy or incorporate this new information. Our world is teeming with invisible life--but it's not ghosts or intelligent designers--it's bacteria floating in the air we breathe.

And the biodiversity of the primordial soup is even more stunning: In the sense that biodiversity is richness, Census microbe hunters found 20,000 kinds floating in a single liter of sea water. Samples were taken from the Atlantic and Pacific, including from an eruptive fissure 1,500 meters deep on a seamount in the Pacific a few hundred kilometers west of Oregon, USA.

Revealed by DNA studies, most of the different kinds of bacteria were unknown and likely rare globally. The richness of the diversity invites speculation about what rare species contribute to their biosphere and an estimate that the kinds of bacteria in the oceans exceed five to 10 million.

The researchers also began assembling the best-ever video of protists (mostly microscopic organisms that are neither animals, plants, or fungi) and to pioneer optical and genetic techniques to extend the limits of knowledge.


http://www.divenews.com/modules.php?op=modload&name=News&file=article&sid=5062&mode=thread&order=0&thold=0

There are so many things along the life continuum--and so many different forms, and we are learning so much everyday (as the above)--how can we have figured this information into a mathematical model...when we didn't know that there was so much life in the invisible air we breath--nor have we come close to identifying all the life-forms and proto life "things" in the ocean. Who would waste time on a math formula trying to prove it couldn't have happened without supernatural help that we don't know exists--when there is so much to learn from substances we are just coming to know the existence of! And these substances fit into a theory already well established which is accumulating more evidence every day (evolution). Anyone who thinks otherwise is lying to themselves or others. If there is an intelligent designer, he sure hasn't been much help in revealing anything about the nature of our world to us--nor is he in evidence as we discover more and more about the world too small to see and the universe too huge to grasp.

[Paul C. Anagnostopoulos]

Since, as you well know, in my view 'what-is' is life (rather than not-life=matter) I have no problem with that statement, as long as terran rna/dna bio-life is what you intend 'life' to mean.
And yet you say that life is nothing special. Making it the fundamental existent is about as special as you can get, no?


No, but I thought you were purporting Modern Ev Theory to be "science".
That still doesn't make a perfect mathmetical model a requirement. And, as I mentioned above, it's actually an impossibility.


As I said before: You have the fossil record; tie that to your argument rather than just pointing at it. We all agree that whatever macroev is, fossils actually demonstrate that it occured.
And yet Kleinman insists that the fossil record can't be the product of evolution.* Now why do we need to tie the fossil record to the mathematical model? Is there some evidence within the fossil record of something other than evolution occuring, some evidence that compels us to weigh it against evolution by working on two competing mathematical models to see which one can better absorb all the evidence? No, there is no evidence of anything except evolution. It's as if you're asking us to apply Occam when there is only one available theory.

When the Creationists provide their theory, then I'll agree that more mathematical work would be useful to make a distinction. Meanwhile, the mathematical work can proceed at its own pace.


~~ Paul

* Or maybe he just insists that it can't be the product of point mutation only. Who knows? Who cares?

[Paul C. Anagnostopoulos]

Oh look, mathematical modeling of something other than point mutation:

http://mbe.oxfordjournals.org/cgi/content/abstract/19/3/278

~~ Paul

[Dr Adequate]

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?
No, the con-ver-gence will be-come less rap-id as we ap-proach the a-symp-tote.

Do you have a clue what you're talking about?

[hammegk]

And yet you say that life is nothing special. Making it the fundamental existent is about as special as you can get, no?
Interesting question from one thought-form to another ... :)


That still doesn't make a perfect mathmetical model a requirement. And, as I mentioned above, it's actually an impossibility.
Agreed.


And yet Kleinman insists that the fossil record can't be the product of evolution.*

* Or maybe he just insists that it can't be the product of point mutation only.

That's the way I understand his point, anyway.


Now why do we need to tie the fossil record to the mathematical model?
Same "reasons" you are working with the model you are running now.


Is there some evidence within the fossil record of something other than evolution occuring, some evidence that compels us to weigh it against evolution by working on two competing mathematical models to see which one can better absorb all the evidence? No, there is no evidence of anything except evolution. It's as if you're asking us to apply Occam when there is only one available theory.
Actually I suggested you go where the data leads.


When the Creationists provide their theory, then I'll agree that more mathematical work would be useful to make a distinction.
They have several more primary problems to be explained by mathematics: Maybe start with the math explaining why baryons attract? ;)


Meanwhile, the mathematical work can proceed at its own pace.
Why not?

[The Atheist]

Interesting debate you have going here. I see John Hewitt's taking part, so I'll join in as well.

John, I said I'd get back to you when I'd studied your site some more and this looks as good a place as any.

I'm always going to like your style when your site is named sexandphilosophy, so you got off to a good start. I see nothing too contentious in what I've seen so far and the same applies to your posts here. As far as I can tell, the differences between you and Paul & the team are not huge.

On to the other interesting character on the thread, Kleinman, the erstwhile "Dr" Alan Kleinman, "PhD". I see the subject of his qualifications and skills has been answered with a "you go find out" attitude.

Ok, Kleinman, I asked Google and was told all about Alan Kleinman, PhD:

http://forums.randi.org/imagehosting/thum_103774592251756de2.jpg (http://forums.randi.org/vbimghost.php?do=displayimg&imgid=3344)

nope. How about, Alan Kleinman, Engineer?

http://forums.randi.org/imagehosting/thum_1037745922543c8689.jpg (http://forums.randi.org/vbimghost.php?do=displayimg&imgid=3346)

nope. How about, Alan Kleinman, MD?

http://forums.randi.org/imagehosting/thum_103774592252fce7e6.jpg (http://forums.randi.org/vbimghost.php?do=displayimg&imgid=3345)

Hmm. You may actually be a doctor of medicine. I confess to being pleased to not be a patient of yours.

I wonder how easy it is to get a degree or PhD (http://www.elearners.com/resources/diploma-mills.asp) these days?

You're the mathematician, Kleinman, work some odds out for me. What is the likelihood of Google having never heard of a living PhD? No publications, nothing? With all your scholarly analysis, nobody's ever heard of you?

[kleinman]

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.
Joobz, you can’t tell the difference between the truth and a lie.
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.)
Joobz, go back to my first post on the Evolutionisdead forum and you will see that my position on what ev shows has not changed.
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.
Microevolution is the only part of the theory of evolution and of abiogenesis which has any scientific basis. I have drawn lines but you refuse to pay attention. I have said that de novo generation of a gene or genetic control mechanism represents macroevolution.
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 problem with your analogy is that laminar flow can be demonstrated with known viscosities and flow velocities while the evolution of binding sites requires unrealistically small genomes with unrealistically high mutation rates in order to occur rapidly, neither of which can be demonstrated in the laboratory nor in field measurements. If you had read Dr Schneider’s publication in Nucleic Acids Research about ev you would have seen the following quote:
Variations of the program could be used to investigate how population size, genome length, number of sites, size of recognition regions, mutation rate, selective pressure, overlapping sites and other factors affect the evolution.
Clearly Dr Schneider intended that his program be used to study these parameters. His model shows how profoundly slow the process of random point mutation and natural selection becomes when you use realistic genome lengths and mutation rates.
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.
The only thing that I continually beat is the data obtained from ev. That data shows that random point mutations and natural selection is far too slow when realistic genome lengths and mutation rates are use in the model to support the theory of evolution. In fact the data shows it is mathematically impossible to evolve anything by random point mutations and natural selection, it is far too slow a process.
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, feel free to inform us of the selection process or mutation mechanism that allow you to evolve a megabase or gigabase genome in the time available. It certainly is not random point mutations and natural selection as described by Dr Schneider’s ev model. Maybe we should give you an elevated head rest for this ride.
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?
Perhaps we should say that your view of ev is evolving.
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.
Now that’s another interesting idea you are presenting.
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.
Just the opposite, ev demonstrates that nothing can evolve de novo by random point mutations and natural selection on a gigabase genome.
If you are supporter of Gould’s hypothesis of punctuated equilibrium, populations would even be smaller.This statement is utterly nonsensical.
Gould’s hypothesis of punctuated equilibrium states that evolution occurs more quickly in small subpopulations. This is in direct contradiction with the results from ev.
Does random point mutation and natural selection have any role in your theory of evolution?Yes.
Why don’t you tell us what it is so I can quote you at a later date? I am always looking for annoyobilia from you.
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.
Fair enough, teach the theory of evolution and intelligent design in philosophy courses. There is a distinction that can be made between the two theories, mathematical modeling of the theory of evolution shows that it is impossible. I don’t think anyone has shown intelligent design is mathematically impossible.
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?
Perhaps natural selection would do something with that critter.
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.)
Mathematics differentiates the hard sciences from the soft sciences. You are a devout believer in evolutionism, it just doesn’t meet the standard of a hard science.
No, but I thought you were purporting Modern Ev Theory to be "science".That still doesn't make a perfect mathmetical model a requirement. And, as I mentioned above, it's actually an impossibility.
Paul, your own model argues against your theory.
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? No, the con-ver-gence will be-come less rap-id as we ap-proach the a-symp-tote.
That’s correct, now why don’t you explain that to Paul.
Ok, Kleinman, I asked Google and was told all about Alan Kleinman, PhD:
You are kidding me. Are you telling me that google doesn’t know everything? Keep looking; I have a few publications out there.

[Dr Adequate]

The Atheist ---

My real name, followed by PhD, the whole surrounded by quotes, gets no hits either.

I have never signed myself that way.

[kjkent1]

The only thing that I continually beat is the data obtained from ev. That data shows that random point mutations and natural selection is far too slow when realistic genome lengths and mutation rates are use in the model to support the theory of evolution. In fact the data shows it is mathematically impossible to evolve anything by random point mutations and natural selection, it is far too slow a process.Your statement here is unnecessarily extreme.

Several recently posted articles in this thread show evidence of other biological mechanisms which may increase the speed of evolutionary change. They are not modeled in ev. This doesn't mean that evolution is mathematically impossible -- it just means that the mechanism has yet to be modeled which will satisfy your stated criterion for accepting evolution as mathematically modeled.

You want ev to work faster, but when asked to do some of the fundamental research yourself, you immediately leap to the conclusion that no mechanism can possibly speed up ev.

Such a conclusion is entirely non-scientific and beneath you. You don't have any math nor any scientific test which demonstrates that any of these other, scientifically observed, biological mechanisms, if modeled, would not increase ev's performance to a satisfactory level.

You have also stated that Dr. Schneider took all of these things into account and so this renders such other mechanisms irrelevant. Dr. Schneider must have a crystal ball, because these mechanisms are only now being published, whereas ev has been in existence since 2000.

The point is that you are now playing the speculation game, in the same manner as you accuse your opponents. At first your comments were inventive and worthy of investigation. But by repeating them ad nauseam, without personally undertaking or even crediting others with the possibility that further research may improve ev, you are aiding in the thread to devolve into a flame war.

This is regrettable.

Thus, your statement that evolution is mathematically impossible is simply not supportable -- you don't have sufficient information to reach this conclusion.

But, be careful what you wish for, because if your goal is to show that ev won't cut the mustard as currently constructed, you may end up pushing someone else to cause it to do just that.

Or, maybe that's actually what you want -- to force the mathematical proof of evolution -- because you're really a closet evolutionarian, yourself.

[dv82matt]

...mathematical modeling of the theory of evolution shows that it is impossible.
In order to show that evolution is mathematically impossible you need to show that it cannot ever (even in principal) be mathematically described. It's pretty obvious that you're merely spouting rhetoric as you haven't even made a token effort to support your contention.

When your entire argument is based on something you made up is it any wonder that people find you annoying?

[kleinman]

The only thing that I continually beat is the data obtained from ev. That data shows that random point mutations and natural selection is far too slow when realistic genome lengths and mutation rates are use in the model to support the theory of evolution. In fact the data shows it is mathematically impossible to evolve anything by random point mutations and natural selection, it is far too slow a process.Your statement here is unnecessarily extreme.
We’ll have to disagree on that. I think the data from ev plainly verifies my statement.
Several recently posted articles in this thread show evidence of other biological mechanisms which may increase the speed of evolutionary change. They are not modeled in ev. This doesn't mean that evolution is mathematically impossible -- it just means that the mechanism has yet to be modeled which will satisfy your stated criterion for accepting evolution as mathematically modeled.
That’s another difference between what I post and what you evolutionarians post. I post the data obtained from your models, you post a URL and call that proof. Once I have finished with ev, I’ll look at some of the other mathematical models for evolution and see if they offer any real mathematical proof for the theory of evolution. I think that time is drawing close because Paul has already been indicating that there is no need for mathematical proof for the theory of evolution. If he abandons ev, that leaves only Dr Schneider and myself as defenders of the validity of the ev model.
You want ev to work faster, but when asked to do some of the fundamental research yourself, you immediately leap to the conclusion that no mechanism can possibly speed up ev.
What you don’t seem to comprehend is that ev works very rapidly with small genomes and high mutation rates. The selection process Dr Schneider designed works extremely well under these circumstances. What happens is the search space increases by 4^G as you lengthen the genome in the model and overwhelms the selection process. Even with this artificially precise selection process, random point mutation and natural selection is still profoundly slow when using larger genomes. The problem in the model is not the selection process; the problem in the model (and for the theory of evolution) is the underlying mathematics.
Such a conclusion is entirely non-scientific and beneath you. You don't have any math nor any scientific test which demonstrates that any of these other, scientifically observed, biological mechanisms, if modeled, would not increase ev's performance to a satisfactory level.
The most commonly stated mechanism that would correct what ev is showing is recombination. However, recombination without error does not have the capability of increasing information in the gene pool and recombination with natural selection can cause the loss of alleles which would reduce the information in the gene pool. If evolutionarians are going to claim the recombination is the main driving mechanism for evolution, you are going to have a hard time explaining different genes in humans and chimpanzees. Are you going to claim that frame shift mutations are the main driving force for evolution? How about recombination errors and polyploidy? Each of these mechanisms are dependent on random point mutations and natural selection to produce new genes and you are back to the ev model. Random point mutations and natural selection is the cornerstone for your theory.
You have also stated that Dr. Schneider took all of these things into account and so this renders such other mechanisms irrelevant. Dr. Schneider must have a crystal ball, because these mechanisms are only now being published, whereas ev has been in existence since 2000.
I have never said that the other mechanisms are irrelevant. I only contend that random point mutations and natural selection is a profoundly slow process as shown by ev. Dr Schneider wrote ev in the early 1980’s.
The point is that you are now playing the speculation game, in the same manner as you accuse your opponents. At first your comments were inventive and worthy of investigation. But by repeating them ad nauseam, without personally undertaking or even crediting others with the possibility that further research may improve ev, you are aiding in the thread to devolve into a flame war.
I love the smell of burning evolutionary theory in the morning!
Thus, your statement that evolution is mathematically impossible is simply not supportable -- you don't have sufficient information to reach this conclusion.
Sure it’s supportable. Why do you think that Paul’s evaluation from ev has evolved from it represents reality, to it represents a small portion of the evolutionary landscape, to who needs mathematics for the theory of evolution?
But, be careful what you wish for, because if your goal is to show that ev won't cut the mustard as currently constructed, you may end up pushing someone else to cause it to do just that.
I want you evolutionarians to work on the mathematics of your theory. Maybe you will come to your senses when you realize your theory doesn’t add up.
Or, maybe that's actually what you want -- to force the mathematical proof of evolution -- because you're really a closet evolutionarian, yourself.
Yeah, right, I’ll dress up in a gorilla suit and march in the next evolutionarian pride parade.

[The Atheist]

The Atheist ---

My real name, followed by PhD, the whole surrounded by quotes, gets no hits either.

I have never signed myself that way.Yes, but then again, you're a slightly more retiring chap than kleinman. I've read far more of your posts than his and I have no idea what your name is. I bet if I knew it, I'd find you ok. Our friend Alan Kleinman PhD doesn't seem to come up as a combination anywhere, either. Can't say I've tried too hard. Having an actual PhD won't make his views any less illegitimate than they are anyway.

[Paul C. Anagnostopoulos]

Gould’s hypothesis of punctuated equilibrium states that evolution occurs more quickly in small subpopulations. This is in direct contradiction with the results from ev.
Let's see what Gould said:

A new species can arise when a small segment of the ancestral population is isolated at the periphery of the ancestral range. Large, stable central populations exert a strong homogenizing influence. New and favorable mutations are diluted by the sheer bulk of the population through which they must spread. They may build slowly in frequency, but changing environments usually cancel their selective value long before they reach fixation. Thus, phyletic transformation in large populations should be very rare—as the fossil record proclaims. But small, peripherally isolated groups are cut off from their parental stock. They live as tiny populations in geographic corners of the ancestral range. Selective pressures are usually intense because peripheries mark the edge of ecological tolerance for ancestral forms. Favorable variations spread quickly. Small peripheral isolates are a laboratory of evolutionary change.
Is Ev simulating the totality of this scenario? I think not.

~~ Paul

[Paul C. Anagnostopoulos]

I post the data obtained from your models, ...
None of which, so far, supports your contentions.


I think that time is drawing close because Paul has already been indicating that there is no need for mathematical proof for the theory of evolution. If he abandons ev, that leaves only Dr Schneider and myself as defenders of the validity of the ev model.
Thanks for quoting me out of context.


I only contend that random point mutations and natural selection is a profoundly slow process as shown by ev.
What you contend is that it proves that macroevolution is impossible. Except when you back off on that statement like you did here.


Why do you think that Paul’s evaluation from ev has evolved from it represents reality, to it represents a small portion of the evolutionary landscape, to who needs mathematics for the theory of evolution?
Could you quote me where I said it represents the totality of the evolutionary landscape? Because you keep repeating this as if it's fact.

And what I said about math was:

Mathematical modeling is not a required bit of evidence for evolution.


Perhaps natural selection would do something with that critter.
But imagine he had siblings with the same mutation. Come on, you can do it.

~~ Paul

[Paul C. Anagnostopoulos]

Are you going to claim that frame shift mutations are the main driving force for evolution? How about recombination errors and polyploidy? Each of these mechanisms are dependent on random point mutations and natural selection to produce new genes and you are back to the ev model. Random point mutations and natural selection is the cornerstone for your theory.
How about deletions, insertions, stutters, inversions, and transpositions? They feel left out of the KTPMNS. Won't you let them be part of your theory, too?

~~ Paul

[hammegk]

Are efforts underway to model those effects, or is everyone jumping on your "it don't need math anyway" idea?

[RecoveringYuppy]

I believe someone cited at least one already. But even without those models, there have been extensive efforts to count such mutations and there is not one observed case of any pairs of species having more than could be accounted for by observed mutation rates.

[kleinman]

Gould’s hypothesis of punctuated equilibrium states that evolution occurs more quickly in small subpopulations. This is in direct contradiction with the results from ev. A new species can arise when a small segment of the ancestral population is isolated at the periphery of the ancestral range. Large, stable central populations exert a strong homogenizing influence. New and favorable mutations are diluted by the sheer bulk of the population through which they must spread. They may build slowly in frequency, but changing environments usually cancel their selective value long before they reach fixation. Thus, phyletic transformation in large populations should be very rare—as the fossil record proclaims. But small, peripherally isolated groups are cut off from their parental stock. They live as tiny populations in geographic corners of the ancestral range. Selective pressures are usually intense because peripheries mark the edge of ecological tolerance for ancestral forms. Favorable variations spread quickly. Small peripheral isolates are a laboratory of evolutionary change.
Is Ev simulating the totality of this scenario? I think not.
So which is ev simulating, the small segment of the ancestral population which is rapidly evolving or the large, stable central populations that exert a strong homogenizing influence which is diluting new and favorable mutations?

I think that mathematics being demonstrated by ev strongly calls into question Gould’s hypothesis of punctuated equilibrium.
I post the data obtained from your models, ...None of which, so far, supports your contentions.
Then why do you withdraw your extrapolations so quickly?
I think that time is drawing close because Paul has already been indicating that there is no need for mathematical proof for the theory of evolution. If he abandons ev, that leaves only Dr Schneider and myself as defenders of the validity of the ev model.Thanks for quoting me out of context.
So why don’t you tell us what ev means to the theory of evolution now so I can quote you out of context on that as well.
I only contend that random point mutations and natural selection is a profoundly slow process as shown by ev.What you contend is that it proves that macroevolution is impossible. Except when you back off on that statement like you did here.Why do you think that Paul’s evaluation from ev has evolved from it represents reality, to it represents a small portion of the evolutionary landscape, to who needs mathematics for the theory of evolution?Could you quote me where I said it represents the totality of the evolutionary landscape? Because you keep repeating this as if it's fact.
Paul, you must know by now that I don’t want or need to make up quotes by you or any one else. You evolutionarians produce more than enough annoyobilia for me to work with.
And what I said about math was: Mathematical modeling is not a required bit of evidence for evolution.
That’s convenient since your own mathematical model provides evidence against your own theory. Since you are excising major portions of science out of your theory, you might as well include that no explanation for the selection process for abiogenesis or your theory of evolution are required. Who needs the principle of cause and effect in the theory of evolution?
Are you going to claim that frame shift mutations are the main driving force for evolution? How about recombination errors and polyploidy? Each of these mechanisms are dependent on random point mutations and natural selection to produce new genes and you are back to the ev model. Random point mutations and natural selection is the cornerstone for your theory.How about deletions, insertions, stutters, inversions, and transpositions? They feel left out of the KTPMNS. Won't you let them be part of your theory, too?
Please include any mechanism or selection process you can imagine in your model. Let’s see if that fixes your accounting problem.

[Paul C. Anagnostopoulos]

So which is ev simulating, the small segment of the ancestral population which is rapidly evolving or the large, stable central populations that exert a strong homogenizing influence which is diluting new and favorable mutations?
Neither, because Ev starts with a random genome.


Then why do you withdraw your extrapolations so quickly?
Which extrapolation did I withdraw? Are you talking about the 200,000,000 guess I made?


Paul, you must know by now that I don’t want or need to make up quotes by you or any one else. You evolutionarians produce more than enough annoyobilia for me to work with.
Okay then, your claim that I said that Ev models the totality of the evolutionary landscape is just a lie.

~~ Paul

[hammegk]

I believe someone cited at least one already. But even without those models, there have been extensive efforts to count such mutations and there is not one observed case of any pairs of species having more than could be accounted for by observed mutation rates.
Perhaps I misunderstand that comment, but I'd say at the moment you couldn't construct a more circular argument if you tried.

[kjkent1]

What you don’t seem to comprehend is that ev works very rapidly with small genomes and high mutation rates. The selection process Dr Schneider designed works extremely well under these circumstances. What happens is the search space increases by 4^G as you lengthen the genome in the model and overwhelms the selection process. Even with this artificially precise selection process, random point mutation and natural selection is still profoundly slow when using larger genomes. The problem in the model is not the selection process; the problem in the model (and for the theory of evolution) is the underlying mathematics.1. Please explain to me why the target gnome must evolve as the result of one long process, rather than as the result of the concatenation of several/many smaller/faster processes.

2. You say that the problem is not in the selection process, but rather in the underlying math. This doesn't seem obvious to me at all. Example: ev conducts its selection process by overwriting one half of a population with a duplicate of the better half. What would happen if ev were modified overwrite the population with the top 1% of the better half?

If you can't provide an immediate mathematically precise answer to the above question, then you cannot conclude unequivocally that the problem with ev is not in the selection process.

[Paul C. Anagnostopoulos]

2. You say that the problem is not in the selection process, but rather in the underlying math. This dpesn't seem obvious to me at all. Example: ev conducts its selection process by overwriting one half of a population with a duplicate of the better half. What would happen if ev were modified overwrrite the population with the top 1% of the better half?
I fooled around with this aspect of Ev awhile back. Myriad has experimented with a selection method that does finer selection between critters with the same mistake counts. Apparently it speeds up evolution. I'm going to add something like this to Ev when I get a chance.

~~ Paul

[dv82matt]

Are efforts underway to model those effects, or is everyone jumping on your "it don't need math anyway" idea?
False dilemma.

A mathematical model such as ev is certainly a welcome even nessessry step, just don't expect it to be without limitations.

I'll put it another way, mathematical models of evolution are nessessary (along with other means) to expand our knowledge of evolution, but a lack of them does not indicate evolution is baseless.

[RecoveringYuppy]

Perhaps I misunderstand that comment, but I'd say at the moment you couldn't construct a more circular argument if you tried.
Then I'll make it clearer. We've counted the differences present in genomes between species, we've measured the mutation rates between generations, we've measured the times involved. In no case have we found a difference in genomes that exceeds the mutation rate times the time available.

[hammegk]

Ok. You suggest modern evolutionary Theory is about the same point geologists Hutton & Lyell were about 1800.

I suspect the Theory is not that far advanced ... ;)

[joobz]

Ok. You suggest modern evolutionary Theory is about the same point geologists Hutton & Lyell were about 1800.

I suspect the Theory is not that far advanced ... ;)
And I suspect that the totality of science is at the same point that wine manufacturing was in the 1400's. 500 years from now, I'm sure our primitive notions of the world will seem quite amusing.:o

But oh well, we do the best with what we've got.:)

[hammegk]

The present is key to the past seems to require adustments to include catastrophism.

Where do you see that in modern ev theory ... other than in the fossil record as writ, I mean. :)


Actual Science (physics & chemistry) seems to be reasonably current rather than 500 years in the past.

[joobz]

Yes, but then again, you're a slightly more retiring chap than kleinman. I've read far more of your posts than his and I have no idea what your name is. I bet if I knew it, I'd find you ok. Our friend Alan Kleinman PhD doesn't seem to come up as a combination anywhere, either. Can't say I've tried too hard. Having an actual PhD won't make his views any less illegitimate than they are anyway.
In defense of fairness, Kleinman has a while back in this thread posted his PhD thesis topic. He's had 2 publications from it. Depending on your field of study that either good or bad. They were modeling papers, which modeling typically pumps out the manuscripts. Having no experiments will do that, but this was in 1980ish and computers weren't so friendly then as they are today.

The only thing I find concerning is that Kleinman's work was in heat transfer. For someone to be well versed in heat transfer but not understand the difference between kinetics and thermodynamics is quite troubling to me.

However, I mark that up to being out of the field for 20+ years and do not doubt that he is knowledgable in what he says he is.

The only thing here is his insistence on lies. We see evolution in action (what he call microevolution). Ev shows evolution can bring about new gene binding sites (what he calls macroevolution). This seems a strong link that evolution is involved in the process.

However, kleinman states that it takes too long (under the conditions he chooses). Ok, that's fine. But then does he suggest that new genes don't form? Or that new species aren't created? Or, if species are created then through what mechanism? He states that microevolution occurs, then what prevents microevolution from going too far? What barriers must be encountered that will prevent the natural selection process? Does this mean that at some point every species will stop microevolving and be near identical?

The distinction of micro vs. macro evolution result in logical deadends. I'm sure we don't understand all of evolution but as we learn more we'll adjust it to fit the data. So far, however, nothing has crept up to tear it completely down, like Kleinman seems to think.

[joobz]

The present is key to the past seems to require adustments to include catastrophism.


Where do you see that in modern ev theory ... other than in the fossil record as writ, I mean. :)
I apologize, but i don't understand this question?
Again, my ignorance shines through.:o



Actual Science (physics & chemistry) seems to be reasonably current rather than 500 years in the past.
to my primitive year 2006 brain, they do seem quite current. But will this hold true in the noncatastrophic future?
We're still missing what gravity is, What a wavefunction is, what the orbitals really are.
On the up shot, we do know enough to do some pretty cool stuff. :D

[Paul C. Anagnostopoulos]

He states that microevolution occurs, then what prevents microevolution from going too far? What barriers must be encountered that will prevent the natural selection process?
The only barrier he has talked about so far is time. Apparently, there is time for microevolution, but not for macroevolution. This means that macroevolution is defined as "any change in allele frequency that cannot occur due to time constraints," thus clearly defining macroevolution as impossible. If it's impossible, why do we even have a name for it?

Obviously, such a definition won't do for Creationists. It has to have happened, just not naturalistically. So we sit back and wait for a definition that makes sense, and then for the evidence supporting that definition. Obviously, any black-and-white definition like "macroevolution is speciation" can't possibly be correct.

Wake me up when it happens.
:s2:


~~ Paul

[kleinman]

So which is ev simulating, the small segment of the ancestral population which is rapidly evolving or the large, stable central populations that exert a strong homogenizing influence which is diluting new and favorable mutations?Neither, because Ev starts with a random genome.
And ev finishes with a random genome except for the binding site region. Does ev simulate anything other than the evolution of binding sites? What good are binding sites without a gene associated with the binding site? Is ev simply a mathematical curiosity that doesn’t say anything about the theory of evolution?

I say that ev is describing something very important about the mathematics of random point mutations and natural selection. It is a profoundly slow process when realistic genome lengths and mutation rates are used. Whether you are describing the evolution of binding sites or entire genes, this process is far to slow to support the theory of evolution.
Then why do you withdraw your extrapolations so quickly?Which extrapolation did I withdraw? Are you talking about the 200,000,000 guess I made?
That extrapolation (guess) as well as your modified extrapolation (guess) of 65,000,000 generations and your numerous statements that you have made about ev.
Paul, you must know by now that I don’t want or need to make up quotes by you or any one else. You evolutionarians produce more than enough annoyobilia for me to work with.Okay then, your claim that I said that Ev models the totality of the evolutionary landscape is just a lie.
Paul, I never claimed you said this. What I did was quote your following statement:
I think Ev rankles the IDers because it is a model of actual life, and also because Schneider is fairly good at advertising it.
Ev does not rankle me, you have back peddled so quickly on ev modeling actual life that is where you got your whiplash and Dr Schneider has stopped advertising his model. I have neither need nor desire to lie about what you say.
What you don’t seem to comprehend is that ev works very rapidly with small genomes and high mutation rates. The selection process Dr Schneider designed works extremely well under these circumstances. What happens is the search space increases by 4^G as you lengthen the genome in the model and overwhelms the selection process. Even with this artificially precise selection process, random point mutation and natural selection is still profoundly slow when using larger genomes. The problem in the model is not the selection process; the problem in the model (and for the theory of evolution) is the underlying mathematics.1. Please explain to me why the target gnome must evolve as the result of one long process, rather than as the result of the concatenation of several/many smaller/faster processes.
Are you proposing that half a binding site evolves one genome and the other half evolves on another genome and they somehow combine to make an entire binding site? If you think that different genetic components can evolve on a variety of different life forms then mix and match to give higher life forms, propose a plausible model. Otherwise, this concept is only suitable for the sci-fi channel.
2. You say that the problem is not in the selection process, but rather in the underlying math. This doesn't seem obvious to me at all. Example: ev conducts its selection process by overwriting one half of a population with a duplicate of the better half. What would happen if ev were modified overwrite the population with the top 1% of the better half?
Feel free to try this and see whether this increases the convergence rate sufficiently to support your theory. What I suspect would happen is that this type of selection process would have a similar effect to increasing population. It would help a little but not enough to rescue your theory.
If you can't provide an immediate mathematically precise answer to the above question, then you cannot conclude unequivocally that the problem with ev is not in the selection process.
Feel free to believe whatever you want about ev.
2. You say that the problem is not in the selection process, but rather in the underlying math. This dpesn't seem obvious to me at all. Example: ev conducts its selection process by overwriting one half of a population with a duplicate of the better half. What would happen if ev were modified overwrrite the population with the top 1% of the better half?I fooled around with this aspect of Ev awhile back. Myriad has experimented with a selection method that does finer selection between critters with the same mistake counts. Apparently it speeds up evolution. I'm going to add something like this to Ev when I get a chance.
There you go kjkent1, Paul and Myriad are going to correct the mathematics of ev and rescue your theory. Of course they have not posted any data.
He states that microevolution occurs, then what prevents microevolution from going too far? What barriers must be encountered that will prevent the natural selection process?The only barrier he has talked about so far is time. Apparently, there is time for microevolution, but not for macroevolution. This means that macroevolution is defined as "any change in allele frequency that cannot occur due to time constraints," thus clearly defining macroevolution as impossible. If it's impossible, why do we even have a name for it?
Paul, if you paid closer attention to my arguments you would know that time is not the only barrier to macroevolution. I have also proposed that natural selection is also a barrier to macroevolution. Every microevolutionary step needed to accomplish the macroevolutionary process would have to provide a selective advantage to the creature. If you consider this concept on the genetic level, every mutation required to generate a gene de novo would have to provide a selective advantage to that creature. What selective advantage is there to half a hemoglobin gene? Your theory requires nonexistent forces to overcome impossible mathematics.

[RecoveringYuppy]

What selective advantage is there to half a hemoglobin gene?
Hemoglobin is not created by one gene. And if you look it up you will find that the subunits of hemoglobin (heme and globin) have a variety of uses in other proteins. In fact, half of some hemoglobins would still be hemoglobins themselves.

[delphi_ote]

Hemoglobin is not created by one gene. And if you look it up you will find that the subunits of hemoglobin (heme and globin) have a variety of uses in other proteins. In fact, half of some hemoglobins would still be hemoglobins themselves.
I'm really suprised to see a creationist hitching their wagon to this horse after the beating Behe took at the Dover trial. When will they learn that molecular biologists work so fast these days, by the time a creationist understands how a particular system behaves well enough to declare, "Aha! But you can't explain this!", there is already a pile of literature just waiting to be plopped down in front of them? You'd think they'd learn to at least do an exhaustive literature search first before declaring something unexplained and impossible without molecular divine intervention.

[fishbob]

Paul, if you paid closer attention to my arguments you would know that time is not the only barrier to macroevolution. I have also proposed that natural selection is also a barrier to macroevolution. Every microevolutionary step needed to accomplish the macroevolutionary process would have to provide a selective advantage to the creature. If you consider this concept on the genetic level, every mutation required to generate a gene de novo would have to provide a selective advantage to that creature. What selective advantage is there to half a hemoglobin gene? Your theory requires nonexistent forces to overcome impossible mathematics.

Underlying all Kleinman's big sciency sounding arguments, we find some very familiar bunk.

Previously Kleinman had let slip that he buys into Dembski's discredited statistics, and now we see that he also buys into Behe's discredited 'irreducible complexity'.

[kjkent1]

Please explain to me why the target gnome must evolve as the result of one long process, rather than as the result of the concatenation of several/many smaller/faster processes.Are you proposing that half a binding site evolves one genome and the other half evolves on another genome and they somehow combine to make an entire binding site? If you think that different genetic components can evolve on a variety of different life forms then mix and match to give higher life forms, propose a plausible model. Otherwise, this concept is only suitable for the sci-fi channel.There is an apparent fusion in the human genome, of the still-separate 1st and 2nd chromosomes found in the modern troglodyte chimpanzee. Now, one could argue that this fusion is either by design or by accident, but let’s continue to steer clear of this issue.

Assuming such fusions are accidental and non-fatal, then this suggests that smaller portions of a genome could be slowly evolving as per the ev model, and then a fusion of material could carry that existing information towards a suddenly very different and unexpected future, which is not currently modeled by ev, and which might speed up the evolutionary process by the order of magnitude which you suggest is mathematically impossible.

Now, if you admit that the process I’m suggesting is possible (n.b., it apparently actually happened in the past), and that it can be mathematically modeled, then you can no longer conclude that evolution is mathematically impossible (although you can certainly contend that evolution, exclusively using the ev model is mathematically impossible).

You say that the problem is not in the selection process, but rather in the underlying math. This doesn't seem obvious to me at all. Example: ev conducts its selection process by overwriting one half of a population with a duplicate of the better half. What would happen if ev were modified overwrite the population with the top 1% of the better half?Feel free to try this and see whether this increases the convergence rate sufficiently to support your theory. What I suspect would happen is that this type of selection process would have a similar effect to increasing population. It would help a little but not enough to rescue your theory.Pardon me, but you “suspect” that it would help a little? This indicates that you don’t “know” what will happen.

With all due respect, your position is that evolution is mathematically impossible, and yet you are now admitting that you don’t “know” for certain what the effect of my proposed selection modification would be. Thus, you don’t really know if evolution is mathematically impossible – rather you only suspect that it is.

You realize that if we were in a courtroom, that the judge would be forced to rule your expert analysis inadmissible because your are permitting your personal bias to influence you?

So, let me repeat my challenge to you, so it’s not lost in the rhetoric: If you can't provide an immediate mathematically precise answer to explain how my above-proposed selection modification will effect ev’s performance, then you cannot conclude unequivocally that the problem with ev is not in the selection process – nor can you conclude that evolution is mathematically impossible.

[Paul C. Anagnostopoulos]

And ev finishes with a random genome except for the binding site region. Does ev simulate anything other than the evolution of binding sites? What good are binding sites without a gene associated with the binding site? Is ev simply a mathematical curiosity that doesn’t say anything about the theory of evolution?
Attention all brain cells! Ev demonstrates that evolution can produce information in DNA.


That extrapolation (guess) as well as your modified extrapolation (guess) of 65,000,000 generations and your numerous statements that you have made about ev.
Did I withdraw the 65 million generation estimate?


I think Ev rankles the IDers because it is a model of actual life, and also because Schneider is fairly good at advertising it.
Yup, I should have said "is a model of a bit of actual life." Did you take me to mean that it models the totality of the evolutionary landscape?


Ev does not rankle me, you have back peddled so quickly on ev modeling actual life that is where you got your whiplash and Dr Schneider has stopped advertising his model.
He has? Checking Web site ...

http://www.lecb.ncifcrf.gov/~toms/papers/ev/


What selective advantage is there to half a hemoglobin gene?
Now that the flagellum and eye are no longer the poster children of irreducible complexity, I guess it's hemoglobin.

http://www.spaceref.com/news/viewpr.html?pid=717

http://www.sciencedaily.com/releases/1999/10/991005071327.htm

http://www.bloodjournal.org/cgi/reprint/78/9/2165

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=8587498&dopt=Citation

~~ Paul

[kleinman]

And ev finishes with a random genome except for the binding site region. Does ev simulate anything other than the evolution of binding sites? What good are binding sites without a gene associated with the binding site? Is ev simply a mathematical curiosity that doesn’t say anything about the theory of evolution?Attention all brain cells! Ev demonstrates that evolution can produce information in DNA.
When you finish waking up from your nap, tell all your brain cells that the production of information by random point mutations and natural selection is profoundly slow when realistic genome lengths and mutation rates are used in your ev model.
That extrapolation (guess) as well as your modified extrapolation (guess) of 65,000,000 generations and your numerous statements that you have made about ev.Did I withdraw the 65 million generation estimate?
Oh, I guess I was mistaken. So you are holding to this value for the evolution of 8 binding sites, each 10 bases wide, with a mutation rate of 10^-6 and a population of 1 meg? This is a far slower rate of acquisition of information than the case Dr Schneider published in Nucleic Acids Research. Do you care to redo his estimate of the amount of time it would require to evolve a human genome by random point mutations and natural selection based on this rate of acquisition of information?
I think Ev rankles the IDers because it is a model of actual life, and also because Schneider is fairly good at advertising it.Yup, I should have said "is a model of a bit of actual life." Did you take me to mean that it models the totality of the evolutionary landscape?
Is that bit a zero or a one?
Ev does not rankle me, you have back peddled so quickly on ev modeling actual life that is where you got your whiplash and Dr Schneider has stopped advertising his model.He has? Checking Web site ...
I check his site regularly. In particular I am looking for an opportunity when he is going to do another public presentation on ev. I would like to attend and hear his answers to these issues we have been talking about here. At one time, Dr Schneider was willing to engage in internet discussions on his model, he no longer does this. By the way, how is your whiplash?
What selective advantage is there to half a hemoglobin gene?Now that the flagellum and eye are no longer the poster children of irreducible complexity, I guess it's hemoglobin.
I’m not talking about multiple component biologic systems; I’m talking about any single gene, whether it be hemoglobin, myoglobin or any other gene. What selective advantage is there to any half completed gene?

Not only is time working against your theory, you have no selective process that would direct the evolution of a gene de novo.

If you want to discuss irreducible complexity, why don’t you tell us what gyrase and helicase were doing before the DNA replicase system evolved, especially since you can’t replicate DNA without this system.

My poster child for this debate about evolution is your very own ev computer model. Such a lovely child you have made.

[Paul C. Anagnostopoulos]

Look at this. A useful gene evolved out of junk DNA:

http://www.eurekalert.org/pub_releases/2006-04/sfeb-esc033106.php

And a model for one way new exons can appear:

http://arstechnica.com/journals/science.ars/2006/9/7/5218

~~ Paul

[kleinman]

Look at this. A useful gene evolved out of junk DNA:

http://www.eurekalert.org/pub_releas...-esc033106.php (http://www.eurekalert.org/pub_releases/2006-04/sfeb-esc033106.php)

And a model for one way new exons can appear:

http://arstechnica.com/journals/scie.../2006/9/7/5218 (http://arstechnica.com/journals/science.ars/2006/9/7/5218)
Can evolutionarians ever post a URL that doesn’t contain the text “appear(s) to be”?

That first URL takes fish stories to a new level. Did you hear the story about the one armed fisherman? He caught one that long!

Anyway, that gene could not have evolved by random point mutations and natural selection, ev shows that.

[Paul C. Anagnostopoulos]

Can evolutionarians ever post a URL that doesn’t contain the text “appear(s) to be”?
Not until they are pretty damn sure, no. Would it matter to your confidence in evolution?


Anyway, that gene could not have evolved by random point mutations and natural selection, ev shows that.
You're a kick, Kleinman.

~~ Paul

[Schneibster]

[FONT=Times New Roman]Can evolutionarians ever post a URL that doesn’t contain the text “appear(s) to be”?Oh! Oh! Look! They admit it's "just a theory!" They might be wrong! Jeebus might triumph yet!

What's the matter, kleinman, having trouble with the fact that your opponents are honest and you suffer by the comparison you invite?

[joobz]

Look at this. A useful gene evolved out of junk DNA:

http://www.eurekalert.org/pub_releases/2006-04/sfeb-esc033106.php

And a model for one way new exons can appear:

http://arstechnica.com/journals/science.ars/2006/9/7/5218

~~ Paul
What are you doing, presenting data the contridicts the entire claim that Kleinman makes?!?! But but, this couldn't have been point mutations and natural selection only. Kleinman said so. He hasn't shown it, but he says so. What more do you need?:p

[The Atheist]

In defense of fairness, Kleinman has a while back in this thread posted his PhD thesis topic. Cheers, I just wondered about the reality as he seems more like KuriousKathy than a scientist. He has the same circularity of argument and inability to open his eyes. No matter, he's keeping you guys amused. Personally, I have better things to do.

[cyborg]

Can evolutionarians ever post a URL that doesn’t contain the text “appear(s) to be”?

This isn't Bible time kleinman.

We leave the arrogance to of dogma to people such as your self.

Keep on fappin'. Disgusting.

[fishbob]

If you want to discuss irreducible complexity, why don’t you tell us what gyrase and helicase were doing before the DNA replicase system evolved, especially since you can’t replicate DNA without this system.

Shifting the burden? Ducking your responsibility?
You want consideration of irreducible complexity, you need to explain how it works.
Behe couldn't. Bet you can't either.

[articulett]

Attention all brain cells! Ev demonstrates that evolution can produce information in DNA.


Did I withdraw the 65 million generation estimate?


Yup, I should have said "is a model of a bit of actual life." Did you take me to mean that it models the totality of the evolutionary landscape?


He has? Checking Web site ...

http://www.lecb.ncifcrf.gov/~toms/papers/ev/


Now that the flagellum and eye are no longer the poster children of irreducible complexity, I guess it's hemoglobin.

http://www.spaceref.com/news/viewpr.html?pid=717

http://www.sciencedaily.com/releases/1999/10/991005071327.htm

http://www.bloodjournal.org/cgi/reprint/78/9/2165

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=8587498&dopt=Citation

~~ Paul

And hemoglobin genes die out on occasion too:

With fervor and clarity, Carroll amasses a glut of facts to refute the twisted logic of the anti-Darwinist camp. Proponents of intelligent design, for example, argue that some supreme being created the first cell four billion years ago with all of its complex biochemical systems complete, including those that were to be used later, say for blood clotting. This, says Carroll, "is utter nonsense that disregards fundamentals of genetics." The rule is "use it or lose it," and indeed, unused DNA code is eroded by constant mutation. For example, the Antarctic icefish, a pale, near-transparent inhabitant of the frigid South Atlantic Ocean, has not only lost its ancestors' power to make oxygen-binding red hemoglobin (which it does not need in the cold oxygen-rich waters) but the two genes that code for hemoglobin have also gone extinct: one has disappeared, and the other remains as a non-coding "molecular fossil," a useless remnant that hints at past use but still resides in the icefish DNA. http://www.discover.com/web-exclusives/carrollinterview/

Hemoglobin molecular fossils!--Now that is something Behe, er... Kleinman didn't expect.

And even more for kleinman to ignore in regards to evolution:

http://www.sciencedaily.com/releases/2006/11/061116084058.htm
When a gene normally found to be active in liver tissue is switched on in muscle tissue--muscle development occurs. That's not even a point mutation--that's just the turning on of a gene that is normally inactive. That is why your model is so bad, Kleinman. It just misses so many avenues for evolutionary change. And we don't need a math formula--we have the DNA--we can decode it (have you heard?)--We can see for ourselves what happened. Darwin could only hypothesize about what the units of inheritance in gametes might be-- We see it--read it--analyze it--decode it. We don't waste our time on math problems proving that it couldn't have happened via point mutations because we already know that it has happened--and point mutations don't have a whole lot to do with it.

[kleinman]

Since Paul has quoted Stephen Gould about his concept of punctuated equilibrium, I thought it worthwhile to discuss this hypothesis a little more. Is there any truth in the concept of punctuated equilibrium and if so, what truth is there? Again, here is the quote Paul posted:
A new species can arise when a small segment of the ancestral population is isolated at the periphery of the ancestral range. Large, stable central populations exert a strong homogenizing influence. New and favorable mutations are diluted by the sheer bulk of the population through which they must spread. They may build slowly in frequency, but changing environments usually cancel their selective value long before they reach fixation. Thus, phyletic transformation in large populations should be very rare—as the fossil record proclaims. But small, peripherally isolated groups are cut off from their parental stock. They live as tiny populations in geographic corners of the ancestral range. Selective pressures are usually intense because peripheries mark the edge of ecological tolerance for ancestral forms. Favorable variations spread quickly. Small peripheral isolates are a laboratory of evolutionary change.
I believe that Gould has made the same inappropriate extrapolation that Darwin made. Darwin observed variations in the beaks of finches. What Darwin was seeing was the diversity a species can have by recombination and natural selection. The recombination and natural selection mechanism is a far more rapid mechanism for altering a gene pool than is random point mutation and natural selection. The difference between the two mechanism is that recombination without error can not create new information in the gene pool nor can it alter the homology of a genome, but recombination can rapidly alter the appearance of a species in a relatively short period of time. A few finches with the appropriate shaped beak on the edge of an ecological niche favorable to that beak shape would quickly favor those genetic properties. Darwin and Gould extrapolated this rapid recombination and natural selection phenomena to the evolution of new species.

Ev demonstrates that the concept of punctuated equilibrium can not be applied to random point mutations and natural selection. Two crucial parameters to this mechanism (time and population size) are limited by the hypothesis of punctuated equilibrium.

The concept of punctuated equilibrium is applicable to recombination and natural selection. You can start with small subpopulations with particular genetic characteristics that could be quickly propagated through this subpopulation. It fits Darwin’s observations of the variation of finch beaks. Recombination and natural selection is a rapid phenomenon that can be replicated in the laboratory. What recombination and natural selection does not fit is the capability of transforming one species to another species. Recombination does not have the capability of generating new information in the gene pool however; recombination with natural selection does have the capability of losing alleles from the gene pool.

[RecoveringYuppy]

Ignoring a slew of points that others have already addressed here, but...

How can you preclude that losing alleles can't lead to a new species?

[kleinman]

Ignoring a slew of points that others have already addressed here, but...

How can you preclude that losing alleles can't lead to a new species?
I have only ignored a slew of speculations.

Evolutionarians believe that the most complicated molecules known can occur by random processes directed by this miraculous force of natural selection so why not create new species by the loss of information. If you are going to define new species by this mechanism, you probably should call this devolution.

In case you haven’t noticed, your arguments are becoming more and more illogical.

What are you recovering from anyway? Apparently you still need to recover from evolutionism. I’ll help you with this cure.

[RecoveringYuppy]

So you can't preclude it. Thanks.

[kleinman]

So you can't preclude it. Thanks.
In case you haven’t noticed, I don’t try to preclude every speculation that comes across this forum. I have focused specifically on the mathematics of ev and the results it shows for random point mutation and natural selection. I will diverge slightly and discuss irreducible complexity and punctuated equilibrium because Dr Schneider raised these issues in his publication on ev.

Ev points out a serious mathematical defect in your theory of evolution. Rather than addressing this mathematical defect in your theory, you try to change the subject to what you feel does prove your theory. I have already acknowledged that there are superficial similarities in the genetic structures of different living things. The problem you evolutionarians have is that you have no way of mathematically explaining how these genomes can transform from one to another or how you could form the genes de novo that make up these genomes. These are more than gaps in your theory; ev shows that random point mutations and natural selection can not accomplish these tasks.

Don’t expect me to respond to every speculation raised on this forum. If you have a mathematical argument, I will attempt to respond.

[kjkent1]

Don’t expect me to respond to every speculation raised on this forum. If you have a mathematical argument, I will attempt to respond.Please respond to my last post in this thread. If my understanding of the science involved is inaccurate, then feel free to educate me.

[hammegk]

...

Assuming such fusions are accidental and non-fatal, then this suggests that smaller portions of a genome could be slowly evolving as per the ev model, and then a fusion of material could carry that existing information towards a suddenly very different and unexpected future, which is not currently modeled by ev, and which might speed up the evolutionary process by the order of magnitude which you suggest is mathematically impossible.
Who could argue with all those 'what-ifs'?


... If you can't provide an immediate mathematically precise answer to explain how my above-proposed selection modification will effect ev’s performance, then you cannot conclude unequivocally that the problem with ev is not in the selection process – nor can you conclude that evolution is mathematically impossible.
We can agree no model exists including that effect(sfaik). Unfortunately, the question remains un-answered.

And, at least for me as I understand the situation, the efficacy of ev as a robust explanatory mechanism, particularly for macroev as seen in the fossil record, seems doubtful.

[Paul C. Anagnostopoulos]

I have already acknowledged that there are superficial similarities in the genetic structures of different living things.
One of us does not understand what the word superficial means. And I mean really doesn't understand.

~~ Paul

[kleinman]

Don’t expect me to respond to every speculation raised on this forum. If you have a mathematical argument, I will attempt to respond.Please respond to my last post in this thread. If my understanding of the science involved is inaccurate, then feel free to educate me.
Your speculations generate more questions than answers. Consider this speculation your have made.
There is an apparent fusion in the human genome, of the still-separate 1st and 2nd chromosomes found in the modern troglodyte chimpanzee. Now, one could argue that this fusion is either by design or by accident, but let’s continue to steer clear of this issue.
The obvious first question is that if this evolutionary genetic event occurred, how is homology maintained between the first two members of the human line? If this fusion was purely accidental, you would have had to have the same fusion occur twice, once in a male and once in a female in order to maintain homology between the two genomes. You are now off and running down your speculation trail.

Why don’t you do some homework and pick up a genetics text and see what kind of genetic diseases are caused by fusion and translocation errors in the meiotic process? When you do, you will understand why I see your speculations as so illogical.
And, at least for me as I understand the situation, the efficacy of ev as a robust explanatory mechanism, particularly for macroev as seen in the fossil record, seems doubtful.
Hey, Dr Schneider used ev to predict the evolution of a human genome and the peer reviewers at Nucleic Acids Research felt this was worthy of being published. So if you are going to argue the validity of ev for modeling macroevolution, take it up with the evolutionarians who wrote and published this model.

[kleinman]

I have already acknowledged that there are superficial similarities in the genetic structures of different living things.One of us does not understand what the word superficial means. And I mean really doesn't understand.
Let me help you out with this Paul. There is a bit of similarity in the genetic landscape.

[kjkent1]

Your speculations generate more questions than answers. Consider this speculation your have made.

The obvious first question is that if this evolutionary genetic event occurred, how is homology maintained between the first two members of the human line? If this fusion was purely accidental, you would have had to have the same fusion occur twice, once in a male and once in a female in order to maintain homology between the two genomes. You are now off and running down your speculation trail.

Why don’t you do some homework and pick up a genetics text and see what kind of genetic diseases are caused by fusion and translocation errors in the meiotic process? When you do, you will understand why I see your speculations as so illogical..

You only responded to the first question in my post. Furthermore, I asked that we steer clear of the speculation of how the event took place, and just assume it for the sake of argument.

I will come back to this first issue, but please respond to the second question.

[cyborg]

If you are going to define new species by this mechanism, you probably should call this devolution.

Kleinman made a funny! Look, look, he so funny!

Apparently you still need to recover from evolutionism. I’ll help you with this cure.

What would that be, one bronze age myth taken twice daily?

[joobz]

Hey, Dr Schneider used ev to predict the evolution of a human genome and the peer reviewers at Nucleic Acids Research felt this was worthy of being published. So if you are going to argue the validity of ev for modeling macroevolution, take it up with the evolutionarians who wrote and published this model.
Statements like these are what perlexes me most about you.
You've published. (twice) but still, you've published your work. You know what it means and you know what was approved in the publishing of the work. There is no claim that it models ALL of evolution. Yet you hide behind the guise of appealing to authority as though it supports your claim.

You know better than this. You've published. Therefore, We are back to the fact that you will just lie to prove you case.

[joobz]

Paul, if you paid closer attention to my arguments you would know that time is not the only barrier to macroevolution. I have also proposed that natural selection is also a barrier to macroevolution. Every microevolutionary step needed to accomplish the macroevolutionary process would have to provide a selective advantage to the creature.
And it does. That's the point. If it is causes harms to the organism, it dies and doesn't propogate that mutation.
eventually you'll understand this point, but for the time being I'll wait for you to continue your claims of impossible without any evidence.

[kleinman]

Apparently you still need to recover from evolutionism. I’ll help you with this cure.What would that be, one bronze age myth taken twice daily?
Oh no, this disease is much more serious, it requires a continuous infusion of the truth, something which evolutionarians are not used to.

[cyborg]

Oh no, this disease is much more serious, it requires a continuous infusion of the truth, something which evolutionarians are not used to.

Oh, and I suppose you have The Truth?

Why don't you just call us Falsites instead of ridiculously mangling the word 'evolution' then? It would encompass the full scale of how wrong we are about everything and how right you are about it.

[Paul C. Anagnostopoulos]

The obvious first question is that if this evolutionary genetic event occurred, how is homology maintained between the first two members of the human line? If this fusion was purely accidental, you would have had to have the same fusion occur twice, once in a male and once in a female in order to maintain homology between the two genomes. You are now off and running down your speculation trail.
Surely you don't think of that as really very speculative at all, do you? (or, shhh ... Przewalski's horse)


Why don’t you do some homework and pick up a genetics text and see what kind of genetic diseases are caused by fusion and translocation errors in the meiotic process? When you do, you will understand why I see your speculations as so illogical.
Hang on. Are you suggesting that this event did not actually occur? The extra telomere was just tossed in by the designer for jollies?


Hey, Dr Schneider used ev to predict the evolution of a human genome and the peer reviewers at Nucleic Acids Research felt this was worthy of being published.
He did? Can you quote him?


Let me help you out with this Paul. There is a bit of similarity in the genetic landscape.
One of us does not understand what "a bit of" means.

~~ Paul

[articulett]

Kleinman made a funny! Look, look, he so funny!



What would that be, one bronze age myth taken twice daily?

That's hysterical. You probably need to wash it down with some holy water (which is regular water that you boil the hell out of).

Sometimes it seems like an intelligent designer put them here just to amuse us, doesn't it?

[articulett]

And it does. That's the point. If it is causes harms to the organism, it dies and doesn't propogate that mutation.
eventually you'll understand this point, but for the time being I'll wait for you to continue your claims of impossible without any evidence.

And his argument is actually weaker than that--because a "microevolution" event CAN get passed on just so long as it's not deleterious (reduces reproductive success)--moreso if it sorts with a beneficial allele (it sits next to a highly conserved gene such as a hox gene). And this neutral mutation becomes part of the "tool box" in the gene pool that might be used to benefit some organism in the future.

So a mutation doesn't even have to be beneficial to an organism--just so long as it's not detrimental--and this gives it the opportunity to become beneficial to some organism in the future. Genomes are being tweaked all the time and you never know which mutations (among the "survivers") will be beneficial nor when.

[Paul C. Anagnostopoulos]

Oh, look: "Hypothesis: First-Degree Inbreeding Facilitates Chromosomal Speciation"

http://evolutionlist.blogspot.com/2006/11/hypothesis-first-degree-inbreeding.html

~~ Paul

[Yahzi]

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"?
Hewitt's argument does not depend on the difference between order and complexity.

Hewitt is not arguing that inanimate things have order, and animate things have complexity. Even without knowing what arcane definitions you are pretending to adhere to, I know that's just silly.

Your sheer inability to grasp Hewitt's point is, quite frankly, only slightly more astounding than your inability to grasp my point.

I have shown that order can arise from simple mechanics and energy - which proves that complexity can arise from simple mechanics and energy. The pedantic differences between order and complexity are simply irrelvant to the discussion at hand. Nobody cares - except for you, as a way to demonstrate your lofty superiority, and Hewitt, as a fig leaf to hide the nakedness of his argument behind.

If you would care to skip over your reading problems, and address the point directly, you could explain why the selection and accrual of ordered states is inadequate to produce complexity. Or, to phrase in the original terms: if granola can produce order from simple mechanics, why can't life?

[Yahzi]

I have stated previously that the informational difference between animate and inanimate is not order, it is complexity.
Are you saying that inanimate things cannot ever be complex?

Are you saying that life is defined by complexity? Does that mean the space shuttle is alive? Or the weather system?

I just argued to Matt that you couldn't possibly be arguing anything quite so silly. But then, I am always prepared to be proven wrong.

Dawkins, in the Selfish gene. This proposal is quite widely considered.
You're wrong.

Does the granola sort itself by chance? It's a simple question. Perhaps you could answer it. Does granola sort itself by chance?

If the answer is no, then you already understand that evolution does not work by chance. If the answer is yes, then you are dumber than a box of cereal.

Read Chance and necessity, by Monod
I'm not asking you to read a book to be educated... I am asking you to shake a box of granola.

No you can't reduce complex systems to fractals in that way.
Yes, you can.

When I talked about compression, I was talking about data compression, not about compressing physical objects.
Do you keep red herrings in your pockets, where they leap out upon your keyboard at uncontrollable intervals? Or do you just have severe reading comprehension problems?

Nobody, anywhere, at any point in this thread, for any reason, mentioned physically compressing objects. This concept did not exist in this thread until you introduced in the above sentence. I have no idea why you introduced it. I suspect you don't, either.

I am not sufficiently au fait with this topic to go into details. You will have to ask someone else for that.
Someone like... say... for instance...

me?

I would add that dv82matt seems to me a thoughtful and intelligent person. You should consider his comments carefully.
I can't tell if you're really that much of a suck-up, or if dv82matt is just a sock-puppet.

[Yahzi]

It is true that I cannot give you a precise definition of "complex".
But you can bust my chops over the precise difference between order and complexity?

[hammegk]

The ability/luck/whatever that terran bioactive stuff we call life has to correctly form chemical bonds of the correct chirality -- that choice being a 50/50 chance skaik-- an uncountable number of times in a row is one separator.

[kleinman]

Oh no, this disease is much more serious, it requires a continuous infusion of the truth, something which evolutionarians are not used to.Oh, and I suppose you have The Truth?

Why don't you just call us Falsites instead of ridiculously mangling the word 'evolution' then? It would encompass the full scale of how wrong we are about everything and how right you are about it.
Cyborg, here are the four cardinal signs and symptoms that enable you to diagnosis evolutionism, speculationitis, denialophilia, hyperextraplopia, and amathematica sciencea. Evolutionarian also tend to be cranky and foul mouthed especially when someone co-opts evolutionarian attempts at mathematics and shows them the flaws in their belief system.
Hey, Dr Schneider used ev to predict the evolution of a human genome and the peer reviewers at Nucleic Acids Research felt this was worthy of being published.He did? Can you quote him?
Paul, you know this is one of my favorite quotes from Dr Schneider’s paper so I will again oblige you.
Likewise, at this rate, roughly an entire human genome of ~4 * 10^9 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. However, since this rate is unlikely to be maintained for eukaryotes, these factors are undoubtedly important in accounting for human evolution.
Since we are already in the process of addressing worldwide populations and ev is calling into question whether this parameter would accelerate evolution sufficiently and sexual recombination without error can not increase information in the gene pool, that leaves interspecies gene transfers. Since you are Dr Schneider’s coworker, perhaps you would explain to us what he means by interspecies gene transfers? I still think he should have included intergalactic gene transfers as well.
Let me help you out with this Paul. There is a bit of similarity in the genetic landscape.One of us does not understand what "a bit of" means.
Let’s see, random point mutations and natural selection represents a bit of the evolutionary landscape and there is a bit of similarity in the genetic landscape. Hmmm.

[cyborg]

Cyborg, here are the four cardinal signs and symptoms that enable you to diagnosis evolutionism, speculationitis, denialophilia, hyperextraplopia, and amathematica sciencea.

So when am I get the mathematics of Jesus? Come on Kleinman, you're not even trying. If you will waste your time trying to debunk a false theory then you'll never have the time to elevate the truth now will you?

Evolutionarian also tend to be cranky and foul mouthed

No, f-ck nut, I tend to be cranky and foul mouthed. How dare you devalue me by assuming everyone else shares these awesome qualities automagically.

especially when someone co-opts evolutionarian attempts at mathematics and shows them the flaws in their belief system.

Well if it's a belief system then mathematics can go to hell.

STEP OFF MY FAITH OR BE CRUSHED HEATHEN.

Dumbass.

You should stick to working with probabilities greater than 1.

[hammegk]

No, f-ck nut, I tend to be cranky and foul mouthed.

True. And that and the off-topic gibberish on computer hardware you sometimes post are so far your most endearing qualities.

[kleinman]

Cyborg, here are the four cardinal signs and symptoms that enable you to diagnosis evolutionism, speculationitis, denialophilia, hyperextraplopia, and amathematica sciencea.So when am I get the mathematics of Jesus? Come on Kleinman, you're not even trying. If you will waste your time trying to debunk a false theory then you'll never have the time to elevate the truth now will you?
How do you know if you are not already getting the mathematics of Jesus? Don’t you remember when you said?
This is some serious ****! Souls are at stake here - right kleinman?
Evolutionarian also tend to be cranky and foul mouthed.No, f-ck nut, I tend to be cranky and foul mouthed. How dare you devalue me by assuming everyone else shares these awesome qualities automagically.
Quick, nurse this is a critical case of evolutionism. Start a large bore iv and infuse 10 million units of truth stat.
especially when someone co-opts evolutionarian attempts at mathematics and shows them the flaws in their belief system.Well if it's a belief system then mathematics can go to hell.

STEP OFF MY FAITH OR BE CRUSHED HEATHEN.

Dumbass.

You should stick to working with probabilities greater than 1.
Cyborg, your have moved up on my list as number two or three favorite annoyees, but you need to know that I have no interest in crushing you.

[Paul C. Anagnostopoulos]

Hey, Dr Schneider used ev to predict the evolution of a human genome ...

Likewise, at this rate, roughly an entire human genome of ~4 * 10^9 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. However, since this rate is unlikely to be maintained for eukaryotes, these factors are undoubtedly important in accounting for human evolution.
Oh, that quote.


Since we are already in the process of addressing worldwide populations and ev is calling into question whether this parameter would accelerate evolution sufficiently and sexual recombination without error can not increase information in the gene pool, that leaves interspecies gene transfers.
Sexual recombination without error? What fantasy world does that occur in?


Since you are Dr Schneider’s coworker, perhaps you would explain to us what he means by interspecies gene transfers?
I think he means something like this:

http://evolutionlist.blogspot.com/2006/11/hypothesis-first-degree-inbreeding.html


Let’s see, random point mutations and natural selection represents a bit of the evolutionary landscape and there is a bit of similarity in the genetic landscape. Hmmm.
A bit of similarity in the genetic landscape? I still think we have a different definition of "a bit."


How do you know if you are not already getting the mathematics of Jesus?
And a different definition of mathematics.

~~ Paul

[Paul C. Anagnostopoulos]

Kleinman, would it be helpful if I stipulate that a complete lack of change (error) in the reproduction of genomes would, indeed, disallow an increase in information? Cuz, like, I'm happy to do that.

~~ Paul

[cyborg]

How do you know if you are not already getting the mathematics of Jesus? Don’t you remember when you said?

You didn't answer the question.

Quick, nurse this is a critical case of evolutionism. Start a large bore iv and infuse 10 million units of truth stat.

Now you're getting it Kleinman.

I have no interest in crushing you.

Good. You know not to bother where you can't succeed in one area at least. Now you just need to realise your abject failures elsewhere.

[cyborg]

True. And that and the off-topic gibberish on computer hardware you sometimes post are so far your most endearing qualities.

Yeah, off-topic. That's it. Only other people are allowed to post computer hardware gibberish - or at least if you like it it's not gibberish. It's your kind of gibberish.

[RecoveringYuppy]

Sexual recombination without error? What fantasy world does that occur in?
Don't be bitter. Surely you don't regret all of your ex'es.

[kleinman]

Since we are already in the process of addressing worldwide populations and ev is calling into question whether this parameter would accelerate evolution sufficiently and sexual recombination without error can not increase information in the gene pool, that leaves interspecies gene transfers.Sexual recombination without error? What fantasy world does that occur in?
So you think that recombination errors are your solution to your mathematical dilemma. Do you think that recombination errors and natural selection won’t be subject to the same 4^G increase in the search space that random point mutation and natural selection is subject to? What fantasy world does that occur in?
Since you are Dr Schneider’s coworker, perhaps you would explain to us what he means by interspecies gene transfers?I think he means something like this:

http://evolutionlist.blogspot.com/20...nbreeding.html[/quote (http://evolutionlist.blogspot.com/20...nbreeding.html%5b/quote%5d%5b/quote)]
Have you run out of your own speculations so soon that you now have to post URLs with other evolutionarian speculations? Tell us what you think these interspecies gene transfers are? Do you think it was interspecies gene transfers that caused the evolution of the human species from its primate ancestor?
Let’s see, random point mutations and natural selection represents a bit of the evolutionary landscape and there is a bit of similarity in the genetic landscape. Hmmm.[quote="Paul"]A bit of similarity in the genetic landscape? I still think we have a different definition of "a bit."
Well, we can file this next to our definitions for species and macro/microevolution.
How do you know if you are not already getting the mathematics of Jesus?And a different definition of mathematics.
I think you should read the Bible; you would be surprised at how much Jesus Christ talks about mathematics.
Kleinman, would it be helpful if I stipulate that a complete lack of change (error) in the reproduction of genomes would, indeed, disallow an increase in information? Cuz, like, I'm happy to do that.
I don’t know if you would get complete agreement with other evolutionarians. Munch_e_cracker on the EvolutionisDead forum postulated that recombination without error might affect the way a gene could be expressed. Whether this represents an increase in information in the Shannon sense, I don’t know. However, if I were trying to defend the evolutionarian position, I would not abandon any version of gene modification whether it is considered a normal biological process or an error in a biological process in order to try an explain macroevolution. I happen to think this is one of the better speculations for the theory of evolution. In this case, you don’t need new genes; you only need to alter the way existing genes are expressed in order to get new species. I see many problems in this concept but that is a discussion for another thread.

If you are asking me to stipulate to the DNA replicase system making a perfect duplicate of a genome disallows an increase in information, that’s ok with me.

[articulett]

Ignoring a slew of points that others have already addressed here, but...

How can you preclude that losing alleles can't lead to a new species?

He can't due to mind blindness-- http://www.cnn.com/2006/TECH/science/12/29/canada.arctic.ap/index.html

They do (see ice fish example above).

[articulett]

So when am I get the mathematics of Jesus? Come on Kleinman, you're not even trying. If you will waste your time trying to debunk a false theory then you'll never have the time to elevate the truth now will you?



No, f-ck nut, I tend to be cranky and foul mouthed. How dare you devalue me by assuming everyone else shares these awesome qualities automagically.

Well if it's a belief system then mathematics can go to hell.

STEP OFF MY FAITH OR BE CRUSHED HEATHEN.

Dumbass.

You should stick to working with probabilities greater than 1.

I didn't know we could say dumbass. (jots note to self: "dumbass-- A-OK")

And, not to sound self important--but I also share the awesome qualities, just not as amusingly--but still...

[joobz]

Over the past 10+pages, many of us have presented new data, new information. Supporting evidence that evolution fits our world view. That evolution explains things well. It isn't perfect, there are holes, but it does the best job.

During these same pages, Kleinman has presented the same wrong evidence over and over and over and over and over and over over and over and over and over and over and over and over and over and over and over and over and over and over and over and over and over and over and over over and over and over and over and over and over over and over and over and over and over and over and over and over and over and over and over and over over and over and over and over and over and over and over and over and over and over and over and over and over and over and over and over and over and over again.

I'm going to side with the facts. Let me know, when Kleinman starts to present some.

[articulett]

Oh, look: "Hypothesis: First-Degree Inbreeding Facilitates Chromosomal Speciation"

http://evolutionlist.blogspot.com/2006/11/hypothesis-first-degree-inbreeding.html

~~ Paul

That was a great article Paul--and it makes sense...especially in speciation such as between us and the apes where fusions or translocations occur--close relatives are likely to share the same freaky gene mutation. On occasion, this is just what a new species needs to get a jump start, plus, as the article indicates, it weeds out those pesky recessive alleles that might lead to problems later. Sure, it's not flattering of thinking of oneself begat via incest, but it must be true--such is the case for each and every individual on the tree of life once sexual reproduction took off--

[kleinman]

During these same pages, Kleinman has presented the same wrong evidence over and over and over and over and over and over over and over and over and over and over and over and over and over and over and over and over and over and over and over and over and over and over and over over and over and over and over and over and over over and over and over and over and over and over and over and over and over and over and over and over over and over and over and over and over and over and over and over and over and over and over and over and over and over and over and over and over and over again.
Were those stutter errors or deletion errors?

[Paul C. Anagnostopoulos]

So you think that recombination errors are your solution to your mathematical dilemma. Do you think that recombination errors and natural selection won’t be subject to the same 4^G increase in the search space that random point mutation and natural selection is subject to?
But you see, Alan, it is the recombination errors (among others) that result in the increase in the size of the genome. The enlarged genome is not random to begin with, so your 4^G search problem is even more irrelevant than it already was.


Have you run out of your own speculations so soon that you now have to post URLs with other evolutionarian speculations? Tell us what you think these interspecies gene transfers are? Do you think it was interspecies gene transfers that caused the evolution of the human species from its primate ancestor?
So we are criticized for speculating, and criticized when we don't speculate. I'll make a deal with you: If you will post one coherent paragraph about what you think is going on, then I will post a paragraph about interspecies gene transfers.


I don’t know if you would get complete agreement with other evolutionarians. Munch_e_cracker on the EvolutionisDead forum postulated that recombination without error might affect the way a gene could be expressed. Whether this represents an increase in information in the Shannon sense, I don’t know.
I don't know what he's talking about.


If you are asking me to stipulate to the DNA replicase system making a perfect duplicate of a genome disallows an increase in information, that’s ok with me.
It there were no mechanisms for change at all, so that every creature were a perfect copy of its parent(s), then evolution would not exist.

~~ Paul

[kleinman]

So you think that recombination errors are your solution to your mathematical dilemma. Do you think that recombination errors and natural selection won’t be subject to the same 4^G increase in the search space that random point mutation and natural selection is subject to?But you see, Alan, it is the recombination errors (among others) that result in the increase in the size of the genome. The enlarged genome is not random to begin with, so your 4^G search problem is even more irrelevant than it already was.
So that’s the fantasy world your theory resides in. You should pay more attention to the way ev converges. As ev gets closer and closer to the perfect creature, the rate of convergence becomes slower and slower. Those nonrandom portions of the newly lengthen genome due to the recombination errors still have to be transformed into new functional genes, unless you are proposing that those new nonrandom portions are already the new functional genes. In addition, this still doesn’t solve your problem of the de novo evolution of genes.
Have you run out of your own speculations so soon that you now have to post URLs with other evolutionarian speculations? Tell us what you think these interspecies gene transfers are? Do you think it was interspecies gene transfers that caused the evolution of the human species from its primate ancestor?So we are criticized for speculating, and criticized when we don't speculate. I'll make a deal with you: If you will post one coherent paragraph about what you think is going on, then I will post a paragraph about interspecies gene transfers.
That’s not quite the point that I am trying to make. What I am saying is that I am not willing to reply to every evolutionarian speculation that is posted on this thread. That includes ones that are posted in person and ones posted in the form of URLs. If you think you can make an argument from something you have read on a web site, distill down what you have read and put it in your words to make your point.

If you want a jump start on interspecies gene transfers, I can think of several possibilities. You can have interspecies gene transfers by viruses and phages to a host. You may also be able to have an interspecies gene transfer by some form of phagocytosis of genetic material that is somehow incorporated into the host cell. Another possible mechanism for interspecies gene transfer would be for nonhomologous life forms having successful recombination.
I don’t know if you would get complete agreement with other evolutionarians. Munch_e_cracker on the EvolutionisDead forum postulated that recombination without error might affect the way a gene could be expressed. Whether this represents an increase in information in the Shannon sense, I don’t know.I don't know what he's talking about.
I think what munch_e_cracker was trying to say is that the development of a creature is dependent on how genes are expressed. For example if the gene(s) that controls the production of growth hormone are somehow selected by recombination to produce more growth hormone, you would get larger organisms without evolving any new genes.
If you are asking me to stipulate to the DNA replicase system making a perfect duplicate of a genome disallows an increase in information, that’s ok with me.It there were no mechanisms for change at all, so that every creature were a perfect copy of its parent(s), then evolution would not exist.
Recombination (without error) and natural selection is clearly a mechanism for change, and a rapid mechanism for change at that. It is this phenomenon which I think has misled evolutionarians to believe that mutations and natural selection could also occur rapidly.

[kjkent1]

Paul, as moderator, would you please clarify the purpose of this thread. Did you set this forum up so that kleinman would have a single locale within which you and he could continue to argue about ev, or were you hoping to brainstorm about methods of refining Dr. Schneider's model or both or something else or what?

[quixotecoyote]

kleinman:


Recombination (without error) and natural selection is clearly a mechanism for change, and a rapid mechanism for change at that.

Can you please explain how this is possible? I do not know of any mechanism which would allow this to happen.

[kleinman]

Paul, as moderator, would you please clarify the purpose of this thread. Did you set this forum up so that kleinman would have a single locale within which you and he could continue to argue about ev, or were you hoping to brainstorm about methods of refining Dr. Schneider's model or both or something else or what?
What’s your problem, do you want to censor me?
Recombination (without error) and natural selection is clearly a mechanism for change, and a rapid mechanism for change at that.Can you please explain how this is possible? I do not know of any mechanism which would allow this to happen.
Here are two obvious examples. Darwin observed that there were striking differences in the sizes and shapes of finch beaks and took this as evidence of macroevolution. What Darwin was seeing was the rapid variation you can obtain by sexual recombination and natural selection. In addition, this was an example of punctuated equilibrium that Gould postulated. Dog breeding is another example of recombination and (not so) natural selection. Striking differences between different dog breeds can be obtained by this process quite rapidly. However, it only takes a few generations for these striking characteristics to disappear when breeding is not closely controlled. These are examples of microevolutionary process.

In contrast to the very rapid changes in shapes and sizes of the creatures possible by recombination without error and natural selection, the ev computer model shows that random point mutations and natural selection is a profoundly slow process for evolving binding sites when realistic parameters are used in the model. The process of random point mutations and natural selection is far to slow a process to explain macroevolution.

[quixotecoyote]

Here are two obvious examples. Darwin observed that there were striking differences in the sizes and shapes of finch beaks and took this as evidence of macroevolution. What Darwin was seeing was the rapid variation you can obtain by sexual recombination and natural selection. In addition, this was an example of punctuated equilibrium that Gould postulated. Dog breeding is another example of recombination and (not so) natural selection. Striking differences between different dog breeds can be obtained by this process quite rapidly. However, it only takes a few generations for these striking characteristics to disappear when breeding is not closely controlled. These are examples of microevolutionary process.

Ahh. Now I understand what you are saying. However, orginally there had to be a finch with a bigger beak in order to be able to sexually recombine the genes in order to spead the trait. This just moves the mutation back a step.

In contrast to the very rapid changes in shapes and sizes of the creatures possible by recombination without error and natural selection, the ev computer model shows that random point mutations and natural selection is a profoundly slow process for evolving binding sites when realistic parameters are used in the model. The process of random point mutations and natural selection is far to slow a process to explain macroevolution.

I have been casually following this thread, and I don't understand the revelance of point mutation alone being profoundly slow. It's been awhile since my college bio, but weren't there 3 or 4 other types of mutation in addition to the sexual recomination you referened earlier? Would this just show that your model would have to model more variables to be complete?

[kleinman]

Here are two obvious examples. Darwin observed that there were striking differences in the sizes and shapes of finch beaks and took this as evidence of macroevolution. What Darwin was seeing was the rapid variation you can obtain by sexual recombination and natural selection. In addition, this was an example of punctuated equilibrium that Gould postulated. Dog breeding is another example of recombination and (not so) natural selection. Striking differences between different dog breeds can be obtained by this process quite rapidly. However, it only takes a few generations for these striking characteristics to disappear when breeding is not closely controlled. These are examples of microevolutionary process.Ahh. Now I understand what you are saying. However, orginally there had to be a finch with a bigger beak in order to be able to sexually recombine the genes in order to spead the trait. This just moves the mutation back a step.
And that is the point of this discussion. Ev is a computer model of how binding sites could have evolved by random point mutations and natural selection and this is a profoundly slow process. Random point mutations and natural selection could not have evolved the bigger beak as shown by the profoundly slow convergence of ev, so what mechanism could have evolved the gene(s) for the bigger beak or for any beak at all?
In contrast to the very rapid changes in shapes and sizes of the creatures possible by recombination without error and natural selection, the ev computer model shows that random point mutations and natural selection is a profoundly slow process for evolving binding sites when realistic parameters are used in the model. The process of random point mutations and natural selection is far to slow a process to explain macroevolution.I have been casually following this thread, and I don't understand the revelance of point mutation alone being profoundly slow. It's been awhile since my college bio, but weren't there 3 or 4 other types of mutation in addition to the sexual recomination you referened earlier? Would this just show that your model would have to model more variables to be complete?
It is my contention that random point mutation and natural selection is the cornerstone to the theory of evolution. Without this mechanism, you have no way to transform the genetic sequences generated by other forms of genetic errors to new useful genes.

[articulett]

Were those stutter errors or deletion errors?

Tandem repeats.

(...get thyself a clue.)

[articulett]

kleinman:

Can you please explain how this is possible? I do not know of any mechanism which would allow this to happen.

I think, by recombination he's referring to sex. And can you get varying phenotypic changes depending on how these genes come together. Yes. For example--if dad donates a Y--the recombinant is a boy. If Dad donates an X--the recombinant is a girl. If there are additive alleles (such as in hair and eye color--height--etc.) then yes...you can have things unlike mom and dad (say inbetween). Or a recominant might have 2 recessive genes and be an albino...or have some other recessive trait. Now, he could be referring to "crossing over" which happens before two gametes form a zygote...but I don't think he's anywhere near that. Recombinantion is just different ways the genes can sort themselves.

So that's my best guess of what he's saying--of course genomes can also have DNA inserted via vectors, but I think he's still on chapter one of "Life and How it Came to Be." Of course, I could be absolutely wrong, and he may be far more brilliant than the rest of us...but I suspect that is probably only true in his head.

[quixotecoyote]

articulett:

You missed post #1343 where I figured that out. (A crime worthy of stoning in some jurisdictions, I might add :p )

kleinman:

It is my contention that random point mutation and natural selection is the cornerstone to the theory of evolution. Without this mechanism, you have no way to transform the genetic sequences generated by other forms of genetic errors to new useful genes.

Which theory of evolution are you referring to? The one I learned had gene duplication as a larger contributor than point mutations.

[kleinman]

It is my contention that random point mutation and natural selection is the cornerstone to the theory of evolution. Without this mechanism, you have no way to transform the genetic sequences generated by other forms of genetic errors to new useful genes.Which theory of evolution are you referring to? The one I learned had gene duplication as a larger effect.
I’m referring to the mushy soft theory of evolution that has no mathematical foundation, only a series of speculations and unscientific extrapolations.

So when they taught you that gene duplication has a larger effect, how do you transform these duplicated genes to new genes?

[quixotecoyote]

I’m referring to the mushy soft theory of evolution that has no mathematical foundation, only a series of speculations and unscientific extrapolations.


Ahh ok. We're talking about different theories. I'm sure the one you're talking about is indeed fatally flawed. As I'm not familiar with that one at all, I'm afraid there's nothing more I can contribute to this conversation.

[Paul C. Anagnostopoulos]

So that’s the fantasy world your theory resides in. You should pay more attention to the way ev converges. As ev gets closer and closer to the perfect creature, the rate of convergence becomes slower and slower. Those nonrandom portions of the newly lengthen genome due to the recombination errors still have to be transformed into new functional genes, unless you are proposing that those new nonrandom portions are already the new functional genes. In addition, this still doesn’t solve your problem of the de novo evolution of genes.
Indeed, but you have absolutely no idea how long it might take for a copy of a gene to evolve a new function. Certainly not from Ev, which appears to be the entire basis of your anti-evolutionism.


If you want a jump start on interspecies gene transfers, I can think of several possibilities. You can have interspecies gene transfers by viruses and phages to a host. You may also be able to have an interspecies gene transfer by some form of phagocytosis of genetic material that is somehow incorporated into the host cell. Another possible mechanism for interspecies gene transfer would be for nonhomologous life forms having successful recombination.
And another possibility is that, long ago, genes freely floated about in some medium that housed many different protospecies.


Recombination (without error) and natural selection is clearly a mechanism for change, and a rapid mechanism for change at that.
What I said was that if there were no mechanisms for change at all, then evolution would not occur.

~~ Paul

[Paul C. Anagnostopoulos]

Paul, as moderator, would you please clarify the purpose of this thread. Did you set this forum up so that kleinman would have a single locale within which you and he could continue to argue about ev, or were you hoping to brainstorm about methods of refining Dr. Schneider's model or both or something else or what?
I started this thread to complain about annoying creationists. It has taken on a life of its own, which has certainly been educational for me.

~~ Paul

[Paul C. Anagnostopoulos]

It is my contention that random point mutation and natural selection is the cornerstone to the theory of evolution. Without this mechanism, you have no way to transform the genetic sequences generated by other forms of genetic errors to new useful genes.
So you must be counting all the following as "point mutations": single base changes; multiple base changes; insertions; deletions; stutters; inversions; translocations.

The problem is, Ev only models one of those, and only beginning with a random genome.

~~ Paul

[kleinman]

I’m referring to the mushy soft theory of evolution that has no mathematical foundation, only a series of speculations and unscientific extrapolations.Ahh ok. We're talking about different theories. I'm sure the one you're talking about is indeed fatally flawed. As I'm not familiar with that one at all, I'm afraid there's nothing more I can contribute to this conversation.
There is no other theory of evolution than the mushy soft theory we have been discussing on this thread.

I guess when you learned that gene duplication has a larger effect; you never thought to ask your instructor how these duplicated genes were transformed to new genes.
So that’s the fantasy world your theory resides in. You should pay more attention to the way ev converges. As ev gets closer and closer to the perfect creature, the rate of convergence becomes slower and slower. Those nonrandom portions of the newly lengthen genome due to the recombination errors still have to be transformed into new functional genes, unless you are proposing that those new nonrandom portions are already the new functional genes. In addition, this still doesn’t solve your problem of the de novo evolution of genes.Indeed, but you have absolutely no idea how long it might take for a copy of a gene to evolve a new function. Certainly not from Ev, which appears to be the entire basis of your anti-evolutionism.
Certainly I have an idea how long it would take to evolve a copy of a gene to a new function. Ev gives us that idea. Your so far un-retracted extrapolation of 65,000,000 generations to evolve 8 binding sites with a width of 10 bases, mutation rate of 10^-6 on a 100k genome and a population of a million give us an idea where the goal posts are. That is the evolution of 80 loci in 65,000,000 generations. So all you have to do is come up with some selection process that would take that duplicated gene to a new functioning gene such that every helpful mutation is selected for in the process. Make your model and prove me wrong and prove your theory right. The mathematics is even less hopeful for evolving the original gene de novo.
If you want a jump start on interspecies gene transfers, I can think of several possibilities. You can have interspecies gene transfers by viruses and phages to a host. You may also be able to have an interspecies gene transfer by some form of phagocytosis of genetic material that is somehow incorporated into the host cell. Another possible mechanism for interspecies gene transfer would be for nonhomologous life forms having successful recombination.And another possibility is that, long ago, genes freely floated about in some medium that housed many different protospecies.
Joobz has not told us how ribose formed long ago and you already have this primordial soup of genes floating around mixing and matching under some unknown selection process.

Is this what you think Dr Schneider was talking about when he mentioned interspecies gene transfers in his paper on ev?
Recombination (without error) and natural selection is clearly a mechanism for change, and a rapid mechanism for change at that.What I said was that if there were no mechanisms for change at all, then evolution would not occur.
Ok.
It is my contention that random point mutation and natural selection is the cornerstone to the theory of evolution. Without this mechanism, you have no way to transform the genetic sequences generated by other forms of genetic errors to new useful genes.So you must be counting all the following as "point mutations": single base changes; multiple base changes; insertions; deletions; stutters; inversions; translocations.

The problem is, Ev only models one of those, and only beginning with a random genome.
Again, ev does not model the evolution of a random genome, ev models the evolution of binding sites on a portion of a random genome, the rest of the genome remains random. Are you going to write an updated version of ev and include these other mechanisms to make your case since random point mutations and natural selection does not support your theory?

Hey all of you, have a safe and happy new year.

[Paul C. Anagnostopoulos]

Again, ev does not model the evolution of a random genome, ev models the evolution of binding sites on a portion of a random genome, the rest of the genome remains random. Are you going to write an updated version of ev and include these other mechanisms to make your case since random point mutations and natural selection does not support your theory?
Ah, so you're not including those other mutations as point mutations. Therefore your strange idea that just single-point substitutions are the cornerstone of evolution has no basis in reality. No one else thinks that. You do have your own personal mushy soft theory of evolution. I was calling it KTPMNS, but perhaps I'll call it KOPMSTE.

~~ Paul

[articulett]

articulett:

You missed post #1343 where I figured that out. (A crime worthy of stoning in some jurisdictions, I might add :p )

kleinman:

Which theory of evolution are you referring to? The one I learned had gene duplication as a larger contributor than point mutations.

I don't think that quote was actually made by me--I never make that sort of emoticon.

[quixotecoyote]

I wasn't quoting you, I was responding to you. Sorry, I still have a tendency to use post conventions from other forums. I have to get in the habit of just putting the posters name in the quote box rather than addressing them before typing.

[kleinman]

Again, ev does not model the evolution of a random genome, ev models the evolution of binding sites on a portion of a random genome, the rest of the genome remains random. Are you going to write an updated version of ev and include these other mechanisms to make your case since random point mutations and natural selection does not support your theory?Ah, so you're not including those other mutations as point mutations. Therefore your strange idea that just single-point substitutions are the cornerstone of evolution has no basis in reality. No one else thinks that. You do have your own personal mushy soft theory of evolution. I was calling it KTPMNS, but perhaps I'll call it KOPMSTE.
When I’ve looked up mutation rates, I don’t recall whether they include all the forms of mutations you are talking about. What I can tell you is that no matter what the form of mutation, you will still be subject to the 4^G search space effect. In addition, you have no selection mechanism that would select for a gene de novo no matter what your mechanism of mutation is. Your theory is still mushy soft with no mathematical basis.

When you think about your primordial soup do you hum, mmm, mmm, good, mmm, mmm, good, evolution soup is mmm, mmm, good?

[articulett]

I wasn't quoting you, I was responding to you. Sorry, I still have a tendency to use post conventions from other forums. I have to get in the habit of just putting the posters name in the quote box rather than addressing them before typing.


I re-read--and you're right--I should have finished reading before posting. You win. Don't stone me.

On the other hand, I now know how to make one of these: :p

[articulett]

I started this thread to complain about annoying creationists. It has taken on a life of its own, which has certainly been educational for me.

~~ Paul

If you post it,--
they will come.

[Paul C. Anagnostopoulos]

In addition, you have no selection mechanism that would select for a gene de novo no matter what your mechanism of mutation is.
If by "gene" you mean "DNA-encoded gene found in modern life," then I suspect you are right. If you mean anything even vaguely resembling the concept of a gene, then you're just being funny.

~~ Paul

[VonNeumann]

Who are the 'annoying creationists'?

Those who believe in the supernatural creative power of 'randomness'?
or
Those who believe in the supernatural creative power of 'design'?

[Senor_Pointy]

Who are the 'annoying creationists'?

Those who believe in the supernatural creative power of 'randomness'?
or
Those who believe in the supernatural creative power of 'design'?

Either. With the not-annoying people being those who understand the difference between "chance" and "natural selection." (Or just selection in general)

[Yahzi]

Who are the 'annoying creationists'?
The ones who refuse to have an honest discussion.

Nothing wrong with having a different point of view. Present your evidence and let's talk about it. But once we've shown why your argument fails, either shut up, or come up with something new. Otherwise prepare to face the opprobrium of being branded... annoying!

:)

[articulett]

I think it's so cool that Paul puts up a post called "annoying creationists"--and they flock to it like moths to a flame...

[Paul C. Anagnostopoulos]

Imagine a world in which the Creationists stop using the stupid, busted, debunked, ridiculous canard "evolution is random." Ah, sweet bliss. We could take the conversation to a whole new level!

~~ Paul

[kleinman]

In addition, you have no selection mechanism that would select for a gene de novo no matter what your mechanism of mutation is.If by "gene" you mean "DNA-encoded gene found in modern life," then I suspect you are right. If you mean anything even vaguely resembling the concept of a gene, then you're just being funny.
What color paint would you like for this corner you are painting yourself into?

So you are proposing that these protospecies in this primordial soup were assembling some type of molecules (RNA strands from RNA bases?) with some type of protoselection process making some type of self replicating protogenes. Now that is protofunny.
Who are the 'annoying creationists'?

Those who believe in the supernatural creative power of 'randomness'?
or
Those who believe in the supernatural creative power of 'design'?
Or c) None of the above
I think it's so cool that Paul puts up a post called "annoying creationists"--and they flock to it like moths to a flame...
Shouldn’t that be “flock to it like a moth to a flame”?
Imagine a world in which the Creationists stop using the stupid, busted, debunked, ridiculous canard "evolution is random." Ah, sweet bliss. We could take the conversation to a whole new level!
Now what’s your problem? Are you tired of talking about the mathematics of ev? Or should I say the protomathematics of ev? Maybe what we have been having here is a protoconversation about the protoevolutionary theory?

Glad you survived New Year’s Eve.

[Paul C. Anagnostopoulos]

So you are proposing that these protospecies in this primordial soup were assembling some type of molecules (RNA strands from RNA bases?) with some type of protoselection process making some type of self replicating protogenes. Now that is protofunny.
Protospecies: Indeed, I don't know how to define species way back at the beginning of life. Do you?

Protoselection process: You don't need the prefix proto- here. Selection is selection.

Protogenes: Be careful. A gene is DNA coding for a protein. I'm not sure what the original gene-like molecules were. Are you?

The point is quite simple: You're talking out of your arse when you say "you have no selection mechanism that would select for a gene de novo."

~~ Paul

[kleinman]

So you are proposing that these protospecies in this primordial soup were assembling some type of molecules (RNA strands from RNA bases?) with some type of protoselection process making some type of self replicating protogenes. Now that is protofunny.Protospecies: Indeed, I don't know how to define species way back at the beginning of life. Do you?
Hey, you evolutionarians can’t define a species so you make up a term protospecies. So why don’t you give us a protodefinition for that term.
Protoselection process: You don't need the prefix proto- here. Selection is selection.
Protoselection-smotoselection, you don’t have any selection process in your protosoup.
Protogenes: Be careful. A gene is DNA coding for a protein. I'm not sure what the original gene-like molecules were. Are you?
You sure protogenes don’t code for protoproteins? The reason why you and I are not sure what the original gene-like molecules were is that there is no evidence for these protomolecules, but don’t let that get in the way of your belief system, it just doesn’t have any scientific basis.
The point is quite simple: You're talking out of your arse when you say "you have no selection mechanism that would select for a gene de novo."
Oh, so you are finally going to tell us what this magical selection process is that allows for evolution of genes de novo?

The point of this thread is that your own computer model shows that your own theory is mathematically impossible and you would rather talk about anything else besides what your model shows. Even with your artificial selection process in your model, you still can’t get rapid enough convergence to support your theory and you can’t tell us what your real selection process is that would evolve genes de novo. Your own computer model reveals the mush of the theory of evolution.

Speculationitis, denialophilia, hyperextraplopia, and amathematica sciencea

[articulett]

So you are proposing that these protospecies in this primordial soup were assembling some type of molecules (RNA strands from RNA bases?) with some type of protoselection process making some type of self replicating protogenes. Now that is protofunny.

Shouldn’t that be “flock to it like a moth to a flame”?

[FONT=Times New Roman][SIZE=3]Now what’s your problem? Are you tired of talking about the mathematics of ev? Or should I say the protomathematics of ev? Maybe what we have been having here is a protoconversation about the protoevolutionary theory?

A moth (singular)...doesn't "flock". "Moths" is plural: "Creationists" is plural. Kleinmann, Hewitt, VonNeumann and Hammegk are people (though I use the term loosely in case of hammy). "people" is plural.

Now that I think of it, I'm not sure moths "flock" (technically), but flames do flicker--kinda' like the photons on a computer screen...where creationists flock.

By the way...speaking of protogenes--you do remember a bit about molecules and compounds form, right--how water is comprised of 2 parts Hydrogen and 1 part Oxygen via a molecular bond? Ice has the same ingredients different bond. The planets we know of have a nice sort of spherical shape to them...remember that there does not anyone running things for atoms to create "stuff"--big stuff like planets and little stuff like amino acids. If you have the elements interacting with energy via a star and an environment that affects "stuff"--you can get things like water and "stuff" that grows in water--

You should see the cool stuff that they are finding in the depths of the ocean. Did you hear about the shark that walks on it's fins? The little hairy lobsteresque thing? There is a lot of weird stuff down there.
See:
http://zaxy.wordpress.com/
http://www.ens-newswire.com/ens/dec2006/2006-12-11-01.asp

but we just recently discovered atoms and DNA, plus were just now getting our first peek at what's down there, but, rest assured, we already know there are tons of "proto" life in the ocean. See! http://www.discover.com/issues/mar-06/cover/
And check this out: http://www.physorg.com/news85857909.html
Heck, we just figured out that we are breathing life all the time: http://www.medicalnewstoday.com/medicalnews.php?newsid=59473

Oh, check this babe: http://rstours.com/html/gal_rosy_lipped.html

That shall be my next avatar, I think.

Instead of worrying about numbers of moths and math problems, you should get out more. Look at what you are missing. There are life forms going up your nose as you read this.

[articulett]

OH...and check out the pygmy elephants--just precious: http://zaxy.wordpress.com/2006/07/06/miniature-elephants-are-a-separate-and-unique-species/

You guys are missing the good stuff--all because you have purposely chosen not to understand evolution. And you live in a time when we can know stuff our ancestors would have died to know.

Bronze age texts are bad places to get scientific info. But it's probably too late to expect any kind of conversion, eh?

Ah well, appreciating what you guys miss, helps me savor the info. all the more.

[joobz]

The point of this thread is that your own computer model shows that your own theory is mathematically impossible and you would rather talk about anything else besides what your model shows. Even with your artificial selection process in your model, you still can’t get rapid enough convergence to support your theory and you can’t tell us what your real selection process is that would evolve genes de novo. Your own computer model reveals the mush of the theory of evolution.
It is almost sad to see you holding so tight to something so wrong. It's like watching a friend hold tight to a relationship that is over and he refuses to accept it.
"Dude, she's just not into you."

"Dude, the facts are just not with you."

[articulett]

It is almost sad to see you holding so tight to something so wrong. It's like watching a friend hold tight to a relationship that is over and he refuses to accept it.
"Dude, she's just not into you."

"Dude, the facts are just not with you."

Reality wants nothing to do with you either, Kleinman.
Even patience is get antsy...

Shoot--here's some old news and it will mean yet another factor in your calculations that will have to be included. http://www.sciencedaily.com/releases/2002/12/021202071449.htm

Gosh, with all this new info. coming out every day do you think it's really possible to calculate what the divisions over how many eons it took to get what we see? Why not just look at what we see and presume that however it happened--it did...and the radiometric dating is telling us over which time period. Come now...you, too, can live in the 21st century with the rest of us.

[articulett]

worms--another creationist conundrum...
http://www.nioo.knaw.nl/ppages/jmiddelburg/downloads/1/Meysman_tree.pdf

[Kotatsu]

Ah, so you're not including those other mutations as point mutations. Therefore your strange idea that just single-point substitutions are the cornerstone of evolution has no basis in reality. No one else thinks that. You do have your own personal mushy soft theory of evolution. I was calling it KTPMNS, but perhaps I'll call it KOPMSTE.

I have an exam tomorrow and thus will do anything to get my mind of those horrible books for a while. Therefore, I started thinking about how similar this new term you use for Kleinman's theory is to the word "compost", and --- while I am not entirely satisfied with the results, especially the need to have a capital "O" in one place, but not in another, in order for it to work --- I suggest an alternative term to be KOMPOSTE (1), which is easier to pronounce than both KTPMNS and KOPMSTE, and, by coincindence also gives a pretty good idea about the contents and quality of the theory without knowing the meaning of any of the words in the title.

I shall now go back to reading too many course books in too little time. Please do not assume that getting rid of the "it seems you haven't posted here in a while"-message in any way motivated the writing of this message.

---
(1) Which natutally means "Kleinman's Own Mindless Pretentions Of Smashing the Theory of Evolution".

[Paul C. Anagnostopoulos]

KOMPOSTE it is, Kotatsu. Excellent acronym.

Now get back to work, you lazy acronymizer!

~~ Paul

[kleinman]

I though it worthwhile to review and discuss why mathematics is so important to this discussion of the theory of evolution. I believe there are two central mechanisms that are used to support the theory of evolution and the mathematical behavior of these two mechanisms are being confused. Those two mechanisms are sexual recombination and natural selection and mutation (of any type) and natural selection. Recombination is not an error type mechanism whereas mutations are an error type mechanism. The mathematics of these two mechanisms are entirely different.

Recombination and natural selection consists of the selection of advantageous alleles from a pool of perhaps a few hundred alleles for a particular gene while mutation and natural selection consists of the selection of advantageous mutations from a pool that is the size of the population.

Again, consider the example of dog breeding. If dog breeding has been occurring for the past 10,000 years and the generation time for dogs is 1 year, you would have 10,000 generations to accomplish the wide spread diversity of the different breeds of dogs. This includes wide spread variation in numerous different properties of the different breeds all accomplished a small number of generations.

Now consider mutation and natural selection. Ev demonstrates the mathematics of random point mutations and natural selection. Unlike recombination and natural selection which can accomplish huge changes in a small number of generations, this particular form of evolutionary process requires billions of generations (if not more) to accomplish a very small change in a same size genome.

What I believe Darwin, Gould and other evolutionists have done is confuse the mathematical behavior of recombination and natural selection with the mathematical behavior of mutations and natural selection. Recombination and natural selection can bring about rapid microevolutionary changes but has never been shown to be able to accomplish a macroevolutionary change (eg evolve birds from reptiles) while ev shows that mutations and natural selection can accomplish occasional microevolutionary changes (eg Sickle cell mutation and drug resistance in bacteria) but is shown by ev to be profoundly slow to accomplish a macroevolutionary change (eg evolve a gene de novo).

Shouldn’t that be “flock to it like a moth to a flame”?A moth (singular)...doesn't "flock". "Moths" is plural: "Creationists" is plural.
It appears that I am the only creationist who has “flocked” to this flame.

And I didn’t flock here, I was invited by Paul.

[delphi_ote]

Recombination and natural selection can bring about rapid microevolutionary changes but has never been shown to be able to accomplish a macroevolutionary change (eg evolve birds from reptiles)
If birds rapidly evolved naturally from reptiles in an observable time frame, that would be evidence against evolution. Speciation happens over time. Divergence to the degree that we would label the two species as belonging to different classes happens over a lot of time. There is evidence that reptiles accumulated adaptive changes that eventually caused their offspring to seem so different, we humans came along and called them something else. That evidence is in the fossil record, not Ev.

[kleinman]

Recombination and natural selection can bring about rapid microevolutionary changes but has never been shown to be able to accomplish a macroevolutionary change (eg evolve birds from reptiles)If birds rapidly evolved naturally from reptiles in an observable time frame, that would be evidence against evolution. Speciation happens over time. Divergence to the degree that we would label the two species as belonging to different classes happens over a lot of time. There is evidence that reptiles accumulated adaptive changes that eventually caused their offspring to seem so different, we humans came along and called them something else. That evidence is in the fossil record, not Ev.
Gould postulated punctuated equilibrium in order to try to explain the lack of evidence in the fossil record; however I believe that Gould inappropriately extrapolated Darwin’s observations of divergence of finch beaks and similar types of recombination events and natural selection to mutation and natural selection.

The vast majority of observed adaptive events are recombination events, not mutation events. What you call evidence in the fossil record is open to interpretation. The mathematics of ev describes how random point mutation and natural selection can accumulate information in a genome. Your interpretation of the fossil record is in conflict with your mathematical model of random point mutations and natural selection. You are doing what I told Dr Schneider months ago that evolutionists would do once they understood the mathematics of ev, evolutionists would discredit ev.

[fishbob]

Numbered for my convenience:

1 - Gould postulated punctuated equilibrium in order to try to explain the lack of evidence in the fossil record; 2 - however I believe that Gould inappropriately extrapolated Darwin’s observations of divergence of finch beaks and similar types of recombination events and natural selection to mutation and natural selection.

1 - I think you got this very wrong - maybe poor phrasing on your part (if so, please clarify), or maybe a poor grasp of the concept (if so, no hope).

2 - What is the basis for your belief? In other words, why do you believe this?

[kleinman]

1 - Gould postulated punctuated equilibrium in order to try to explain the lack of evidence in the fossil record; 2 - however I believe that Gould inappropriately extrapolated Darwin’s observations of divergence of finch beaks and similar types of recombination events and natural selection to mutation and natural selection.1 - I think you got this very wrong - maybe poor phrasing on your part (if so, please clarify), or maybe a poor grasp of the concept (if so, no hope).

2 - What is the basis for your belief? In other words, why do you believe this?
The following is a quote of Gould that previously was posted by Paul.
A new species can arise when a small segment of the ancestral population is isolated at the periphery of the ancestral range. Large, stable central populations exert a strong homogenizing influence. New and favorable mutations are diluted by the sheer bulk of the population through which they must spread. They may build slowly in frequency, but changing environments usually cancel their selective value long before they reach fixation. Thus, phyletic transformation in large populations should be very rare—as the fossil record proclaims. But small, peripherally isolated groups are cut off from their parental stock. They live as tiny populations in geographic corners of the ancestral range. Selective pressures are usually intense because peripheries mark the edge of ecological tolerance for ancestral forms. Favorable variations spread quickly. Small peripheral isolates are a laboratory of evolutionary change.
I added the bold face to two of the sentences. In the first bold face sentence, Gould is speaking about mutations. It is clear from the mathematics from ev that the larger the population, the more rapid the evolution (at least for random point mutations). However, if you consider a small population with advantageous alleles and recombination rather than mutations, Gould’s postulate makes sense.

The second bold faced sentence also makes sense if you are talking about recombination and natural selection. Pygmy elephants could rapidly evolve to their larger relatives that we see today by recombination and natural selection without their being much evidence in the fossil record because of the rapid transition from the small form to the large form. If you consider the analogy of dog breeding, you have the variation in size from Chihuahuas to Great Danes in fewer than 10,000 generations.

Gould should have been using the word recombination, not mutation in his postulate and then his theory would match observations.

[kjkent1]

The following is a quote of Gould that previously was posted by Paul.

I added the bold face to two of the sentences. In the first bold face sentence, Gould is speaking about mutations. It is clear from the mathematics from ev that the larger the population, the more rapid the evolution (at least for random point mutations). However, if you consider a small population with advantageous alleles and recombination rather than mutations, Gould’s postulate makes sense.

The second bold faced sentence also makes sense if you are talking about recombination and natural selection. Pygmy elephants could rapidly evolve to their larger relatives that we see today by recombination and natural selection without their being much evidence in the fossil record because of the rapid transition from the small form to the large form. If you consider the analogy of dog breeding, you have the variation in size from Chihuahuas to Great Danes in fewer than 10,000 generations.

Gould should have been using the word recombination, not mutation in his postulate and then his theory would match observations.

Are Chihuahuas and Great Danes still members of the same species? I can't imagine that it would be reasonably likely for the two "breeds" to be able procreate without human intervention.

[hammegk]

Er, the definition of species is still evolving. :)

http://humboldt.edu/~kll1/speciesdef.html

That paper purports to be last updated in 1998. Perhaps someone can provide a few definitions more to get us all up to date?

[kleinman]

The following is a quote of Gould that previously was posted by Paul.

I added the bold face to two of the sentences. In the first bold face sentence, Gould is speaking about mutations. It is clear from the mathematics from ev that the larger the population, the more rapid the evolution (at least for random point mutations). However, if you consider a small population with advantageous alleles and recombination rather than mutations, Gould’s postulate makes sense.

The second bold faced sentence also makes sense if you are talking about recombination and natural selection. Pygmy elephants could rapidly evolve to their larger relatives that we see today by recombination and natural selection without their being much evidence in the fossil record because of the rapid transition from the small form to the large form. If you consider the analogy of dog breeding, you have the variation in size from Chihuahuas to Great Danes in fewer than 10,000 generations.

Gould should have been using the word recombination, not mutation in his postulate and then his theory would match observations.Are Chihuahuas and Great Danes still members of the same species? I can't imagine that it would be reasonably likely for the two "breeds" to be able procreate without human intervention.
The two breeds maintain homologous chromosomes. A “pure bred” Chihuahua/Great Dane pair might have difficulty mating because of their extreme size difference but it is easy to imagine a Chihuahua interbreeding with a small mutt giving larger offspring than the Chihuahua parent and a Great Dane interbreeding with a large mutt giving smaller offspring than the Great Dane parent and the offspring of these “pure bred” dogs interbreeding. This can all be done without human intervention.

[kjkent1]

The two breeds maintain homologous chromosomes. A “pure bred” Chihuahua/Great Dane pair might have difficulty mating because of their extreme size difference but it is easy to imagine a Chihuahua interbreeding with a small mutt giving larger offspring than the Chihuahua parent and a Great Dane interbreeding with a large mutt giving smaller offspring than the Great Dane parent and the offspring of these “pure bred” dogs interbreeding. This can all be done without human intervention.

You avoided the question. A small mutt is not a Great Dane. A small mutt is a cross between a Great Dane and something(s) else, and may in fact, be more something else than Great Dane.

And, to be clear, a male Great Dane wouldn't just "have difficulty mating, because of their extreme size differences." A male Great Dane would almost certainly kill the female Chihuahua, if not during mating, then during the birth of the pups.

As for the reverse circumstance of a male Chihuahua mating with a female Great Dane, when you get me a photo of those two dogs tied together, that's when I'll buy into that imagery.

So, I'll repeat the question, are Great Danes and a Chihuahuas members of the same "species?"

[kleinman]

The two breeds maintain homologous chromosomes. A “pure bred” Chihuahua/Great Dane pair might have difficulty mating because of their extreme size difference but it is easy to imagine a Chihuahua interbreeding with a small mutt giving larger offspring than the Chihuahua parent and a Great Dane interbreeding with a large mutt giving smaller offspring than the Great Dane parent and the offspring of these “pure bred” dogs interbreeding. This can all be done without human intervention.You avoided the question. A small mutt is not a Great Dane. A small mutt is a cross between a Great Dane and something(s) else, and may in fact, be more something else than Great Dane.

And, to be clear, a male Great Dane wouldn't just "have difficulty mating, because of their extreme size differences." A male Great Dane would almost certainly kill the female Chihuahua, if not during mating, then during the birth of the pups.

As for the reverse circumstance of a male Chihuahua mating with a female Great Dane, when you get me a photo of those two dogs tied together, that's when I'll buy into that imagery.

So, I'll repeat the question, are Great Danes and a Chihuahuas members of the same "species?"
Do you think that all the members of a species have to be the same size?

[kjkent1]

Do you think that all the members of a species have to be the same size?

You're giving a splended demonstration of being unable to define when microevolutionary change ends and macroevolutionary change begins.

A Great Dane is enormously bigger than a Chihuahua, not in some cases, but in every case.

http://www.akc.org/breeds/great_dane/index.cfm

http://www.akc.org/breeds/chihuahua/index.cfm

But, suppose there is a dwarf? If you admit that a dwarf Great Dane is possible, then you admit the possiblity of some very substantial and immediate changes due to random mutation -- changes which could irrevocably prevent any future procreation between what were formerly members of the same "species."

Is a Chihuahua a dwarf Great Dane? Is a dwarf Great Dane a Great Dane? A dwarf Great Dane would be equally unable to breed with a full size Great Dane as would a Great Dane and a Chihuahua.

All of this begs the question of when speciation occurs. It is inescapable that if you define Great Dane and Chihuahua as the American Kennel Club defines them, that there is near zero probability of their ever mating again without human intervention. Howevever if you define the dogs differently, then you will get a different result.

So, once more, are Great Danes and Chihuahuas different species?

[Paul C. Anagnostopoulos]

That paper purports to be last updated in 1998. Perhaps someone can provide a few definitions more to get us all up to date?
Good luck. The definition of species is not as slippery as macroevolution, but it's right up there on the slick scale.


You're giving a splended demonstration of being unable to define when microevolutionary change ends and macroevolutionary change begins.
Agreed. I sure as heck wouldn't base my definition of macroevolution on a definition of species. It's slippery all the way down.

Continua are very difficult to partition. We have to do it in ethics, but I see no reason why we have to do it in biology.

~~ Paul

[hammegk]

Can an evolutionarian wave his arms fast enough to actually gain altitude? :)

[Kotatsu]

Can an evolutionarian wave his arms fast enough to actually gain altitude? :)

Yes. I use it all the time. I think I've saved several thousands of my local currency in bus fares over the last six months alone! Of course, this would depend on the individual evolutionarian's body weight, arm strength, the local wind and weather conditions, whether or not he/she is carrying anything, and several other factors; please consider my simple "Yes" an affirmation that it is indeed possible under certain conditions, not as an universal positive.

Question: What is actually "arm-waving" as used by Hammegk here? I've seen it several times in this thread and elsewhere, but I'm not really sure I understand what it means.

[kleinman]

Do you think that all the members of a species have to be the same size?You're giving a splended demonstration of being unable to define when microevolutionary change ends and macroevolutionary change begins.
Kjkent1, you are doing a splendid demonstration of swatting at gnats when an elephant is stomping on your head. You are attempting to split hairs with this species argument concerning Chihuahuas and Great Danes when you are missing this huge mathematical difference between mutation and natural selection and recombination and natural selection.

Mutation and natural selection is a profoundly slow process while recombination and natural selection is a rapid process. You can not extrapolate the rapid changes that are possible by recombination and natural selection to mutation and natural selection. This is what Darwin and Gould have done and caused evolutionists to go down a hundred plus year long rabbit trail.
That paper purports to be last updated in 1998. Perhaps someone can provide a few definitions more to get us all up to date?Good luck. The definition of species is not as slippery as macroevolution, but it's right up there on the slick scale.
Let’s start firming up the definition of macroevolution. Start with the de novo evolution of a gene.
You're giving a splended demonstration of being unable to define when microevolutionary change ends and macroevolutionary change begins.Agreed. I sure as heck wouldn't base my definition of macroevolution on a definition of species. It's slippery all the way down.
Hey Paul, we agree on this one. Does that mean you are soon going to retract this statement?

[Paul C. Anagnostopoulos]

Have you noticed that antievolutionites demand that things be continuous when it suits them (e.g., fossil record), but also demand that things be discrete when it suits them (e.g., species, macroevolution)? Is this because these things are really continuous/discrete, or is it just convenient?

~~ Paul

[Paul C. Anagnostopoulos]

Question: What is actually "arm-waving" as used by Hammegk here? I've seen it several times in this thread and elsewhere, but I'm not really sure I understand what it means.
It means he thinks you don't know what you're talking about, but you stubbornly refuse to use the word mu. If you would just say moo, he would be happy.

~~ Paul

[kleinman]

Have you noticed that antievolutionites demand that things be continuous when it suits them (e.g., fossil record), but also demand that things be discrete when it suits them (e.g., species, macroevolution)? Is this because these things are really continuous/discrete, or is it just convenient?
Since I am the primary antievolutionite on this thread, I will take this statement as addressed to me. It is you evolutionarians that are claiming that the fossil record is your proof for evolution. Now that the huge mathematical difference between mutation and natural selection and recombination and natural selection is now apparent (in part because of your good work on ev), the explanation of the fossil record become more sensible. The changes in the fossil record are explained by recombination and natural selection events. Punctuated equilibrium explains why there are no transitional form fossils seen for intraspecies microevolutionary events (such as pygmy elephants to the large forms we see today, ring species and many other examples) and the lack of fossils for extraspecies macroevolutionary events such as the transition from reptiles to birds. Unless the transition from reptiles to birds is accomplished by recombination and natural selection by punctuated equilibrium, you should see large numbers of transitional forms due to the slow action of mutation and natural selection. Paul, you do good work and I appreciate it very much.

[PixyMisa]

Mutation and natural selection is a profoundly slow process while recombination and natural selection is a rapid process.

Except, of course, when the reverse is true. Thousands of years of selective breeding and all dogs are dogs. A single transposition error (http://www.nmsr.org/nylon.htm) and we have a species of bacteria with an ability never seen before.

It all depends on what sort of changes you are looking for.

For example:

It is clear from the mathematics from ev that the larger the population, the more rapid the evolution (at least for random point mutations).Which simply isn't correct. A larger population allows for more instances of mutation; however, this does not result in speciation unless the mutations are propagated and accumulate over time. That is far more likely in a small, isolated population than in a large, widespread one. What the large population ends up with is more genetic variation; what it doesn't do is evolve.

[PixyMisa]

Since I am the primary antievolutionite on this thread, I will take this statement as addressed to me. It is you evolutionarians that are claiming that the fossil record is your proof for evolution.
Not just that; we have also observed speciation for all sensible definitions of the term. We also have the evidence of molecular evolution, of nuclear and mitochondrial DNA. The molecular evidence runs directly against your hypothesis.

Now that the huge mathematical difference between mutation and natural selection and recombination and natural selection is now apparent (in part because of your good work on ev)Your interpretation of the mathematics of these processes is completely wrong.

Punctuated equilibrium explains why there are no transitional form fossils seen for intraspecies microevolutionary events (such as pygmy elephants to the large forms we see today, ring species and many other examples) and the lack of fossils for extraspecies macroevolutionary events such as the transition from reptiles to birds.Except that this is also completely wrong. We have an abundance of transitional fossils... except, as far as I know, for bats.

Unless the transition from reptiles to birds is accomplished by recombination and natural selection by punctuated equilibrium, you should see large numbers of transitional forms due to the slow action of mutation and natural selection. And we do see large numbers of transitional forms.

What's more, it simply isn't possible, genetically, for recombination to result in phyletic evolution (such as reptiles to birds). There are new genes all over the place, changes in the numbers of chromosomes, all sorts of differences.

[PixyMisa]

Oh, and the definition of macroevolution is a simple one:

Microevolution: Change.
Macroevolution: More change.

[hgc]

Question: What is actually "arm-waving" as used by Hammegk here? I've seen it several times in this thread and elsewhere, but I'm not really sure I understand what it means.
Welcome to hammyworld. He's got a whole snarkabulary that you will never penetrate.

[kjkent1]

Except, of course, when the reverse is true. Thousands of years of selective breeding and all dogs are dogs. A single transposition error (http://www.nmsr.org/nylon.htm) and we have a species of bacteria with an ability never seen before.

This sort of brings me back to my point about Chihuahuas and Great Danes. The statement that "all dogs are dogs," is just our choice as humans to arbitrarily classify a certain group of life forms as "dogs", and as all being contained within the same species. Yes, all dogs continue to share important features, and their DNA is compatible. But if physical reproductive isolation were considered the primary speciation determiner, then a Chihuahua and a Great Dane would no longer be members of the same species, because they cannot, as a practical matter, procreate.

Furthermore, suppose that the "Eugenics" movement of the early-mid 1900s had caught on. Suppose we were actively creating breeds of humans, for size, shape, strength and intellect, etc. Within a few hundred years our view of what is a "human" would be markedly different. And, I suggest that if one of these human breeds were considerably more fit than all of its competitors, that those competitors would very quickly disappear from the biological landscape.

Like it or not, we humans are an extremely ruthless species.

We don't like to think about these things, because of our cultural history. Eugenics is almost a code word for "NAZI," because of how the Third Reich chose to deal with the creation of a superior race.

But, were we, as humans to become suddenly and considerably less "moral," I strongly suspect that we would witness a very profound evolution of the species within our own lifetimes.

[kleinman]

Mutation and natural selection is a profoundly slow process while recombination and natural selection is a rapid process.Except, of course, when the reverse is true. Thousands of years of selective breeding and all dogs are dogs. A single transposition error (http://www.nmsr.org/nylon.htm) and we have a species of bacteria with an ability never seen before.
This is a good example of a single mutation that can cause a microevolutionary change. Natural selection in this case takes and existing peptidase and modifies it so a synthetic organic molecule (nylon) can be decomposed. Now if the original peptidase were to evolve, that would be macroevolution.
It is clear from the mathematics from ev that the larger the population, the more rapid the evolution (at least for random point mutations).Which simply isn't correct. A larger population allows for more instances of mutation; however, this does not result in speciation unless the mutations are propagated and accumulate over time. That is far more likely in a small, isolated population than in a large, widespread one. What the large population ends up with is more genetic variation; what it doesn't do is evolve.
I haven’t noticed any previous posts from you but it seems you are not familiar with the data posted from Dr Schneider’s ev program. This computer model simulates random point mutations and natural selection. The mathematics of random point mutation and natural selection is completely different from the mathematics of recombination and natural selection. You are confusing these two mathematical processes. You need to study this thread and a related thread-http://www.evolutionisdead.com/forum/viewtopic.php?t=348&sid=f42b17926a042f8bf08e0eb2cc13c212 (http://www.evolutionisdead.com/forum/viewtopic.php?t=348&sid=f42b17926a042f8bf08e0eb2cc13c212) in order to understand the distinction. You will then have some understanding of the effects of population on random point mutation and natural selection.
Since I am the primary antievolutionite on this thread, I will take this statement as addressed to me. It is you evolutionarians that are claiming that the fossil record is your proof for evolution.Not just that; we have also observed speciation for all sensible definitions of the term. We also have the evidence of molecular evolution, of nuclear and mitochondrial DNA. The molecular evidence runs directly against your hypothesis.
What you are doing is extrapolating the observation of similarity between genomes of different life forms to that they evolved from one another. The flaw in your argument is that the differences are too great to be accounted for by mutations and natural selection to make the transformation. Not only does random point mutation and natural selection fail to account for the evolution of one species to the next, the de novo evolution of genes is a mathematical impossibility. There is no known selection mechanism to evolve a gene de novo and Dr Schneider’s ev computer model with an unrealistic selection process shows how profoundly slow random point mutations and natural selection is for evolving binding sites de novo.
Now that the huge mathematical difference between mutation and natural selection and recombination and natural selection is now apparent (in part because of your good work on ev)Your interpretation of the mathematics of these processes is completely wrong.
My interpretation of the mathematics is based on an evolutionist written, peer reviewed and published computer model of random point mutations and natural selection and the observed behavior of recombination and natural selection, for example dog breeding. What is the mathematical basis of your interpretation?
Punctuated equilibrium explains why there are no transitional form fossils seen for intraspecies microevolutionary events (such as pygmy elephants to the large forms we see today, ring species and many other examples) and the lack of fossils for extraspecies macroevolutionary events such as the transition from reptiles to birds.Except that this is also completely wrong. We have an abundance of transitional fossils... except, as far as I know, for bats.
The fossil record is open to interpretation. Your interpretation of the fossil record conflicts with the mathematical results obtained from ev.
Unless the transition from reptiles to birds is accomplished by recombination and natural selection by punctuated equilibrium, you should see large numbers of transitional forms due to the slow action of mutation and natural selection.And we do see large numbers of transitional forms.
This is the evolutionist version of the Rorschach test. You are seeing what you want to see in the fossil record. You have not come to grips with the fact that you have a big mathematical problem in your theory.
What's more, it simply isn't possible, genetically, for recombination to result in phyletic evolution (such as reptiles to birds). There are new genes all over the place, changes in the numbers of chromosomes, all sorts of differences.
Again, what you don’t understand yet is that recombination and natural selection is a rapid mechanism for change. It is this mechanism that Darwin was observing when trying to explain the differences between finch beaks, not mutation and natural selection. It also is the mechanism that Gould should have used when postulating his hypothesis of punctuated equilibrium rather than mutation and natural selection. There is no way to explain mathematically all the new genes required to evolve reptiles to birds. Random point mutations and natural selection is a profoundly slow process as shown by the ev computer model. All the other forms of mutations that are being raised by evolutionists are governed by the same mathematics as is random point mutations and natural selection.
Oh, and the definition of macroevolution is a simple one:

Microevolution: Change.
Macroevolution: More change.
Conceptually this may be the case. Perhaps you would like to tell us what the selection process that would evolve a gene de novo?

[kjkent1]

Again, what you don’t understand yet is that recombination and natural selection is a rapid mechanism for change. It is this mechanism that Darwin was observing when trying to explain the differences between finch beaks, not mutation and natural selection. It also is the mechanism that Gould should have used when postulating his hypothesis of punctuated equilibrium rather than mutation and natural selection. There is no way to explain mathematically all the new genes required to evolve reptiles to birds. Random point mutations and natural selection is a profoundly slow process as shown by the ev computer model. All the other forms of mutations that are being raised by evolutionists are governed by the same mathematics as is random point mutations and natural selection.

I wonder if the answer is in the selection method? ;-)

Ev's method is extremely simplistic, apparently quite arbitrary and not at all like what happens in nature (ev simply and mindlessly kills off one half of the population which is less fit, and replaces it with a copy of the more fit half).

I suspect that a more natural model of a bacterial evolution (ev is clearly an asexual model) would be to kill off nearly the entire population except for the organism which has the mutation permitting survival under the current environmental stress, and then multiply that organism.

Of course, ev doesn't model any particular environmental stress, either. If it did, then that stress would tend to limit the survival of the population to those creatures whose mutations provide them with the best opportunity to survive.

Ev operates in an almost totally random style, as if the environment in which its creatures live is under a stress that simply kills off one half of the population which is "less perfect," as defined by ev.

This is not how it happens in nature. In nature, perfect is defined by the ability of the creature to survive long enough to procreate in the present environment. This may mean, for example, that only the bacteria which has developed the required antibiotic resistance will survive, and all the other bacteria will die.

I don't think your constant pounding on ev's slow mutation rate is reasonable, because you are arguing that ev doesn't realistically model evolution of the species in nature. I doubt that Dr. Schneider would disagree with that assessment.

[kleinman]

Again, what you don’t understand yet is that recombination and natural selection is a rapid mechanism for change. It is this mechanism that Darwin was observing when trying to explain the differences between finch beaks, not mutation and natural selection. It also is the mechanism that Gould should have used when postulating his hypothesis of punctuated equilibrium rather than mutation and natural selection. There is no way to explain mathematically all the new genes required to evolve reptiles to birds. Random point mutations and natural selection is a profoundly slow process as shown by the ev computer model. All the other forms of mutations that are being raised by evolutionists are governed by the same mathematics as is random point mutations and natural selection.I wonder if the answer is in the selection method? ;-)
Now if you could select the correct selection method! :c)
Ev's method is extremely simplistic, apparently quite arbitrary and not at all like what happens in nature (ev simply and mindlessly kills off one half of the population which is less fit, and replaces it with a copy of the more fit half).
Ev’s selection method is actually quite precise. A weight matrix is traversed along the genome and if a match is found, that determines the location of a binding site. If the binding site is in the appropriate portion of the genome, that match is considered correct, if the match is not in the binding site region, it is considered an error, if the weight matrix does not locate a binding site where it should be located, that is an error as well. Then the half of the population with the fewest errors is duplicated. I agree that this selection process is not a realistic simulation; however it does give a rapidly evolving selective process. This can be seen how quickly binding sites evolve on short genomes. The mathematical probability effect becomes more apparent with longer genomes. This mathematical effect would appear no matter what your choice of selection process is. The search space increases at 4^G.

So let’s say you want to model a more realistic selection process. How would you do this? Pick an example of a gene you would want to evolve, for example, the hemoglobin gene. The hemoglobin molecule is about 150 amino acids long which would require 450 bases to code for this protein. Paul previously proposed that the presence of oxygen in the atmosphere was the selective pressure for the formation of hemoglobin. So as primitive microorganisms were being nonezymatically oxidized by the newly available free oxygen and you are getting mutations to the genome that are being selected for the production of hemoglobin. How does this happen? You get the appropriate first base for the sequence but it doesn’t yet code for the needed protein so is not selected for, the first base appears only randomly. Then you get the second base in the sequence, but still this doesn’t code for a protein and therefore does not offer any selective advantage. You only get a selective advantage when you have sufficient number of bases to code for a useful protein. There is no selection process known that would take you to the point of evolving a useful gene de novo.
I suspect that a more natural model of a bacterial evolution (ev is clearly an asexual model) would be to kill off nearly the entire population except for the organism which has the mutation permitting survival under the current environmental stress, and then multiply that organism.
This sound reasonable, I suspect this is what happens with bacterial populations that are not resistant to an antibiotic. The question is whether this kind of selection pressure will evolve a gene de novo or only allows for microevolutionary processes.
Of course, ev doesn't model any particular environmental stress, either. If it did, then that stress would tend to limit the survival of the population to those creatures whose mutations provide them with the best opportunity to survive.
Bacteria are subject to multiple different environmental stresses.
Ev operates in an almost totally random style, as if the environment in which its creatures live is under a stress that simply kills off one half of the population which is "less perfect," as defined by ev.
If you watch how ev converges, you see that as the binding sites become more evolved, the rate of convergence slows down. The number of helpful mutations are the highest when the binding site region is the most random.
This is not how it happens in nature. In nature, perfect is defined by the ability of the creature to survive long enough to procreate in the present environment. This may mean, for example, that only the bacteria which has developed the required antibiotic resistance will survive, and all the other bacteria will die.
One of the things that happens when a bacteria develops resistance to an antibiotic is that these bacteria have to expend energy to maintain this resistance. Once the antibiotic is removed, nonresistant bacteria are at a selective advantage. For example sulfa drugs were overused 30 or 40 years ago and many bacteria developed resistance to these drugs. Sulfa drugs fell out of favor for a while and bacterial resistant to these drugs declined to the point where sulfa drugs again have become useful (although resistance is again reappearing).
I don't think your constant pounding on ev's slow mutation rate is reasonable, because you are arguing that ev doesn't realistically model evolution of the species in nature. I doubt that Dr. Schneider would disagree with that assessment.
That pounding you are feeling is the elephant that is stomping on your head as you try to figure out if Chihuahuas and Great Danes are the same species. Anyway, it is not the slow mutation rate; it is the slow evolution by random point mutations and natural selection that ev is showing. Again, even with this unrealistic but very precise selection process, ev can not overcome the mathematical limitations imposed by this problem.

[kjkent1]

Now if you could select the correct selection method! :c)

Ev’s selection method is actually quite precise. A weight matrix is traversed along the genome and if a match is found, that determines the location of a binding site. If the binding site is in the appropriate portion of the genome, that match is considered correct, if the match is not in the binding site region, it is considered an error, if the weight matrix does not locate a binding site where it should be located, that is an error as well. Then the half of the population with the fewest errors is duplicated. I agree that this selection process is not a realistic simulation; however it does give a rapidly evolving selective process. This can be seen how quickly binding sites evolve on short genomes. The mathematical probability effect becomes more apparent with longer genomes. This mathematical effect would appear no matter what your choice of selection process is. The search space increases at 4^G.I follow your analysis right up to the point where you jump to the conclusion that that the mathematical effect would appear no matter the choice of selection process. It seems to me that if it were as obvious as you assert, that you would be able to express the problem mathematically. I've asked you to do this before, and you have refused on the same grounds, i.e., that your suspicions are sufficient.


This seems to be a real gate to any further progress in the discussion. Neither side seems willing to do any science -- instead, both sides seem content to claim that they are right and that it's obvious.


Well, it's not at all obvious to me, and it would be wonderful if someone would prove/disprove your hypothesis on this point:


Can the ev selection mechanism be modified to overcome the slow mutation rate in longer genomes?

So let’s say you want to model a more realistic selection process. How would you do this? Pick an example of a gene you would want to evolve, for example, the hemoglobin gene. The hemoglobin molecule is about 150 amino acids long which would require 450 bases to code for this protein. Paul previously proposed that the presence of oxygen in the atmosphere was the selective pressure for the formation of hemoglobin. So as primitive microorganisms were being nonezymatically oxidized by the newly available free oxygen and you are getting mutations to the genome that are being selected for the production of hemoglobin. How does this happen? You get the appropriate first base for the sequence but it doesn’t yet code for the needed protein so is not selected for, the first base appears only randomly. Then you get the second base in the sequence, but still this doesn’t code for a protein and therefore does not offer any selective advantage. You only get a selective advantage when you have sufficient number of bases to code for a useful protein. There is no selection process known that would take you to the point of evolving a useful gene de novo.As it stands right now, how long would it take ev to evolve 450 bases?

Edit: I just thought of another point. You seem to be suggesting that some pre-hemoglobin molecule is floating around in the Pacific Ocean, just waiting to randomly form into de novo hemoglobin. Isn't reality more like there is some complex life form with an already developed genome, which first mutates for a selective advantage -- not necessarily hemoglobin -- and then over time, continues to evolve until one day hemoglobin, or something close to it is finally defined?

If this is how evolution really works, then your example of evolving a 450 base gene, directly to hemoglobin, is irrelevant. It's just another version of the already-discredited creationist "tornado through the junkyard creates a 747" example.

Anyway, it is not the slow mutation rate; it is the slow evolution by random point mutations and natural selection that ev is showing. Again, even with this unrealistic but very precise selection process, ev can not overcome the mathematical limitations imposed by this problem.You keep repeating this, however neither you nor your opponents have provided any affirmative proof to resolve this issue. This is unfortunate.

[Paul C. Anagnostopoulos]

Can the ev selection mechanism be modified to overcome the slow mutation rate in longer genomes?
Myriad has made a proposal. I plan to implement a variant of it in Evj. It will be interesting to see what happens. Have you seen a description of this proposal?

~~ Paul

[PixyMisa]

Now if the original peptidase were to evolve, that would be macroevolution.
Are you saying that changes in enzymes are macroevolution? Categorically?

Edit: Or are you saying this only applies for "new" enzymes, for some definition of "new" which does not include new enzymes that we have actually observed evolving?

I haven’t noticed any previous posts from you but it seems you are not familiar with the data posted from Dr Schneider’s ev program. This computer model simulates random point mutations and natural selection.
Very badly, it would seem.

What you are doing is extrapolating the observation of similarity between genomes of different life forms to that they evolved from one another.
Yes.

The flaw in your argument is that the differences are too great to be accounted for by mutations and natural selection to make the transformation.No.

Not only does random point mutation and natural selection fail to account for the evolution of one species to the next, the de novo evolution of genes is a mathematical impossibility.See the example I just linked to, that you just commented on. Looky! A new gene! It's not "de novo", but then other new genes aren't "de novo" either.
Again, what you don’t understand yet is that recombination and natural selection is a rapid mechanism for change.
But it is impossible to get phyletic evolution (or any major change, really) this way. And yet we do see phyletic evolution. That has to come from mutation.

There is no way to explain mathematically all the new genes required to evolve reptiles to birds.There are two major problems with your thesis: First, the genes are really there; second, we have seen this happening.

Conceptually this may be the case. Perhaps you would like to tell us what the selection process that would evolve a gene de novo?
Genes don't evolve "de novo". They evolve from existing genes via mutations. See example already provided.

[PixyMisa]

Ev's method is extremely simplistic, apparently quite arbitrary and not at all like what happens in nature (ev simply and mindlessly kills off one half of the population which is less fit, and replaces it with a copy of the more fit half).
Well, that would be something of a problem if you are trying to accurately model genetic propagation!

[PixyMisa]

Ev’s selection method is actually quite precise. A weight matrix is traversed along the genome and if a match is found, that determines the location of a binding site. If the binding site is in the appropriate portion of the genome, that match is considered correct, if the match is not in the binding site region, it is considered an error, if the weight matrix does not locate a binding site where it should be located, that is an error as well. Then the half of the population with the fewest errors is duplicated. I agree that this selection process is not a realistic simulation; however it does give a rapidly evolving selective process.

Albeit one that has no bearing on reality. This completely misrepresents the real dynamics of genetic variation in any population, and is particularly egregious when it comes to sexual reproduction.

[kjkent1]

Myriad has made a proposal. I plan to implement a variant of it in Evj. It will be interesting to see what happens. Have you seen a description of this proposal?

~~ Paul

No, I haven't seen Myriad's proposal (and, I probably wouldn't have understood it even though I had). I'd love to review it.

[Paul C. Anagnostopoulos]

I'm going to implement a simple variant of his proposal. Right now, Ev has three methods for breaking ties between creatures when it goes to kill off the worst half and replicate the best half. The idea is to add a fourth method for breaking the ties. Tie-breaking turns out to happen quite often, especially with large populations (selective sweeps occur continuously due to Ev's simplistic model).

If two creatures are tied in their number of mistakes, Evj will select the one with the lowest absolute difference between the valuations of the binding sites and the threshold. This provides a finer-grained selection process which distinguishes between two creatures with the same mistake count, selecting for the one that is, in some sense, closer to reducing its mistake count.

It will be interesting to see how this speeds up the evolution of a perfect creature, if at all. It's all a bit of a tangent, since it was not the purpose of Ev to model realistic genetic variation.

~~ Paul

[kleinman]

Ev’s selection method is actually quite precise. A weight matrix is traversed along the genome and if a match is found, that determines the location of a binding site. If the binding site is in the appropriate portion of the genome, that match is considered correct, if the match is not in the binding site region, it is considered an error, if the weight matrix does not locate a binding site where it should be located, that is an error as well. Then the half of the population with the fewest errors is duplicated. I agree that this selection process is not a realistic simulation; however it does give a rapidly evolving selective process. This can be seen how quickly binding sites evolve on short genomes. The mathematical probability effect becomes more apparent with longer genomes. This mathematical effect would appear no matter what your choice of selection process is. The search space increases at 4^G.I follow your analysis right up to the point where you jump to the conclusion that that the mathematical effect would appear no matter the choice of selection process. It seems to me that if it were as obvious as you assert, that you would be able to express the problem mathematically. I've asked you to do this before, and you have refused on the same grounds, i.e., that your suspicions are sufficient.
The selection process that Dr Schneider uses in his model is very efficient. This is seen by the rapid convergence when small genomes are used in the model. Even with this very efficient selection process, convergence slows down profoundly as you length the genome. The problem you face is not an efficient selection process, Dr Schneider already has designed an efficient selection process. The problem is that as the genome is lengthened, this efficient selection process is overwhelmed by the increase in the search space (4^G). The dominant parameter in this mathematical model by far is the genome length. I don’t think you can design a selection process that is orders of magnitude faster than the one Dr Schneider has designed and overcome the effect of the increasing genome length. This is fundamental in the mathematics of this problem. These are the grounds for my suspicions when you suggest alternative selection processes. Contact Dr Schneider about this, he has defended his selection process for years.
This seems to be a real gate to any further progress in the discussion. Neither side seems willing to do any science -- instead, both sides seem content to claim that they are right and that it's obvious.
You lack patience as well as understanding. When you debate such deeply ingrained thinking such as those convinced of the validity of the theory of evolution, it takes time.
Well, it's not at all obvious to me, and it would be wonderful if someone would prove/disprove your hypothesis on this point:
Have you run a single case with ev? In order to get a sense of the mathematical behavior of this computer model, you need to do a systematic parametric study. That may explain why it is not obvious to you.
Can the ev selection mechanism be modified to overcome the slow mutation rate in longer genomes?
It not accurate to describe the problem this way. It is the number of mutation/selection cycles necessary to increase the information in the genome which is increasing as you increase the genome length. I don’t believe you can modify the selection process and reduce the number of mutation/selection cycles by orders of magnitude. Myriad is trying to do this and he is a good mathematician and we’ll wait and see. None of the other mathematicians who inhabit this site have offered a solution. In order for this model to support the theory of evolution, you need a selection process that is orders of magnitude faster than Dr Schneider’s selection process. I don’t believe that such a selection process exists.
So let’s say you want to model a more realistic selection process. How would you do this? Pick an example of a gene you would want to evolve, for example, the hemoglobin gene. The hemoglobin molecule is about 150 amino acids long which would require 450 bases to code for this protein. Paul previously proposed that the presence of oxygen in the atmosphere was the selective pressure for the formation of hemoglobin. So as primitive microorganisms were being nonezymatically oxidized by the newly available free oxygen and you are getting mutations to the genome that are being selected for the production of hemoglobin. How does this happen? You get the appropriate first base for the sequence but it doesn’t yet code for the needed protein so is not selected for, the first base appears only randomly. Then you get the second base in the sequence, but still this doesn’t code for a protein and therefore does not offer any selective advantage. You only get a selective advantage when you have sufficient number of bases to code for a useful protein. There is no selection process known that would take you to the point of evolving a useful gene de novo.As it stands right now, how long would it take ev to evolve 450 bases?
I did one small series where I varied site width up to 15 bases. In that series, the rate of convergence was independent of base width. I don’t know if that behavior would remain constant to a base width of 450. When I get a chance, I’ll try running more cases with a wider width to see if such a case is possible. In addition, you don’t have a selection process.
Anyway, it is not the slow mutation rate; it is the slow evolution by random point mutations and natural selection that ev is showing. Again, even with this unrealistic but very precise selection process, ev can not overcome the mathematical limitations imposed by this problem.You keep repeating this, however neither you nor your opponents have provided any affirmative proof to resolve this issue. This is unfortunate.
I keep repeating this because very few people posting on this thread have run any cases with ev or if they have run cases, they don’t post the results. If you do a systematic parametric study with ev, you will understand what I am saying, until then, I’ll keep repeating myself.
Now if the original peptidase were to evolve, that would be macroevolution.Are you saying that changes in enzymes are macroevolution? Categorically?

Edit: Or are you saying this only applies for "new" enzymes, for some definition of "new" which does not include new enzymes that we have actually observed evolving?
What I am saying is that the de novo evolution of a gene is macroevolution. The example of the transposition of a base pair enabling an existing peptidase to lyse nylon represents a microevolutionary process.
I haven’t noticed any previous posts from you but it seems you are not familiar with the data posted from Dr Schneider’s ev program. This computer model simulates random point mutations and natural selection.Very badly, it would seem.
The peer reviewers and editors of Nucleic Acids Research don’t seem to think so, they published Dr Schneider’s work. Dr Schneider is the head of computational molecular biology at the National Cancer Institute. Dr Schneider believes his computer model simulates reality and so do I.
What you are doing is extrapolating the observation of similarity between genomes of different life forms to that they evolved from one another.Yes.
That’s only half the story. You have to show how these genomes can transform from one to another. Dr Schneider’s model shows that this is mathematically impossible (at least for random point mutations and natural selection).
Not only does random point mutation and natural selection fail to account for the evolution of one species to the next, the de novo evolution of genes is a mathematical impossibility.See the example I just linked to, that you just commented on. Looky! A new gene! It's not "de novo", but then other new genes aren't "de novo" either.
There are lots of examples like this. These are examples of microevolution which I believe occurs. It is the de novo evolution of genes that I don’t believe occurs.
Again, what you don’t understand yet is that recombination and natural selection is a rapid mechanism for change.But it is impossible to get phyletic evolution (or any major change, really) this way. And yet we do see phyletic evolution. That has to come from mutation.
You have convinced yourself that you see phyletic evolution but this view is contradicted by the mathematics shown by Dr Schneider’s computer model.
There is no way to explain mathematically all the new genes required to evolve reptiles to birds.There are two major problems with your thesis: First, the genes are really there; second, we have seen this happening.
I don’t argue that reptiles and birds to not have genes. What I argue is that you can’t make the transition from the reptile to the bird genome by random point mutations and natural selection. The process is profoundly slow, too slow to accomplish this transition. This is demonstrated by the ev computer model.
Conceptually this may be the case. Perhaps you would like to tell us what the selection process that would evolve a gene de novo?Genes don't evolve "de novo". They evolve from existing genes via mutations. See example already provided.
Where did these existing genes come from?
Ev's method is extremely simplistic, apparently quite arbitrary and not at all like what happens in nature (ev simply and mindlessly kills off one half of the population which is less fit, and replaces it with a copy of the more fit half).Well, that would be something of a problem if you are trying to accurately model genetic propagation!
I’ll let Dr Schneider statement about his model answer this:
A good simulation does not attempt to simulate everything; only the essential components are modeled. For the issue at hand, the form of the genetic code is not relevant; information measured by Shannon's method is more general than that.
Ev’s selection method is actually quite precise. A weight matrix is traversed along the genome and if a match is found, that determines the location of a binding site. If the binding site is in the appropriate portion of the genome, that match is considered correct, if the match is not in the binding site region, it is considered an error, if the weight matrix does not locate a binding site where it should be located, that is an error as well. Then the half of the population with the fewest errors is duplicated. I agree that this selection process is not a realistic simulation; however it does give a rapidly evolving selective process.Albeit one that has no bearing on reality. This completely misrepresents the real dynamics of genetic variation in any population, and is particularly egregious when it comes to sexual reproduction.
How would you know, have you even looked at the model. Paul wrote an online version of the model. You should study it. You would get an interesting lesson in the mathematics of random point mutation and natural selection. And as you have already said the following about recombination and natural selection:
But it is impossible to get phyletic evolution (or any major change, really) this way.
You are correct, you can not increase the information in the gene pool by recombination without error, but you can lose alleles (information in the gene pool) by recombination with natural selection.

You all have a good weekend.

[kjkent1]

I don’t believe you can modify the selection process and reduce the number of mutation/selection cycles by orders of magnitude. Myriad is trying to do this and he is a good mathematician and we’ll wait and see. None of the other mathematicians who inhabit this site have offered a solution. In order for this model to support the theory of evolution, you need a selection process that is orders of magnitude faster than Dr Schneider’s selection process. I don’t believe that such a selection process exists.

If you're a scientist, then you will stop using the phrase, "I don't believe..." and start actually testing your hypotheses. You are obviously a good mathematician, so you should be able to describe the mathematics of possible selection methods, OR, you should reprogram the algorithm and test your theory, empirically. Otherwise, your repeated claims about impossible evolution are exactly the same sort of "religion" as you decry in your opponents (I'll continue to repeat this until you recognize that this is a deficiency in your own analysis of the problems with ev).

I did one small series where I varied site width up to 15 bases. In that series, the rate of convergence was independent of base width. I don’t know if that behavior would remain constant to a base width of 450. When I get a chance, I’ll try running more cases with a wider width to see if such a case is possible. In addition, you don’t have a selection process.Thanks, that would be great.

Also, you didn't address my last issue, and I think it's a reasonable one. So I'll repeat it:

You seem to be suggesting that some pre-hemoglobin molecule is floating around in the Pacific Ocean, just waiting to randomly form into de novo hemoglobin. Isn't reality more like there is some complex life form with an already developed genome, which first mutates for a selective advantage -- not necessarily hemoglobin -- and then over time, continues to evolve until one day hemoglobin, or something close to it is finally defined?

If this is how evolution really works, then your example of evolving a 450 base gene from a random genome, directly to hemoglobin, is irrelevant. It's just another version of the already-discredited creationist "tornado through the junkyard creates a 747" example.

[Myriad]

I'm going to implement a simple variant of his proposal. Right now, Ev has three methods for breaking ties between creatures when it goes to kill off the worst half and replicate the best half. The idea is to add a fourth method for breaking the ties. Tie-breaking turns out to happen quite often, especially with large populations (selective sweeps occur continuously due to Ev's simplistic model).

If two creatures are tied in their number of mistakes, Evj will select the one with the lowest absolute difference between the valuations of the binding sites and the threshold. This provides a finer-grained selection process which distinguishes between two creatures with the same mistake count, selecting for the one that is, in some sense, closer to reducing its mistake count.

It will be interesting to see how this speeds up the evolution of a perfect creature, if at all. It's all a bit of a tangent, since it was not the purpose of Ev to model realistic genetic variation.

Paul, are you using the total absolute difference of all error sites? Or of all binding sites plus all error nonbinding sites? Or something else (surely not all the potential sites in the whole genome)?

I have one qualm about this experiment, which is as much an aesthetic concern as anything else. I share Dr. Schneider's reluctance to allow the internal workings of the sorting algorithm to affect the results (though in the end he didn't manage to completely eliminate all incidental effects of the sort, hence what used to be termed 'deaths not due to selection'). Tiebreaking occurs only between pairs of organisms that happen to be equidistant from the beginning and end of the list after the sort. Hence, how much "churn" occurs from generation to generation within the tied population will effect how genetic changes selected by tiebreaking can spread through the population. If the same individuals tend to stay aligned with one another from generation to generation, transfer of tiebreaker-winning genomes through the population will be different than if the tied population gets more thoroughly mixed each generation.

To avoid this, I changed the whole selection procedure to eliminate the sort, and instead place each bug at a location in a grid and have each compete against its (up to) four adjacent neighbors each generation. For the record, my own finer-grained selection method is to break ties in number of mistakes in favor of a creature whose single worst mistake has the lesser absolute value. If still tied, the original occupant of the position wins, and beyond that (if the tied top competitors for a position do not include the original occupant) a random choice is made.

It's probably not a big problem. In the version you're building, if there's even a little bit of churn in the tied population -- such as should be caused by just a few "fatal" (mistake-increasing) mutations per generation even if the sorting algorithm tends to keep the survivors in the same order -- then changes favorably selected by the tiebreaker should be able to spread through the population adequately, probably at a rate comparable to the bugs-on-a-grid version (for small populations at least). But you might have to watch out for a few situations, such as very low mutation rates per base, where the behavior of the sorting algorithm (and hence, precise values of population) could make a large difference.

I haven't been able to do any new experiments for a while, and now something's come up that will prevent me from doing any for a few more weeks yet. When I can get back to it, I need to do more overnight-and-longer runs with the modified selection, and I'm in the process of writing versions to simulate having large "evolved" portions of the genome (for which a given fraction of all mutations is fatal) and to try it with sexual recombination. I look forward to seeing some interesting results in 07!

Respectfully,
Myriad

[delphi_ote]

What you call evidence in the fossil record is open to interpretation.
Hand waving does not a convincing argument make.

[PixyMisa]

What I am saying is that the de novo evolution of a gene is macroevolution.

Genes do not evolve de novo. That is in fact a contradiction in terms.

The peer reviewers and editors of Nucleic Acids Research don’t seem to think so, they published Dr Schneider’s work.

That means they thought the paper was worth publishing, not that they agreed with it.

That’s only half the story. You have to show how these genomes can transform from one to another. Dr Schneider’s model shows that this is mathematically impossible (at least for random point mutations and natural selection).

And it is clear that Dr Schneider's model doesn't handle population genetics in any way remotely resembling reality, so the results from it are not useful in forming any conclusions relating to population genetics, and phyletic evolution clearly does relate to population genetics.

There are lots of examples like this. These are examples of microevolution which I believe occurs. It is the de novo evolution of genes that I don’t believe occurs.

NOBODY believes that de novo evolution of genes occurs.

I don’t argue that reptiles and birds to not have genes. What I argue is that you can’t make the transition from the reptile to the bird genome by random point mutations and natural selection. The process is profoundly slow, too slow to accomplish this transition. This is demonstrated by the ev computer model.

And as has been pointed out, there is no reason to believe that the computer model in question is a plausible representation of reality.

Where did these existing genes come from?

They are existing genes. What sort of question is that?

I’ll let Dr Schneider statement about his model answer this:
A good simulation does not attempt to simulate everything; only the essential components are modeled. For the issue at hand, the form of the genetic code is not relevant; information measured by Shannon's method is more general than that.

The form of the genetic code is absolutely relevant to the transmission of genetic modifications and to the evolutionary process; Dr Schneider's assertions to the contrary are disingenuous at best.

How would you know, have you even looked at the model.

Yes.

Paul wrote an online version of the model. You should study it. You would get an interesting lesson in the mathematics of random point mutation and natural selection. And as you have already said the following about recombination and natural selection:
But it is impossible to get phyletic evolution (or any major change, really) this way.

You are correct, you can not increase the information in the gene pool by recombination without error, but you can lose alleles (information in the gene pool) by recombination with natural selection.

Which explains nothing. We know that phyletic evolution cannot occur through recombination. We know that phyletic evolution occurs. We know that there is a mechanism for this. Your entire argument against this mechanism is a single computer model which we know is deeply flawed precisely in the way it models this mechanism. Therefore we have no reason at all to consider the argument valid.

[Paul C. Anagnostopoulos]

Paul, are you using the total absolute difference of all error sites? Or of all binding sites plus all error nonbinding sites? Or something else (surely not all the potential sites in the whole genome)?
I haven't decided, though I'm leaning to the minimum absolute difference of just the binding sites. The total absolute difference probably makes more sense though, doesn't it?

~~ Paul

[Paul C. Anagnostopoulos]

The form of the genetic code is absolutely relevant to the transmission of genetic modifications and to the evolutionary process; Dr Schneider's assertions to the contrary are disingenuous at best.
The purpose of Ev is not to model genetic propagation in nature, but to demonstrate that information can evolve in a genome. For this purpose, the exact encoding of the information is irrelevant.

Please note: Most of the detailed behavior of Ev that we have been discussing has nothing to do with Schneider's original intent. He did not claim to model the complete evolutionary landscape, and certainly not phyletic evolution.

The fact that Kleinman has decided to co-opt Ev as the be-all-end-all of evolutionary modeling is his problem, not Dr. Schneider's.*

~~ Paul

* Disclosure: I have only an informal working relationship with Dr. Schneider. I am not employed by him, nor have I been paid by him.

[Paul C. Anagnostopoulos]

We know that phyletic evolution cannot occur through recombination.
Hmm. I wonder if it's possible that control regions could change substantially enough to cause a phyletic event?

~~ Paul

[hammegk]

And if it did, then all you need to do is find it as factor in the fossil record to demonstrate phyletic gradualism is meaningful.

[Paul C. Anagnostopoulos]

And if it did, then all you need to do is find it as factor in the fossil record to demonstrate phyletic gradualism is meaningful.
A speciation event by recombination, if it can occur at all, would be instantaneous.

But now you're not arguing that phyletic gradualism doesn't occur at all, are you?

http://www.nature.com/nature/journal/v309/n5965/abs/309250a0.html

~~ Paul

[hammegk]

But now you're not arguing that phyletic gradualism doesn't occur at all, are you?


To date, not leading to a result that would demonstrate a macro-evolutionary event that would be agreed to as such by all who examined it.

We're always back to your favorite question. "What stops micro from becoming macro?" vs mine "Other than the fossil record, where have you seen macro-ev -- lab, model, nature?" and then we can discuss the multitude of definitions of species.



I'll forego the crack about arm-waving and talking louder. :p

[Paul C. Anagnostopoulos]

We're always back to your favorite question. "What stops micro from becoming macro?" vs mine "Other than the fossil record, where have you seen macro-ev -- lab, model, nature?" and then we can discuss the multitude of definitions of species.
Which brings us back to the definition of macroevolution. Speciation? Seen it. New function? Seen it. New gene from nothing? Ridiculous.

When it's a continuum, it's difficult to pick a point and give it a new name, and it's even more difficult to come up with an argument why nature would never cross that line. The goalpost is on wheels for easy moving.

~~ Paul

[hammegk]

Gee, that's beginning to sound un-falsifiable. Do you hold other religious beliefs?

[Paul C. Anagnostopoulos]

Gee, that's beginning to sound un-falsifiable. Do you hold other religious beliefs?
What sounds unfalsifiable?

~~ Paul

[PixyMisa]

The purpose of Ev is not to model genetic propagation in nature, but to demonstrate that information can evolve in a genome. For this purpose, the exact encoding of the information is irrelevant.

For that purpose, yes, you're quite right.

Please note: Most of the detailed behavior of Ev that we have been discussing has nothing to do with Schneider's original intent. He did not claim to model the complete evolutionary landscape, and certainly not phyletic evolution.Ah. Sorry. I looked at some information about it and saw that it was hardly a comprehensive model, and did not support many claims made for it by third parties, but given your explanation it would appear that the model is adequate for its intended purpose, and the fault lies with the inappropriate claims and not the model.

The fact that Kleinman has decided to co-opt Ev as the be-all-end-all of evolutionary modeling is his problem, not Dr. Schneider's.Quite, and I apologize to Dr Schneider for any offense my remarks may have caused.

[PixyMisa]

Hammy, define "macro-evolution" and we'll try to answer any questions you might have about it.

The working definition for "macro-evolution" appears to be "whatever scientists don't have direct evidence for... yet".

As Paul said, we've observed speciation, for any meaningful definition of speciation. We've seen new functions arise, some traceable to individual mutations. We haven't seen genes "evolve de novo", because that doesn't happen.

Is speciation not macro enough? Where do you draw the line?

[hammegk]

Paul: Goalposts on wheels.

Which quite nicely describes the entire edifice you call "modern Theory", and which remains a just-so-story.

[PixyMisa]

Yes, we noticed. And given that, is there any reason we should pay any attention to your input?

[hammegk]

The working definition for "macro-evolution" appears to be "whatever scientists don't have direct evidence for... yet".
Outside the reality of the fossil record, you have zilch.

.... we've observed speciation, for any meaningful definition of speciation. ...
Yeah, it's easy when "meaningful definition" is another moving goalpost; need another? no problem ... it's only words. (flap, flap, flap .. ;) )

[RecoveringYuppy]

How do you explain away the taxonomic classifications and DNA differences?

[PixyMisa]

Outside the reality of the fossil record, you have zilch.

Completely wrong.

We have observed new species evolve. Pick your definition of "species" - one that is scientifically valid, please - and we have observed a speciation event according to that definition.

Yeah, it's easy when "meaningful definition" is another moving goalpost; need another? no problem ... it's only words. (flap, flap, flap .. ;) )You seem confused.

There are a number of valid ways to determine whether two populations represent distinct species. For ALL of those distinctions, we have observed speciation.

We are not moving goalposts; we are covering all possible locations for the goalposts.

Now, Hammy, your turn: Define macro-evolution. You seem to attribute some meaning to the term; tell us what that is.

[hammegk]

How do you explain away the taxonomic classifications and DNA differences?
Why, yes species exist. Fossils so demonstrate them as does what we see as we look at existing life. That is not the question.

This is.

We have observed new species evolve. Pick your definition of "species" - one that is scientifically valid, please - and we have observed a speciation event according to that definition.
What you have done is move the goalposts on wheels to define "speciation" and then pretend you've demonstrated how speciation occurs -- there are cats & dogs, species, and we all know basically what I mean by species.

A speciation event has not been demonstarted in labs, models, or nature. And please spare us a re-gurgitation of the pap that demonstrates -- in the lab and in nature -- the bacteria that remain bacteria, birds that remain birds, plants that remain the same plant, ring species that remain the same species. Remain, that is, until the appropriate and needed re-definition of species has been provided to cover each specific case. Nor do we need to review the fossils, which at least do demonstrate new species occuring.

It would not bother my worldview an iota if you actually found an event that demonstrates speciation (that the world would acclaim as proof of what some name macro-ev). What bothers me is the pretense you have done so, and that all who don't accept results to date as that proof are dunces.

[RecoveringYuppy]

Can you explain a little more why speciation isn't speciation??

[hammegk]

Other than to ask if you call cats dogs, not really.

However, as my buddy drkitten likes to point out I'm not even scientifically semi-literate. Perhaps you can educate me. Once cladistics identifies the proposed common ancestor of those different species, can a genotype for that ancestor be proposed? If so, if not now, soon ... build one; let's see if it's a viable phenotype.

[Paul C. Anagnostopoulos]

Outside the reality of the fossil record, you have zilch.
You appear to have missed the evidence from genomic analysis. Now granted, that is a recent development, but do please pay attention.


A speciation event has not been demonstarted in labs, models, or nature. And please spare us a re-gurgitation of the pap that demonstrates -- in the lab and in nature -- the bacteria that remain bacteria, birds that remain birds, plants that remain the same plant, ring species that remain the same species.
Wait, you want to see birds turn into something else? I thought we were talking about speciation events. Or did I misunderstand your convoluted sentence here?


Nor do we need to review the fossils, which at least do demonstrate new species occuring.
If you trust that the fossil record shows speciation, then you should trust that genomic analysis shows speciation. Either they both show speciation, or god has rigged the evidence in both cases.*

Now, what was that definition of macroevolution, again?

~~ Paul

* Can you say "endogenous retroviruses"?

[RecoveringYuppy]

Cats to dogs would not be a speciation event.

[hammegk]

Agreed.

Since you, me and Paul basically cross posted while I edited, I'll repeat:

...
Perhaps you can educate me. Once cladistics identifies the proposed common ancestor of those different species (say, dogs & cats ... whatever), can a genotype for that ancestor be proposed? If so, if not now, soon ... build one; let's see if it's a viable phenotype.

[Paul C. Anagnostopoulos]

However, as my buddy drkitten likes to point out I'm not even scientifically semi-literate. Perhaps you can educate me. Once cladistics identifies the proposed common ancestor of those different species, can a genotype for that ancestor be proposed? If so, if not now, soon ... build one; let's see if it's a viable phenotype.
In general, I'm not sure how you can work backward completely accurately, given that the mutations that led to the different species are more or less random. And how would you ever know about features of the common ancestor that have disappeared?

http://www.elasmo-research.org/education/classification/cladistics.htm

~~ Paul

[RecoveringYuppy]

How many old DNA samples do we have? We know of some that are 30,000 years old and they fall in to the tree where we'd expect. How far back will the doubters insist on?

[Dr Adequate]

There is no way to explain mathematically all the new genes required to evolve reptiles to birds. Oooh, you thought of a new lie!

Of course, you can't substantiate your halfwitted lie, 'cos it's a lie, but it does seem to be one you haven't told before.

Hey, look everyone, kleinman thought of a new lie!

[Dr Adequate]

Other than to ask if you call cats dogs, not really.

However, as my buddy drkitten likes to point out I'm not even scientifically semi-literate. Perhaps you can educate me. Once cladistics identifies the proposed common ancestor of those different species, can a genotype for that ancestor be proposed? Of course not, you drivelling halfwit.

Before you beg us to educate you, try reading a basic textbook on the subject until you understand it.

If drkitten called you "not even scientifically semi-literate", that is putting it very mildly.

[kjkent1]

Perhaps you can educate me. Once cladistics identifies the proposed common ancestor of those different species (say, dogs & cats ... whatever), can a genotype for that ancestor be proposed? If so, if not now, soon ... build one; let's see if it's a viable phenotype.

Instead of constantly using the Socratic Method to get others to constantly answer a different question than the one actually asked, why don't you just provide a precise definition of what you would personally accept as a "speciation event," and then let's see if someone else here can provide the published evidence to satisfy your definition.

It just gets so damn boring to watch the constant circling between opponents. Once and a while, someone needs to step forward and take the risk of getting hit back.

Note: This is where you would ordinarily respond with, "OK, why don't you propose a definition for speciation," thereby avoiding having to do it yourself, so that if someone else later satisfies my definition, you can continue to deny the proof, because you never accepted my definition.

[hammegk]

Of course not,
Gee, data. Thanks. I took Paul's comment as a "no", but he didn't seem quite so sure.


you drivelling halfwit.
Temper, temper, little fella ...


Before you beg us to educate you, try reading a basic textbook on the subject until you understand it.
I've done a bit of research, but that point eluded me.


If drkitten called you "not even scientifically semi-literate", that is putting it very mildly.
And you, sir, are an ass (but most here already know that).

Now, please have a nice day, before you give yourself an aneurism.

[hammegk]

Instead of constantly using the Socratic Method to get others to constantly answer a different question than the one actually asked, why don't you just provide a precise definition of what you would personally accept as a "speciation event," and then let's see if someone else here can provide the published evidence to satisfy your definition.
Yeah, we all wish someone, somewhere, could provide more substantive definitions than currently exist. Cheer up, someone may as soon as they identify something new they want to tout as a "speciation". Sorry. I can't.

Note: This is where you would ordinarily respond with, "OK, why don't you propose a definition for speciation," thereby avoiding having to do it yourself, so that if someone else later satisfies my definition, you can continue to deny the proof, because you never accepted my definition.
Been there, done that.

Er, the definition of species is still evolving.

http://humboldt.edu/~kll1/speciesdef.html

That paper purports to be last updated in 1998. Perhaps someone can provide a few definitions more to get us all up to date?
Would you care to offer a new one?



Meanwhile, DrAdequate may choose enlighten us as to where the math is that demonstrates the reptile to bird sequence. If it does not exist, what does that make the Dr other than the usual kettle?

[kjkent1]

Oh well, I tried. Your response was as I predicted.

[Paul C. Anagnostopoulos]

Yeah, we all wish someone, somewhere, could provide more substantive definitions than currently exist. Cheer up, someone may as soon as they identify something new they want to tout as a "speciation". Sorry. I can't.
So you argue emphatically about speciation, god, and free will without being able to give a definition of any of them. I'm at a loss to understand where the content is.

~~ Paul

[hammegk]

That's something we can agree on.

[Paul C. Anagnostopoulos]

Hammy and I agree on something! Time for a beer!

Oh, wait ...

~~ Paul

[kjkent1]

So you argue emphatically about speciation, god, and free will without being able to give a definition of any of them. I'm at a loss to understand where the content is.

~~ Paul

The content is irrelevant. Hammegk's goal is to maintain superiority over all debate opponents by demonstrating that he cannot be outargued on any subject.

The technique can be summarized as "skillful avoidance." It involves:

1. Never directly answering a question, because that leads to someone later using your previous answer to prove you wrong.

2. Rely on the implicit hole in every conclusion that nothing can be proven absolutely true or false, because ultimately, everything is dependent on the belief of the observer in the accuracy of his observations.

3. When all else fails, resort to sarcasm in order to draw a hostile emotional response from your opponent -- and then when you obtain the response -- criticize the responder for making an ad hominem.

Persistent use of this technique can effectively destroy any useful online debate in an unmoderated forum, because it tends to divert the conversation from the substantive, to the purely argumentative.

[hammegk]

Damn. Is that what I'm doing? Sucked you right in it seems.

Back near topic, do no responses to my question on definitions mean y'all haven't made up a new one since 1998? Paulie, where are 'ya? You're the guy who ceaselessly whines for definitions.

[kjkent1]

Damn. Is that what I'm doing? Sucked you right in it seems.

Back near topic, do no responses to my question on definitions mean y'all haven't made up a new one since 1998? Paulie, where are 'ya? You're the guy who ceaselessly whines for definitions.

You were asked directly to provide your personal definition of what would satisfy you as a speciation event.

You are now exhibiting propensity #1, as previously described, by refusing to answer, and trying to get others to answer instead.

Please stop wasting everyone's time, and answer the question.

[hammegk]

I've stated a number of times I have no answer.

Move on.

[Paul C. Anagnostopoulos]

Back near topic, do no responses to my question on definitions mean y'all haven't made up a new one since 1998? Paulie, where are 'ya? You're the guy who ceaselessly whines for definitions.
I ceaselessly whine for definitions when people insist on chit-chatting about concepts that appear to be undefined: god, free will, macroevolution. If you don't make claims about these things, I won't whine for definitions.

~~ Paul

[joobz]

Actually the question is somewhat interesting. I'd guess that the insect kingdom would offer some answers to this question on speciation. Unfortunately, I'm not an entomologist and can't speak intelligently on the subject. What defines differences between ant species?

HOwever,on a related note, a quick search pulled this article on the speciation of plant-insect systems in tandem.
http://www.pnas.org/cgi/content/full/96/22/12626

Seems one main assumption that has been made in this debate, that of speciation being an event that occurs in isolation from other species is just wrong. In fact it seems that genetic drift of completely different species can influence the evolution of another species. A point that is at once obvious, but seems to be ignored in this thread. or at least not discussed.

[kjkent1]

I've stated a number of times I have no answer.

Move on.

If you have no answer, then what is your objection to the definitions provided by evolution advocates, and their proofs that speciation occurs?

If your objection is that they have moved the goal post, then why does this bother you? Science must be open to new proofs.

[PixyMisa]

What you have done is move the goalposts on wheels to define "speciation" and then pretend you've demonstrated how speciation occurs

Either you are lying, or you are utterly ignorant on the topic. I won't speculate as to which.

there are cats & dogs, species, and we all know basically what I mean by species.

Okay, I'll go for hopelessly ignorant. Cats and dogs are different families, Felidae and Canidae respectively, in the order Carnivora.

A speciation event has not been demonstarted in labs, models, or nature.

Wrong, wrong, and wrong.

And please spare us a re-gurgitation of the pap that demonstrates -- in the lab and in nature -- the bacteria that remain bacteria, birds that remain birds, plants that remain the same plant, ring species that remain the same species.

So, you are demanding phyletic change - change at the level of the phylum - or even at the level of the kingdom? Do you know how rare that is, how long it takes? Do you understand that this is several orders of magnitude away from speciation?

Well, clearly you don't.

Remain, that is, until the appropriate and needed re-definition of species has been provided to cover each specific case.

Wrong. The definitions of species came first. Since then, we have observed examples for all of those definitions.

Nor do we need to review the fossils, which at least do demonstrate new species occuring.

And why not?

It would not bother my worldview an iota if you actually found an event that demonstrates speciation (that the world would acclaim as proof of what some name macro-ev). What bothers me is the pretense you have done so, and that all who don't accept results to date as that proof are dunces.

Hammy, you don't have the faintest clue what you are talking about. You are embarrassing yourself.

[PixyMisa]

I've stated a number of times I have no answer.

Then how do you presume to argue the point?

[articulett]

And you, sir, are an ass (but most here already know that).


I think that is a common delusion of the biggest asses. I suspect that if a poll were taken, you'd be at the top of ass heap, and Dr. Adequate probably wouldn't even have his nomination seconded. And I know how you feel about me, but I relish being in the company of your enemies--they are the more intelligent members on this forum from what I've gathered-- But what I want to know is who on this forum do you think "gets you"? Even other creationists tend not to engage you--I think you may have confused the voices in your head with the support of others.

;)

[articulett]

Then how do you presume to argue the point?

Just by ad homs, as usual.

Now that we've "invented" molecular genetics--we get a snapshot of speciation as it's occurring... There are many hybrids and speciating plants and animals, and evolution just makes surviving branches of the tree more different through time. Humans become more of the mutations that helped them survive--and Chimps become more chimpish as the gene pool they draw from is from their surviving ancestors. We can look at both genomes and extrapolate what was conserved (useful for both species) and what diverged--benefiting one group over another in the survival.

This is like having a close up picture of atoms to let us know that they are "real"--that what we understand about them is true and continually being refined. Given the length of time for speciation to occur in complex organisms, I can't imagine how much more obvious the evidence could be. Creationists seem purposefully ignorant--purposely unwilling to see the obvious. They avoid definitions and continuums and all lines of thought that might lead to the possibility that the entities' responsible for their existence were far from almighty...

It boils down to an ego thing, doesn't it?--that's why Hammegk has to use ad homs. He's trying to elevate himself by putting others down, because his arguments have no merit. And he sees himself as so very glorious that he can't imagine that his existence is other than purposeful and pre-ordained. The world exists to bring forth him. I suspect my cat thinks the same.

[PixyMisa]

He's trying to elevate himself by putting others down, because his arguments have no merit. And he sees himself as so very glorious that he can't imagine that his existence is other than purposeful and pre-ordained.

So it would seem to me. I have seen him make a positive contribution - twice, I think - but as for the other 99.9%...

The world exists to bring forth him. I suspect my cat thinks the same.
Yes, but cats have concrete evidence for their belief. Clearly mankind exists to open cupboards and operate can-openers.

[PixyMisa]

I've stated a number of times I have no answer.
Move on.

We can't move on from this point, because this is the entirety of your argument.

We have definitions for species (http://www.talkorigins.org/faqs/faq-speciation.html#part2).

Given each of those definitions, we have observed speciation events (http://www.talkorigins.org/faqs/faq-speciation.html#part5).

You wish to dispute this, but given any of those definitions, the fact is that speciation has been observed.

If you want to claim otherwise, you have to either (a) provide an alternative definition of species, or (b) refute a whole bunch of thoroughly documented examples.

Since you choose to do neither, your position is rendered invalid.

Again, for the term macro-evolution. Evolution is simply the action of natural selection upon genetic variability. The smallest unit of change is the single gene, and we have certainly observed this to happen. These changes accumulate; we have observed this to happen. There is no known mechanism for enforcing a limit upon the accumulation of changes.

So if you want to assert a definition for macro-evolution that is not simply an arbitrary quantification of accumulated genetic change, you must first propose and then demonstrate the reality of such a limit.

You have not even attempted to do this, so your disputes involving macro-evolution are also rendered invalid.

[joobz]

I think that is a common delusion of the biggest asses. I suspect that if a poll were taken, you'd be at the top of ass heap, and Dr. Adequate probably wouldn't even have his nomination seconded. And I know how you feel about me, but I relish being in the company of your enemies--they are the more intelligent members on this forum from what I've gathered-- But what I want to know is who on this forum do you think "gets you"? Even other creationists tend not to engage you--I think you may have confused the voices in your head with the support of others.
;)
I'll stand up for hammegk. :) Although, i doubt he'll want me in his corner. I do not think i have earned much clout or respect to be considered a useful ally.:o

I haven't followed the recent exchange too too closely, but I can say that I've almost always enjoyed his presence in threads. He, in my estimation, is worlds more enjoyable to read than Kleinman and others of his ilk who are demonstrably liars.

I agree that hammagk tends to be obscure and not offer much substance or background into his comments, but i've always google-fu-ed a bit about comments he's made (e.g., dualism, just-so stories, objective humanism, materialism...) to try and figure out what he's getting at. It's taught me a bit about some aspects of philosophy that I, as an engineer, never bothered to look into.

And maybe it's me being new to the boards, but he never really said evolution is a lie or that it is impossible or that creationism is the key. It seems that he is just playing the skeptical observer here. Although, i do wish he would provide a definition of speciation that he would agree with or most agree with.

[PixyMisa]

The problem is, as far as I can tell, Hammy doesn't know the meaning of most of the terms he uses. Certainly in anything scientific (as we see here), but also in matters philosophical. He will make an obscure reference, but he will never explain what he means by it.

Take a look at what he says regarding speciation. He claims that the field of evolutionary biology is not merely wrong but constructed of deliberate lies, but he has nothing, nothing, to back up his assertions.

This is the hammecratic method in a nutshell.

The only reason you can't prove he is lying is that he never takes an unambiguous position on anything - except that everyone but him is somehow wrong.

[PixyMisa]

Ah, that's it!

You and I are skeptics.

Hammy is a cynic.

[joobz]

Ah, that's it!

You and I are skeptics.

Hammy is a cynic.
We'll his avatar does say Curmudgeon.;)
ALthough, I always thought his admitted world view, objective humanism, was quite optimistic. And appealing to someone who is currently re-evaluating his religious-philisophical outlook.

[Kotatsu]

A speciation event has not been demonstarted in labs, models, or nature. And please spare us a re-gurgitation of the pap that demonstrates -- in the lab and in nature -- the bacteria that remain bacteria, birds that remain birds, plants that remain the same plant, ring species that remain the same species. Remain, that is, until the appropriate and needed re-definition of species has been provided to cover each specific case.

I'm not at work now (it being Sunday), and it's been perhaps half a year since I read about it last, but does not the allopolyploidy experiments of Song et al. (or was it Soltis & Soltis who did it first?) where the progeny after five (or six? [1]) generations were both genotypically and phenotypically different from both parent species --- does not this count as a case where lab experiments have shown the possibility of speciation where the progeny does not resemble the parents in some significant aspects? I don't think they called the progeny "new species", though.

---
(1) I could check all these details tomorrow. Notice that I am by necessity vague and may change my description of their papers when I get the oppurtunity to read them again. This is not due to deceptiveness.

[Kotatsu]

Back near topic, do no responses to my question on definitions mean y'all haven't made up a new one since 1998?

I seem to have missed the relevance of 1998, probably due to oversight, but I'd suggest that the whole barcoding things --- with all its shortcomings --- is some sort of new definition (or at least redefinition, restatement, refinement, or other permutation of one of the older definitions) of species that has come about since 1998. For oligochaetes, it actually seems to work quite well in general; I have no idea if it generally works for other groups, but know that it does not work for some types of beetles.

[articulett]

So it would seem to me. I have seen him make a positive contribution - twice, I think - but as for the other 99.9%...


Yes, but cats have concrete evidence for their belief. Clearly mankind exists to open cupboards and operate can-openers.

I think underestimated his Hammy's negative contributions--he's up to nearly 8000 posts--you need at least one more space in your decimal--or if you haven't read them all, then I suppose there could be a third positive contribution, making 99.9% slightly more accurate.

Yes, my dogs think I'm god; my cats think they're gods.

[Paul C. Anagnostopoulos]

Seems one main assumption that has been made in this debate, that of speciation being an event that occurs in isolation from other species is just wrong. In fact it seems that genetic drift of completely different species can influence the evolution of another species. A point that is at once obvious, but seems to be ignored in this thread. or at least not discussed.
You bastage! You've just made the definitions of macroevolution and species even more difficult to pin down.


I agree that hammagk tends to be obscure and not offer much substance or background into his comments, but i've always google-fu-ed a bit about comments he's made ...
Make sure you Google mu. You'll need to know that one.

~~ Paul

[Myriad]

A conceptual portrait of creationists examining the fossil record:

C: You want me to believe that everything is made of atoms. Like, a table is made of atoms, right?

S: That's right.

C: Here is a picture of a table. Please point out the atoms.

S: It's all atoms, but the individual atoms are too small to see in that picture.

C: Then show me a picture where you can see the atoms.

S: No problem. Here's a scanning tunneling microscope image of atoms.

C: Of course those are atoms. I never denied that atoms exist. But are they the kind of atoms that a table is made of?

S: Yes.

C: I don't see a table. Please point out the table in your picture of atoms.

S: The table is too large to see in that picture.

C: Then show me a picture where you can see the table.

... and so on, and so on ...

Respectfully,
Myriad

[hammegk]

If your objection is that they have moved the goal post, then why does this bother you?
Circular arguments, where one begins by assuming the answer, bother me when presented as 'proof' the original assumption was correct.


Science must be open to new proofs.
Then find one, and present it.

Either you are lying, or you are utterly ignorant on the topic. I won't speculate as to which.
I see. Who pissed on your corn-flakes?


Okay, I'll go for hopelessly ignorant. Cats and dogs are different families, Felidae and Canidae respectively, in the order Carnivora.
Hmm. You seriously suggest that the ability of humans to order things, and draw imaginary lines to provide boxes that are then named, is our best evidence demonstrating a speciation event?


Wrong, wrong, and wrong.
Opinion, opinion, opinion; undemonstrated by other than wishful thinking -- hey, let's move the edge of our imaginary box here! Yeah, that'll convince the rubes.


So, you are demanding phyletic change - change at the level of the phylum - or even at the level of the kingdom? Do you know how rare that is, how long it takes? Do you understand that this is several orders of magnitude away from speciation?

Well, clearly you don't.
Yeah, we both wish that darn fossil record -- or data anywhere -- would shed some light on a speciation event.


Wrong. The definitions of species came first. Since then, we have observed examples for all of those definitions.
The definitions make good, infinitely malleable, just-so-stories, anyway.


And why not?
Fine. Make your review.


Hammy, you don't have the faintest clue what you are talking about. You are embarrassing yourself.
You concern for me is touching.


We can't move on from this point, because this is the entirety of your argument.
I see. So the whole of Modern Evolutionary Theory rests on my ability to provide a definition of species?


We have definitions for species (http://www.talkorigins.org/faqs/faq-speciation.html#part2).

Given each of those definitions, we have observed speciation events (http://www.talkorigins.org/faqs/faq-speciation.html#part5).

You wish to dispute this, but given any of those definitions, the fact is that speciation has been observed.
And the fact that you, and most materialists, find that absolutely convincing, is the final 'proof'?


If you want to claim otherwise, you have to either (a) provide an alternative definition of species, or (b) refute a whole bunch of thoroughly documented examples.
I do? ROFL.


Again, for the term macro-evolution. Evolution is simply the action of natural selection upon genetic variability. The smallest unit of change is the single gene, and we have certainly observed this to happen. These changes accumulate; we have observed this to happen. There is no known mechanism for enforcing a limit upon the accumulation of changes.
Yup. I agree. Now all you need is a demonstrable macro-ev event.


So if you want to assert a definition for macro-evolution that is not simply an arbitrary quantification of accumulated genetic change, you must first propose and then demonstrate the reality of such a limit.
I must?

You have not even attempted to do this, so your disputes involving macro-evolution are also rendered invalid.
Thanks for sharing your opinion in this matter.

I'll stand up for hammegk. :) Although, i doubt he'll want me in his corner. I do not think i have earned much clout or respect to be considered a useful ally.:o
Thanks. Why not? And, why wouldn't you be a useful ally?


I agree that hammagk tends to be obscure and not offer much substance or background into his comments, but i've always google-fu-ed a bit about comments he's made (e.g., dualism, just-so stories, objective humanism, materialism...) to try and figure out what he's getting at. It's taught me a bit about some aspects of philosophy that I, as an engineer, never bothered to look into.
Thank you.


And maybe it's me being new to the boards, but he never really said evolution is a lie or that it is impossible or that creationism is the key. It seems that he is just playing the skeptical observer here.
Yeah, and it's a crummy job, but someone needs to do it.


Although,i do wish he would provide a definition of speciation that he would agree with or most agree with.
I wish I could, too.

The problem is, as far as I can tell, Hammy doesn't know the meaning of most of the terms he uses.
And your problem is that you are wrong in that assessment.


Certainly in anything scientific (as we see here), but also in matters philosophical. He will make an obscure reference, but he will never explain what he means by it.

Take a look at what he says regarding speciation. He claims that the field of evolutionary biology is not merely wrong but constructed of deliberate lies, but he has nothing, nothing, to back up his assertions.
Other than the fact that it's the definition of speciation that has no meaning. Back to just-so-stories.


The only reason you can't prove he is lying is that he never takes an unambiguous position on anything - except that everyone but him is somehow wrong.
Waaah. Life is a bitch, and then you die.

We'll his avatar does say Curmudgeon.;)
ALthough, I always thought his admitted world view, objective humanism, was quite optimistic.
Ouch! Objective idealism!

I'm not at work now (it being Sunday), and it's been perhaps half a year since I read about it last, but does not the allopolyploidy experiments of Song et al. (or was it Soltis & Soltis who did it first?) where the progeny after five (or six? [1]) generations were both genotypically and phenotypically different from both parent species --- does not this count as a case where lab experiments have shown the possibility of speciation where the progeny does not resemble the parents in some significant aspects? I don't think they called the progeny "new species", though.
Each Kingdom has it's own challenges in interpretation, although Plantae doesn't get much play.

---
(1) I could check all these details tomorrow. Notice that I am by necessity vague and may change my description of their papers when I get the oppurtunity to read them again. This is not due to deceptiveness.
Your added comments will be welcomed.

I seem to have missed the relevance of 1998, probably due to oversight,
I'd previously provide a link with a plethora of 'species definitions' that was compiled in 1998.


but I'd suggest that the whole barcoding things --- with all its shortcomings --- is some sort of new definition (or at least redefinition, restatement, refinement, or other permutation of one of the older definitions) of species that has come about since 1998. For oligochaetes, it actually seems to work quite well in general; I have no idea if it generally works for other groups, but know that it does not work for some types of beetles.
I don't understand the 'barcoding' comment.

Er, and I almost hate to say it, but, A worm is a worm. :D

[delphi_ote]

Circular arguments, where one begins by assuming the answer, bother me when presented as 'proof' the original assumption was correct.
Darwin started with the physical evidence and developed a theory to explain it. This theory has been vindicated many times over by multiple independent lines of evidence. There's no circular argument coming from the science camp. Implying that scientists need to agree on a perfect definition of species before they can explain the origin of species is as absurd as demanding they have a mathematically precise definition of "red" and "pink" before they can explain the origin of colors.

[Paul C. Anagnostopoulos]

Yup. I agree. Now all you need is a demonstrable macro-ev event.
Are you willing to define exactly what you mean by demonstrable here?

~~ Paul

[PixyMisa]

I see. Who pissed on your corn-flakes?

No one, but you pissed in this discussion.

Hmm. You seriously suggest that the ability of humans to order things, and draw imaginary lines to provide boxes that are then named, is our best evidence demonstrating a speciation event?In a sense, yes.

Species are named after the fact based on a variety of criteria. The same goes for every layer of the taxonomy, up through genera and families all the way to kingdoms, and at every level there is some degree of arbitrariness in the distinctions made. Often - when whole ranges of intermediary species have gone extinct - the distinction is clear. Other times, not.

But we have workable definitions of the term species, definitions that have proved themselves useful in the study of biology, and by any and all of those definitions, speciation events have been observed.

Opinion, opinion, opinion; undemonstrated by other than wishful thinking -- hey, let's move the edge of our imaginary box here! Yeah, that'll convince the rubes.Again, a demonstration of your ignorance and your desperate struggle to avoid honest debate.

You have been invited to select one of the accepted definition of species
or to provide your own. You have done neither, so your argument is meaningless.

Yeah, we both wish that darn fossil record -- or data anywhere -- would shed some light on a speciation event.Meaning what?

The definitions make good, infinitely malleable, just-so-stories, anyway.False. The definitions are specific. For each and every one of the definitions, we have observed speciation.

Fine. Make your review.I see no need to do so, given that your entire argument is specious; I just want to know why you said what you said.

You concern for me is touching.Oh, I'm not concerned; just making an observation.

I see. So the whole of Modern Evolutionary Theory rests on my ability to provide a definition of species? No. Any potential value of your participation here rests on your ability to provide a definition of species. Evolutionary Theory will get on just fine without you.

And the fact that you, and most materialists, find that absolutely convincing, is the final 'proof'?What are you talking about?

We have definitions for the term species. For each of those definitions, we have observed speciation events. That's simply a statement of fact.

I do? ROFL.Well, you could continue to make ill-informed remarks and be regarded by all as an ignoramus; your choice.

Yup. I agree. Now all you need is a demonstrable macro-ev event.By my definition of macro-evolution, a number of such events have already been documented.

If you disagree, explain why.

I must?Or pursue the alternative outlined above, yes. I believe that exhausts the possibilities.

And your problem is that you are wrong in that assessment.Well, yes, there's an assertion. Evidence?

Other than the fact that it's the definition of speciation that has no meaning. Back to just-so-stories.Which definition of species (and hence, of speciation) do you disagree with, and why?

Waaah. Life is a bitch, and then you die.Do you have anything worthwhile to say here?

[PixyMisa]

Are you willing to define exactly what you mean by demonstrable here?

I'm not sure there's a lot of point in him doing so, given that he flatly refuses to define macro-evolution.

[PixyMisa]

Hammy, to sum up:

You are disputing the scientific position on speciation, but you neither accept the scientific definition of speciation nor provide your own.

You are raising questions regarding macro-evolution, but neither accept the scientific definition of macro-evolution nor provide your own.

Until you do, your statements on these subjects are semantically null. They cannot be interpreted, let alone answered. They don't mean anything.

Do you intend to correct this failing?

[kjkent1]

Hammy, to sum up:

You are disputing the scientific position on speciation, but you neither accept the scientific definition of speciation nor provide your own.

You are raising questions regarding macro-evolution, but neither accept the scientific definition of macro-evolution nor provide your own.

Until you do, your statements on these subjects are semantically null. They cannot be interpreted, let alone answered. They don't mean anything.

Do you intend to correct this failing?

hammegk has provided a dozen definitions for speciation/macro-evolution. He wants you to prove them all. However, after you do, he will surprise you by telling you that none of those definitions are sufficient to satisfy his requirements.

Then, when you ask him again for his requirements, he will tell you that he doesn't have any -- but that he knows yours don't satisfy.

The objective is to maintain a non-substantive argument in order to prove superiority over others who outside of an anonymous internet forum, would be credited with superior education and intellect. But, on the internet, where no one can be forced to answer a direct question, hammegk's debating technique cannot be overcome, except by either refusing to discuss anything with him, or banning him from the forum.

Of course, you can choose to adopt the identical debating technique. But, hammegk will not give up -- not ever. So, you will be stuck orbiting with him at the argument "event horizon" indefinitely. Because, while you may have a life off the internet, hammegk's life "is" this internet, and beating you at an argument on any/every subject is what he lives for.

The empirical evidence for this is readily available. hammegk has nearly 8,000 posts on this website. And, if you're interested, I can show you another website where I believe that he has 16,000+ more.

[joobz]

Ouch! Objective idealism!
Oops, that's what I meant. i was writing that late last night inbetween writing a grant due on monday.:)

My mind was more concerned about polymeric antioxidants and treatment of vascular oxidative stress.

[hammegk]

If there be a poster elsewhere with 16,000+ posts it isn't me. :confused:

Here a couple years ago I lost about 3000 courtesy of a management fracas and resulting db re-org. As to spending way too much time on this forum, I plead guilty. Sue me.

[Paul C. Anagnostopoulos]

If you will define sue and lawyer, I'll get right on it. :D

~~ Paul

[Yahzi]

And you, sir, are an ass (but most here already know that).
Once again Hamme uses words with regard to their actual meanings.

Dr. Adequate is what is known as a wit. Quite distinct from an ass, insomuch as wit is intentionally amusing.

[Yahzi]

Hammegk's goal is to maintain superiority over all debate opponents by demonstrating that he cannot be outargued on any subject.
A trick he learned from Socrates. Too bad we can't teach him the trick the Athenians finally figured out for dealing with it. :D

Persistent use of this technique can effectively destroy any useful online debate in an unmoderated forum, because it tends to divert the conversation from the substantive, to the purely argumentative.
May I suggest the /ignore feature as a moderating influence?

Wouldn't it be wonderful if you could click on a poster and see how many active members have them on /ignore? Someday, in a more perfect internet...

[kjkent1]

A trick he learned from Socrates. Too bad we can't teach him the trick the Athenians finally figured out for dealing with it. :D

I wish no one harm -- just an opportunity to learn.

Socrates, used his method to narrow the argument to a reasoned conclusion, rather than to extend it ad infinitum. And, that makes all the difference.

[articulett]

If there be a poster elsewhere with 16,000+ posts it isn't me. :confused:

Here a couple years ago I lost about 3000 courtesy of a management fracas and resulting db re-org. As to spending way too much time on this forum, I plead guilty. Sue me.

I don't want to sue you. I just would like you to learn some of the coolest information humans have had the privilege of knowing. You don't even have to give up your intelligent designer or become a "fundamentalist materialist" or "closet dualist" to understand speciation and how we know what we know. You've heard of Francis Collins, right? The same technology that allows us to do forensic testing and paternity testing, is also useful for showing how closely species are related. It's really really interesting and cool. It's even pretty easy to understand. You see this information as some sort of threat to a paradigm, but it's just information that's really interesting to know--people here want to share it with you. It's information you can "decipher" for yourself--prove it or disprove it to yourself. But you seem to have a knee-jerk reaction that protects you from even examining the evidence, and I suspect that it's because you think your salvation is at stake. But Francis Collins is an evangelical Christian who heads up the official human genome project. You can at least be on the same page as everyone else regarding speciation which will lend credence to what you have to say. Read some of what he writes because you really do sound like Myriad's example. Really.

[Unnamed]

I haven't decided, though I'm leaning to the minimum absolute difference of just the binding sites. The total absolute difference probably makes more sense though, doesn't it?

Paul (and Myriad),

I confess that I didn't follow the last few days of the thread, but I just made this small change to Evj (in the scoreChromosome method), and I thought I would let you know.


! sortValue = mistakes = spuriousHits = 0;
for (int p = 0; p <= chromosome.length - width; ++p) {
if ((valuation[p] = siteValuation(p, width)) >= threshold) {
if (!siteInd[p]) {
if (p < availablePos) mistakes += gene; else mistakes += nongene;
! sortValue += Math.abs(valuation[p] - threshold);
++spuriousHits;
}
} else {
if (siteInd[p]) {
mistakes += missed;
! sortValue += Math.abs(valuation[p] - threshold);
}
}
}

! //sortValue = mistakes; // We will sort on the mistake


As a result, the number of generations to perfect creature went down by a factor of 3.0 in my tests (7 runs for each version, pop. 128, sites 256, default for everything else). I ran a few tests with 512 sites and the effect is even more impressive.

What I did was, for each mistake, to add the distance between the valuation and threshold, and use the result as the sorting order. This is a finer measure than the raw number of mistakes, but it still goes to zero when mistakes = 0, so it converges to the same place.

I didn't touch anything that had to do with ties, but I guess that using sortValue instead of mistakes would help even more.

ETA: I ran examples with genome length 1024 and 2048, and the difference is just astonishing.

[Paul C. Anagnostopoulos]

Very cool, Unnamed! Thanks for trying that variation.

Would you be willing to run a set of experiments with your variant of Evj? If so, use these parameters:

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

Then vary the genome size from 1024 by factors of 2 and record the number of generations to perfect creature. I've run this model up to a genome size of 128K.

~~ Paul

[Kotatsu]

Each Kingdom has it's own challenges in interpretation, although Plantae doesn't get much play.
Your added comments will be welcomed.

I haven't had time to look at it today, but it is Song et al. 1995 (PNAS 92, 7719-7723) I referred to. I'll bring it home with me tonight and read it later. Reading through the abstract, though, it seems I must have imagined the "phenotypical" part (1).

I'd previously provide a link with a plethora of 'species definitions' that was compiled in 1998. I don't understand the 'barcoding' comment.

Barcoding is, briefly (2), an idea put forward by Paul Hebert and colleagues, which is based on the assumption that while the within-species differences of the COI gene will be quite low (0-5%, I think), the between-species differences will be much higher (10-20%; with a saturation at about 23% in oligochaetes at least). Between these two differences, there will be a "barcoding gap", which will make it possible to determine to which species (3) a given sample belongs, regardless of phylum.

To clarify: If comparing closely related species in, say, a family, there should in theory be no overlap between the curve that shows the distribution of within-species differences within the family an dthat describing the distribution of between-species differences.If the higher Within-species difference in 5% and the lowest between-species difference is 10%, addition of a new species of the same family should not result in any differences between this species and any of the other which is in the range of 5-10%. The actual ranges seem to differ widely between different groups of animals.

In oligochaetes, this works quite well, actually. I've been working with several families (4), and while saturation is reached in most cases (i.e. division into subfamilies and higher taxonomical ranks is rare, ambiguous, and sometimes wrong), morphologically identified species fall in the same clades, implying that they are fairly homogenous. In some cases, unidentified samples have been placed in a certain clade, and this placement has been confirmed by morphological studies, so the idea seems to hold water. However, if anything, our work has revealed that there is likely a lot of undescribed oligochaetes out there, just waiting to be found; several "common" species are most likely not monophyletic, which will prove dangerous, as several of them are used as model organisms.

Sadly, however, the barcoding assumptions are not universal and - some suggest - not supported by data when sampling is done over a sufficiently large area. Samples with intermediate differences regularly appear, and the papers of Hebert and colleagues (the Costa Rican butterflies, the North American birds and others) with which they gallumph so proudly through current scientific journals apparently fall apart somewhat when larger geographical areas are examined. I attended a conference recently where there was an example of European water beetles (I have forgotten which genus, and it is not very essential). In this example, the barcoding gap failed to present itself once several populations from every area was used. And, of course, COI can't be used at all in Cnidarians. Still, it may be of some use if refined.

Er, and I almost hate to say it, but, A worm is a worm. :D

Certainly --- depending on how you define "worm" --- but my comment was rather in connection to the species concept part of barcoding, not as a comment on speciation. Even if speciation was proven to be impossible, but barcoding gave the same results as it does today, barcoding could still work as a species concept in at least some groups. If another gene, or a set of genes, is used, it might be used universally!

---
(1) However, the study is done on three Brassica species, and unless I am mistaken, allopolyploid progeny of these do show extensive phenotypical differences from the parental species. However, I am not a botanist.
(2) And possibly not very correctly.
(3) These species would initially have to be sorted out by other means, using other species concepts; barcoding - as I understand it - works only when you already have a basic database with which to compare.
(4) Namely: Almidae, Capilloventridae, Enchytraeidae, Lumbricidae, Lumbriculidae, Megascolecidae, Opistocystidae, Phreodrilidae, Propappidae, Randiellidae, and Tubificidae (including Naididae).

[kleinman]

I don’t believe you can modify the selection process and reduce the number of mutation/selection cycles by orders of magnitude. Myriad is trying to do this and he is a good mathematician and we’ll wait and see. None of the other mathematicians who inhabit this site have offered a solution. In order for this model to support the theory of evolution, you need a selection process that is orders of magnitude faster than Dr Schneider’s selection process. I don’t believe that such a selection process exists.If you're a scientist, then you will stop using the phrase, "I don't believe..." and start actually testing your hypotheses. You are obviously a good mathematician, so you should be able to describe the mathematics of possible selection methods, OR, you should reprogram the algorithm and test your theory, empirically. Otherwise, your repeated claims about impossible evolution are exactly the same sort of "religion" as you decry in your opponents (I'll continue to repeat this until you recognize that this is a deficiency in your own analysis of the problems with ev).
I believe that Dr Schneider’s selection process shows that macroevolution is impossible by random point mutations and natural selection. You evolutionarians need to prove your own theory. It appears that some are finally trying.
I did one small series where I varied site width up to 15 bases. In that series, the rate of convergence was independent of base width. I don’t know if that behavior would remain constant to a base width of 450. When I get a chance, I’ll try running more cases with a wider width to see if such a case is possible. In addition, you don’t have a selection process.Thanks, that would be great.
This series will take quite a bit of time to run.
Also, you didn't address my last issue, and I think it's a reasonable one. So I'll repeat it:

You seem to be suggesting that some pre-hemoglobin molecule is floating around in the Pacific Ocean, just waiting to randomly form into de novo hemoglobin. Isn't reality more like there is some complex life form with an already developed genome, which first mutates for a selective advantage -- not necessarily hemoglobin -- and then over time, continues to evolve until one day hemoglobin, or something close to it is finally defined?

If this is how evolution really works, then your example of evolving a 450 base gene from a random genome, directly to hemoglobin, is irrelevant. It's just another version of the already-discredited creationist "tornado through the junkyard creates a 747" example.
I suggest nothing of the kind. It is evolutionarians who speculate that there was a time when there were small self replicating molecules that somehow evolved to the life forms we know today. There was a time when hemoglobin did not exist. The construction of this molecule (and associate gene) had to start from some point.
I'm going to implement a simple variant of his proposal. Right now, Ev has three methods for breaking ties between creatures when it goes to kill off the worst half and replicate the best half. The idea is to add a fourth method for breaking the ties. Tie-breaking turns out to happen quite often, especially with large populations (selective sweeps occur continuously due to Ev's simplistic model).

If two creatures are tied in their number of mistakes, Evj will select the one with the lowest absolute difference between the valuations of the binding sites and the threshold. This provides a finer-grained selection process which distinguishes between two creatures with the same mistake count, selecting for the one that is, in some sense, closer to reducing its mistake count.

It will be interesting to see how this speeds up the evolution of a perfect creature, if at all. It's all a bit of a tangent, since it was not the purpose of Ev to model realistic genetic variation.Paul, are you using the total absolute difference of all error sites? Or of all binding sites plus all error nonbinding sites? Or something else (surely not all the potential sites in the whole genome)?

I have one qualm about this experiment, which is as much an aesthetic concern as anything else. I share Dr. Schneider's reluctance to allow the internal workings of the sorting algorithm to affect the results (though in the end he didn't manage to completely eliminate all incidental effects of the sort, hence what used to be termed 'deaths not due to selection'). Tiebreaking occurs only between pairs of organisms that happen to be equidistant from the beginning and end of the list after the sort. Hence, how much "churn" occurs from generation to generation within the tied population will effect how genetic changes selected by tiebreaking can spread through the population. If the same individuals tend to stay aligned with one another from generation to generation, transfer of tiebreaker-winning genomes through the population will be different than if the tied population gets more thoroughly mixed each generation.
Myriad makes a good point here. If you design a selection method that reduces the importance of errors in the nonbinding site region, you can reduce the effect of the increasing genome length. In the limit, if you choose a selection method that completely ignores errors in the nonbinding site region, the rate of convergence should become independent of genome length when you use a mutation rate fixed to a number of bases.
What you call evidence in the fossil record is open to interpretation.Hand waving does not a convincing argument make.
Are you talking about evolutionarian hand waving or creationist hand waving about the fossil record?
What I am saying is that the de novo evolution of a gene is macroevolution.Genes do not evolve de novo. That is in fact a contradiction in terms.
Ok, then explain how you can take a series of microevolutionary steps from the first base of the hemoglobin gene to the fully formed gene. Don’t forget to tell us what the selection process is.
The peer reviewers and editors of Nucleic Acids Research don’t seem to think so, they published Dr Schneider’s work.That means they thought the paper was worth publishing, not that they agreed with it.
I exchanged some email with one of the editors. I think he agrees with it.
That’s only half the story. You have to show how these genomes can transform from one to another. Dr Schneider’s model shows that this is mathematically impossible (at least for random point mutations and natural selection).And it is clear that Dr Schneider's model doesn't handle population genetics in any way remotely resembling reality, so the results from it are not useful in forming any conclusions relating to population genetics, and phyletic evolution clearly does relate to population genetics.
I love posting these quotes from Dr Schneider’s web site.

The following quotes were taken from Dr Schneider’s blog web page: http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html)

The following are Dr Schneider’s responses to a critique of his paper Evolution of biological information by Dr Stephen E Jones.

"Schneider's paper is misleadingly titled: "Evolution of biological information". But it is just a *computer* simulation. No actual *biological* materials (e.g. genomes of nucleic acids, proteins, etc) were used, nor does Schneider propose that his simulation be tested with *real* genomes or proteins Actual biological materials were used to determine the original hypothesis. Read the literature: Schneider1986 (http://www.lecb.ncifcrf.gov/~toms/paper/schneider1986)

It only becomes *real* biological information and random mutation and natural selection, when the simulation is tested in the *real* world, using *real* DNA, proteins, with *real* mutations and a *real* environment does the selecting. It is significant that Schneider does not propose this, presumably because he knows it wouldn't work.You are very bad at reading my mind, I have considered doing this experiment. Given the right conditions, it WILL WORK. Do you have th gumption to do the experiment yourself? That's the way real science works! FURTHERMORE, if you read the literature, you will recognize that related experiments have been repeatedly done for 20 years. Look up SELEX.

In the rest of the paper he uses the single word "selection". I take this as a tacit admission that his model is not a simulation of *real* biological natural selection. No. A rose is a rose by any other name. Selection is selection whether it be natural (generally meaning the environment of earth), breeding (by humans usually, though perhaps some ants select their fungi), SELEX or in a computer simulation. Of COURSE it is a simulation of natural selection! The paper would not be relevant to biology and would not have been published in a major scientific journal if it were not!

Schneider lets slip that there is another unrealistic element in his (and indeed all) computer simulations in that it (they) "does not correlate with time": So? Run the program slower if you want. Make one generation per 20 minutes to match rapid bacterial growth. THIS WILL NOT CHANGE THE FINIAL RESULT!

Well, when Schneider's simulation is actually tested with *real* "life" (e.g. a bacterium), and under *real* mutation and natural selection it gains information, then, and only then, would "creationists" be favourably impressed. But if they are like me, they would already be impressed (but unfavourably) that Schneider does not mention in his paper that his simulation should now be so tested in the *real* "biological" world. 1. The simulation was of phenomena in the "real" world.
2. Dr. Jones is invited yet again to do an experiment.

The following is a response Dr Schneider made to a statement made by David Berlinski (http://www.discovery.org/scripts/viewDB/index.php?command=view&id=51&isFellow=true).

Where attempts to replicate Darwinian evolution on the computer have been successful, they have not used classical Darwinian principles, and where they have used such principles, they have not been successful. The ev program disproves this statement since it uses classical Darwinian principles and was successful.

The previous statements are clear that Dr Schneider believes that ev simulates the real world.
There are lots of examples like this. These are examples of microevolution which I believe occurs. It is the de novo evolution of genes that I don’t believe occurs.NOBODY believes that de novo evolution of genes occurs.
That’s reassuring, because it is completely illogical to believe such a thing. So where do you believe genes came from?
I don’t argue that reptiles and birds do not have genes. What I argue is that you can’t make the transition from the reptile to the bird genome by random point mutations and natural selection. The process is profoundly slow, too slow to accomplish this transition. This is demonstrated by the ev computer model.And as has been pointed out, there is no reason to believe that the computer model in question is a plausible representation of reality.
You might find that Dr Schneider doesn’t agree with your view. I am sure that I don’t.
Where did these existing genes come from?They are existing genes. What sort of question is that?
Unless you believe that genes are eternal, they had to come into being somehow.
I’ll let Dr Schneider statement about his model answer this:A good simulation does not attempt to simulate everything; only the essential components are modeled. For the issue at hand, the form of the genetic code is not relevant; information measured by Shannon's method is more general than that.The form of the genetic code is absolutely relevant to the transmission of genetic modifications and to the evolutionary process; Dr Schneider's assertions to the contrary are disingenuous at best.
Do you think genetic code is eternal?
How would you know, have you even looked at the model?Yes.
Since ev is a mathematical model, you should be able to enumerate what you think is wrong about the model. Why don’t you tell us what is wrong with this simulation of random point mutations and natural selection?
Paul wrote an online version of the model. You should study it. You would get an interesting lesson in the mathematics of random point mutation and natural selection. And as you have already said the following about recombination and natural selection:But it is impossible to get phyletic evolution (or any major change, really) this way.You are correct, you can not increase the information in the gene pool by recombination without error, but you can lose alleles (information in the gene pool) by recombination with natural selection.Which explains nothing. We know that phyletic evolution cannot occur through recombination. We know that phyletic evolution occurs. We know that there is a mechanism for this. Your entire argument against this mechanism is a single computer model which we know is deeply flawed precisely in the way it models this mechanism. Therefore we have no reason at all to consider the argument valid.
What I am trying to explain here is that recombination and natural selection can give rapid phenotypic changes in a species. It is this rapid phenomena that Darwin inappropriately extrapolated to mutation and natural selection when he was interpreting the differences between finch beaks in isolated populations. Gould did the same when he postulated his concept of punctuated equilibrium. This concept is applicable to recombination and natural selection but not to mutation and natural selection.
The form of the genetic code is absolutely relevant to the transmission of genetic modifications and to the evolutionary process; Dr Schneider's assertions to the contrary are disingenuous at best.The purpose of Ev is not to model genetic propagation in nature, but to demonstrate that information can evolve in a genome. For this purpose, the exact encoding of the information is irrelevant.

Please note: Most of the detailed behavior of Ev that we have been discussing has nothing to do with Schneider's original intent. He did not claim to model the complete evolutionary landscape, and certainly not phyletic evolution.

The fact that Kleinman has decided to co-opt Ev as the be-all-end-all of evolutionary modeling is his problem, not Dr. Schneider's.*

*Disclosure: I have only an informal working relationship with Dr. Schneider. I am not employed by him, nor have I been paid by him.
I tend to agree that this discussion has nothing to do with Dr Schneider’s original intent for ev, however Dr Schneider has gone far beyond his original intent. Consider what Dr Schneider has proposed on his FAQ page at:
http://www.lecb.ncifcrf.gov/~toms/paper/ev/faq-for-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/faq-for-ev.html)
Why don't you do a real biological experiment instead of just a computer model?The primary reason is that we don't have infinite resources and time. If you have the resources (a molecular biology lab), are interested in doing an experiment, and would like to discuss it please contact me (toms@ncifcrf.gov?subject=Ev%20Bench%20Experiment) .
Paul, what part of the evolutionary landscape is Dr Schneider trying to model and then do a real biological experiment?

Don’t forget, I also co-opted the micro/macroevolution concept as well. There is so little else in the theory of evolution that is worth co-opting.
We know that phyletic evolution cannot occur through recombination.Hmm. I wonder if it's possible that control regions could change substantially enough to cause a phyletic event?
Paul, where did you get that idea?
And if it did, then all you need to do is find it as factor in the fossil record to demonstrate phyletic gradualism is meaningful.
Consider that phylum are simply a categorization scheme that can be defined any way you want. Since Gould hypothesis of punctuated equilibrium fits more logically with recombination and natural selection, it is less likely to find evidence of gradualism (on the macroevolutionary scale) by the mechanism of recombination and natural selection.
The purpose of Ev is not to model genetic propagation in nature, but to demonstrate that information can evolve in a genome. For this purpose, the exact encoding of the information is irrelevant.For that purpose, yes, you're quite right.
Too bad the author of the computer model says something different. And this is a peer reviewed and published model. Dr Schneider wants to do experiments verifying his model.
Please note: Most of the detailed behavior of Ev that we have been discussing has nothing to do with Schneider's original intent. He did not claim to model the complete evolutionary landscape, and certainly not phyletic evolution.Ah. Sorry. I looked at some information about it and saw that it was hardly a comprehensive model, and did not support many claims made for it by third parties, but given your explanation it would appear that the model is adequate for its intended purpose, and the fault lies with the inappropriate claims and not the model.
Paul, continue to diminish the value of ev. Why did you waste your time writing the java version of the program?
The fact that Kleinman has decided to co-opt Ev as the be-all-end-all of evolutionary modeling is his problem, not Dr. Schneider's.Quite, and I apologize to Dr Schneider for any offense my remarks may have caused.
As I told Dr Schneider months ago when we were discussing his model, when the full mathematical behavior of the model became known to evolutionarians, they would discredit his model. Now his own programmer has devalued the model. Paul, does ev have any scientific merit?
However, as my buddy drkitten likes to point out I'm not even scientifically semi-literate. Perhaps you can educate me. Once cladistics identifies the proposed common ancestor of those different species, can a genotype for that ancestor be proposed? If so, if not now, soon ... build one; let's see if it's a viable phenotype.In general, I'm not sure how you can work backward completely accurately, given that the mutations that led to the different species are more or less random. And how would you ever know about features of the common ancestor that have disappeared?
Paul! You used the word random. So you can’t work backwards and ev shows you can’t work forward, which way are you going from here?
There is no way to explain mathematically all the new genes required to evolve reptiles to birds.Oooh, you thought of a new lie!

Of course, you can't substantiate your halfwitted lie, 'cos it's a lie, but it does seem to be one you haven't told before.

Hey, look everyone, kleinman thought of a new lie!
Scatequate, why would I lie to you? You are my favorite annoyee. I would much rather use logic on you. Ev is my substantiation. You have heard of ev, haven’t you? Ev is a computer simulation of random point mutation and natural selection and when you use realistic parameters in the model, the rate of evolution is profoundly slow, too slow to evolve any gene de novo. Of course, when you get to infinity, everything happens in one generation.

Scatequate, we can try to get a cubicle for you next to kjkent1 so you can learn the mathematics of ev together.
Back near topic, do no responses to my question on definitions mean y'all haven't made up a new one since 1998? Paulie, where are 'ya? You're the guy who ceaselessly whines for definitions.I ceaselessly whine for definitions when people insist on chit-chatting about concepts that appear to be undefined: god, free will, macroevolution. If you don't make claims about these things, I won't whine for definitions.
What about macroevolution=de novo evolution of a gene? Of course PixyMisa believes genes are eternal.
Circular arguments, where one begins by assuming the answer, bother me when presented as 'proof' the original assumption was correct.Darwin started with the physical evidence and developed a theory to explain it. This theory has been vindicated many times over by multiple independent lines of evidence. There's no circular argument coming from the science camp. Implying that scientists need to agree on a perfect definition of species before they can explain the origin of species is as absurd as demanding they have a mathematically precise definition of "red" and "pink" before they can explain the origin of colors.
Darwin inappropriately extrapolated the rapid changes that can occur with recombination and natural selection to the profoundly slow mechanism of mutation and natural selection. Evolutionarians continue to make this same erroneous extrapolation. With respects to mathematically precise definitions of colors, that has existed for years. It is called the frequency spectrum of light.
Yup. I agree. Now all you need is a demonstrable macro-ev event.Are you willing to define exactly what you mean by demonstrable here?
Macroevolution=de novo evolution of a gene.
I haven't decided, though I'm leaning to the minimum absolute difference of just the binding sites. The total absolute difference probably makes more sense though, doesn't it?Paul (and Myriad),

I confess that I didn't follow the last few days of the thread, but I just made this small change to Evj (in the scoreChromosome method), and I thought I would let you know.
Finally, an evolutionarian is doing some mathematics. Unnamed, since you are modifying the java code, perhaps you or Paul would post the names of the corresponding variables and functions in the Pascal version of the program. Are you ignoring the “spuriousHits” and only using “mistakes” when you doing your sort?

[hammegk]

To an illiterate dolt such as myself Kotatsu's comments add to the complexity of defining 'species'.

Perhaps y'alls old standby talkorigins needs updating?

Their most significant summary of speciation is:
Confirmation:
Speciation of numerous plants, both angiosperms and ferns (such as hemp nettle, primrose, radish and cabbage, and various fern species) has been seen via hybridization and polyploidization since the early 20th century. Several speciation events in plants have been observed that did not involve hybridization or polyploidization (such as maize and S. malheurensis).

Some of the most studied organisms in all of genetics are the Drosophila species, which are commonly known as fruitflies. Many Drosophila speciation events have been extensively documented since the seventies. Speciation in Drosophila has occurred by spatial separation, by habitat specialization in the same location, by change in courtship behavior, by disruptive natural selection, and by bottlenecking populations (founder-flush experiments), among other mechanisms.

Several speciation events have also been seen in laboratory populations of houseflies, gall former flies, apple maggot flies, flour beetles, Nereis acuminata (a worm), mosquitoes, and various other insects. Green algae and bacteria have been classified as speciated due to change from unicellularity to multicellularity and due to morphological changes from short rods to long rods, all the result of selection pressures.

Speciation has also been observed in mammals. Six instances of speciation in house mice on Madeira within the past 500 years have been the consequence of only geographic isolation, genetic drift, and chromosomal fusions. A single chromosomal fusion is the sole major genomic difference between humans and chimps, and some of these Madeiran mice have survived nine fusions in the past 500 years (Britton-Davidian et al. 2000).


Need I say Mice is Mice? :D

[cyborg]

Every time I hear you bang on about somebody else doing mathematics I cannot help but recall your own misgivings about it kleinman.

And the fact I see precious little of it coming from you.

I see someone else's work, a program, and you, running a program (or not as the case may be when doing so would be inconvenient to you). I don't see that as YOU doing any work at all.

Unbelievably conceited.

[kleinman]

Every time I hear you bang on about somebody else doing mathematics I cannot help but recall your own misgivings about it kleinman.

And the fact I see precious little of it coming from you.

I see someone else's work, a program, and you, running a program (or not as the case may be when doing so would be inconvenient to you). I don't see that as YOU doing any work at all.

Unbelievably conceited.
In case you haven’t notice, I did the parametric study with ev and posted these results which show the mathematical behavior of ev. I have run hundreds of cases with this mathematical model. So stop whining because you don’t like the results from this evolutionarian model which disproves your own theory. You need to fix your own mathematical models (if they can be fixed).

I know I am not saying much. All I am saying is the ev computer model shows that macroevolution by random point mutations and natural selection is mathematically impossible when realistic genome lengths and mutation rates are used in the model, that the model contradicts Gould’s hypothesis of punctuated equilibrium and that huge populations do not reduce the generations for convergence sufficiently to contradict either of the two propositions.

Anyway, I like co-opting evolutionarian ideas. The problem is there are so few worth co-opting.

[kjkent1]

Paul (and Myriad),

I confess that I didn't follow the last few days of the thread, but I just made this small change to Evj (in the scoreChromosome method), and I thought I would let you know.


! sortValue = mistakes = spuriousHits = 0;
for (int p = 0; p <= chromosome.length - width; ++p) {
if ((valuation[p] = siteValuation(p, width)) >= threshold) {
if (!siteInd[p]) {
if (p < availablePos) mistakes += gene; else mistakes += nongene;
! sortValue += Math.abs(valuation[p] - threshold);
++spuriousHits;
}
} else {
if (siteInd[p]) {
mistakes += missed;
! sortValue += Math.abs(valuation[p] - threshold);
}
}
}

! //sortValue = mistakes; // We will sort on the mistake


As a result, the number of generations to perfect creature went down by a factor of 3.0 in my tests (7 runs for each version, pop. 128, sites 256, default for everything else). I ran a few tests with 512 sites and the effect is even more impressive.

What I did was, for each mistake, to add the distance between the valuation and threshold, and use the result as the sorting order. This is a finer measure than the raw number of mistakes, but it still goes to zero when mistakes = 0, so it converges to the same place.

I didn't touch anything that had to do with ties, but I guess that using sortValue instead of mistakes would help even more.

ETA: I ran examples with genome length 1024 and 2048, and the difference is just astonishing.

Unnamed (or anyone else who understands what's going on here),

Would you mind explaining to us mere mortals how your programming change relates to real-world biological behaviors. We wouldn't want some creationist, such as Dr. Kleinman to claim (1) that your modifications do not/cannot actually appear in nature, and/or (2) that you are "smuggling" an "intelligent design" into the process of evolution.

[cyborg]

In case you haven’t notice, I did the parametric study with ev and posted these results which show the mathematical behavior of ev.

Yes, I noticed. The point still remains - I don't actually see what you have done apart from run someone else's program and post the results.

So stop whining because you don’t like the results from this evolutionarian model which disproves your own theory. You need to fix your own mathematical models (if they can be fixed).

As has been pointed out so many times before:

1) ev is not the totality of evolution. It's not even close.
2) It was written to show one objective, which it shows. You have unreasonably extrapolated its predictive abilities far beyond its capabilities.

You might as well just go ahead and tell me that Einsteinian physics is wrong because the Newtonian mathematics of Quake doesn't demonstrate any of its effects.

I know I am not saying much. All I am saying is the ev computer model shows that macroevolution by random point mutations and natural selection is mathematically impossible

Yes you say that but still have failed to tell us what macroevolution is - MATHEMATICALLY. This is incredibly important because if you cannot quantify it then it cannot possibly be mathematically demonstrated as such. You simply throw out the assertion time and time again.

You cannot show macroevolution is impossible in ev if you cannot say what constitutes macroevolution - genome lengths and mutation rates be damned. They don't matter until you can tell us that.

[Paul C. Anagnostopoulos]

Would you mind explaining to us mere mortals how your programming change relates to real-world biological behaviors. We wouldn't want some creationist, such as Dr. Kleinman to claim (1) that your modifications do not/cannot actually appear in nature, and/or (2) that you are "smuggling" an "intelligent design" into the process of evolution.
The smuggling issue has already been addressed:

http://www.lecb.ncifcrf.gov/~toms/paper/ev/dembski/rebuttal.html

Ev's normal selection method is quite discrete: A creature with fewer binding mistakes is selected over one with more. These new schemes make a finer distinction between creatures with the same number of mistakes. It is as if stronger binding is favored over weaker binding, even when the number of sites bound is the same. The idea of weak binding appears in the literature:

http://www.pnas.org/cgi/content/abstract/102/20/7097

That said, a person can certainly argue that Ev is not modeling the precise kinds of selection that occur in nature. But Ev's point is simply to show that information can evolve in a genome.

~~ Paul

[Kotatsu]

To an illiterate dolt such as myself Kotatsu's comments add to the complexity of defining 'species'.

Please, if I am at some point too technical, confusing or vague, state which point that is, so that I may elucidate. Barcoding is nothing very difficult, but failure to communicate what I mean may have resulted, as English is not my first language.

However: I have now read Song's et al. article again, and they do mention phenotypic divergence as well, though only briefly:

"Phenotypic variation among F5 plants within each polyploid provided additional evidence for genetic divergence. Fertilities among F5 plants ranged from 0% to 24.9% for the AB/BA synthetics and from 0% to 100% for the AB/BA synthetics [Should probably read "AC/CA"]. F5 plants also varied for morphological traits, such as leaf shape and color, branching patterns, and number of side shoots."

A = Brassica rapa
B = B. nigra
C = B. oleracea
AB and BA corresponds to the natural polyploid hybrid B. juncea, and AC and CA to the natural polyploid hybrid B. napus. BC and CB would --- if I understand things correctly --- correspond to the natural polyploid hybrid B. carinata, but don't take my word for it.

F5 is the fifth generation (self-pollinated) of the various synthetic polyploid hybrids. Interestingly, the genetic variation between the F5 plants and their diploid parents are 9.6% for AB, 8.2% for BA, 4.1% for AC, and 3.7% for CA --- all just in five generations!

As an aside, I noticed in Soltis & Soltis, 1995 (PNAS 92, pp 8089-8091) a quotation to a study by Soltis et al., 1995 (Am J Bot 82, says "in press" in my paper, why I don't know the page numbers) wherein is shown that Tragopogon mirus and Tragopogon miscellus may have formed as many as 9 to 21 times just in the last 50 years (now 60 years) due to allopolyploidization. I shall see if I can get that article tomorrow.

Need I say Mice is Mice? :D

So you are looking for an example of speciation in which the resulting taxa is not only a new species, genus, or tribe but a new family or even new order?

[kleinman]

In case you haven’t notice, I did the parametric study with ev and posted these results which show the mathematical behavior of ev.Yes, I noticed. The point still remains - I don't actually see what you have done apart from run someone else's program and post the results.
That about sums it up. So why are you evolutionarians so annoyed?
So stop whining because you don’t like the results from this evolutionarian model which disproves your own theory. You need to fix your own mathematical models (if they can be fixed).As has been pointed out so many times before:

1) ev is not the totality of evolution. It's not even close.
2) It was written to show one objective, which it shows. You have unreasonably extrapolated its predictive abilities far beyond its capabilities.

You might as well just go ahead and tell me that Einsteinian physics is wrong because the Newtonian mathematics of Quake doesn't demonstrate any of its effects.
So what is the relativistic effect in the theory of evolution that will fix the mathematics that ev reveals for random point mutations and natural selection?
I know I am not saying much. All I am saying is the ev computer model shows that macroevolution by random point mutations and natural selection is mathematically impossibleYes you say that but still have failed to tell us what macroevolution is - MATHEMATICALLY. This is incredibly important because if you cannot quantify it then it cannot possibly be mathematically demonstrated as such. You simply throw out the assertion time and time again.

You cannot show macroevolution is impossible in ev if you cannot say what constitutes macroevolution - genome lengths and mutation rates be damned. They don't matter until you can tell us that.
# of generations to accomplish de novo evolution of a gene by random point mutations and natural selection > time available

As an example of this equation, Paul has estimated that it would take 65,000,000 generations to evolve 80 loci on a 100k genome with a population of 1,000,000. This is done with a highly idealized very accurate selection process on a genome that is still at least a factor of 5 shorter genome than any known free living organism, yet is still much, much slower that recombination and natural selection.
Would you mind explaining to us mere mortals how your programming change relates to real-world biological behaviors. We wouldn't want some creationist, such as Dr. Kleinman to claim (1) that your modifications do not/cannot actually appear in nature, and/or (2) that you are "smuggling" an "intelligent design" into the process of evolution.[quote="Paul"]The smuggling issue has already been addressed:

http://www.lecb.ncifcrf.gov/~toms/pa.../rebuttal.html[/quote (http://www.lecb.ncifcrf.gov/~toms/pa.../rebuttal.html%5b/quote%5d%5b/quote)]
The code fragment Unnamed posted appears to be weighting errors in the binding and non-binding site regions. What is the value assigned to the variables “gene” and “nongene”. If you set nongene=0 then you are ignoring errors in the nonbinding site region of the genome. That is equivalent to ignoring harmful mutations.
Ev's normal selection method is quite discrete: A creature with fewer binding mistakes is selected over one with more. These new schemes make a finer distinction between creatures with the same number of mistakes. It is as if stronger binding is favored over weaker binding, even when the number of sites bound is the same. The idea of weak binding appears in the literature:

http://www.pnas.org/cgi/content/abstract/102/20/7097 (http://www.pnas.org/cgi/content/abstract/102/20/7097)
That modification that Unnamed appears to be changing much more than the threshold.
That said, a person can certainly argue that Ev is not modeling the precise kinds of selection that occur in nature. But Ev's point is simply to show that information can evolve in a genome.
Now that’s a laugh. What kind of precise selection process that occur in nature would evolve a gene de novo? You must have drunk more than a few beers after celebrating that issue of agreement with hammegk in order to come up with this idea.

Sure ev shows that information can evolve in a genome. It just takes more time than the history of the earth to get a gene de novo.

[cyborg]

That about sums it up. So why are you evolutionarians so annoyed?

Annoyed? Hardly. It's more that it's staggering how arrogant you are with your call to 'evolutionists' to do the maths when you're basically saying that they have! You're the one who has done bugger all.

So what is the relativistic effect in the theory of evolution that will fix the mathematics that ev reveals for random point mutations and natural selection?

Way to go Mr Does-Not-Get-The-Point.

You using ev to disprove evolution is the equivalent of using Quake to disprove Einsteinian physics.

Do you get that Quake is an entirely insufficient representation of real world physics or not?

Do you get that ev is an entirely insufficient representation of real world evolution or not?

# of generations to accomplish de novo evolution of a gene by random point mutations and natural selection > time available

That does not answer the question.

That is your conclusion. I require the mathematical definition of macroevolution. That may require something like algebra. I would like a logical analysis of the ev program please. I would like to see the logical conditions for macroevolution occurring - an assessment of the change of state of the genome represented in the ev environment. An example. Anything tangible.

If you cannot tell us what a macroevolutionary event would be in ev I fail to see how you can tell us that ev shows it is impossible - irrelevant of how accurately it captures the real world processes.

[Unnamed]

Would you be willing to run a set of experiments with your variant of Evj? If so, use these parameters:

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

Then vary the genome size from 1024 by factors of 2 and record the number of generations to perfect creature. I've run this model up to a genome size of 128K.
These are my results so far (genome size, mutations, run 1, run 2, run 3):
1024, 2, 190, 197, 206
2048, 4, 219, 210, 262
4096, 8, 256, 256, 268
8192, 16, 322, 357, 332
16384, 32, 394, 375, 366
32768, 32, 474, 474, 430
65536, 32, (running)
I am using the seeds 0, 1 and 2. The cases where the generations to perfect creature are the same have different seeds, so it's a coincidence or the software didn't update the seed.

Starting at 32768, the number of mutations was fixed at 32, because the application won't let me increase it and I didn't notice that until now.

I changed the tie-breaking algorithm to use sortValue (the sum of the strengths of the mistakes) instead of the number of mistakes. This helps a bit, but not much. I also added some overflow protection.

Finally, an evolutionarian is doing some mathematics. Unnamed, since you are modifying the java code, perhaps you or Paul would post the names of the corresponding variables and functions in the Pascal version of the program. Are you ignoring the “spuriousHits” and only using “mistakes” when you doing your sort?
I am not familiar with the Pascal version. I couldn't get it to run on my computer and never looked at the code. I am adding all kinds of mistakes.


Would you mind explaining to us mere mortals how your programming change relates to real-world biological behaviors. We wouldn't want some creationist, such as Dr. Kleinman to claim (1) that your modifications do not/cannot actually appear in nature, and/or (2) that you are "smuggling" an "intelligent design" into the process of evolution.
The smuggling issue has already been addressed:

http://www.lecb.ncifcrf.gov/~toms/paper/ev/dembski/rebuttal.html

Ev's normal selection method is quite discrete: A creature with fewer binding mistakes is selected over one with more. These new schemes make a finer distinction between creatures with the same number of mistakes. It is as if stronger binding is favored over weaker binding, even when the number of sites bound is the same. The idea of weak binding appears in the literature:

http://www.pnas.org/cgi/content/abstract/102/20/7097

My idea (actually a misinterpretation of Myriad's idea) was to replace the number of mistakes, which is very coarse, with the sum of the strength of the mistakes, which is a finer grained measure. The selection step can then distinguish between "weak" mistakes and "strong" mistakes. Actually, my version prefers creatures with many weak mistakes over ones with fewer but stronger mistakes.

The code fragment Unnamed posted appears to be weighting errors in the binding and non-binding site regions. What is the value assigned to the variables “gene” and “nongene”. If you set nongene=0 then you are ignoring errors in the nonbinding site region of the genome. That is equivalent to ignoring harmful mutations.

That modification that Unnamed appears to be changing much more than the threshold.
I don't use the weight variables "gene" and "nongene", and in any case I was running with them set to 1 all the time.

My modification was to replace "mistakes" with "sum of strength of mistakes". That was all. I didn't change what a mistake was, I didn't ignore spurious hits and I didn't ignore non-gene mistakes.

Now, I can't find the old results because the thread is huge. Does this version scale better than the original with genome size?

[kjkent1]

What kind of precise selection process that occur in nature would evolve a gene de novo? You must have drunk more than a few beers after celebrating that issue of agreement with hammegk in order to come up with this idea.

Sure ev shows that information can evolve in a genome. It just takes more time than the history of the earth to get a gene de novo.

Your argument is subtly "evolving" (or maybe you're just adding a little more argument and subtly moving the goalpost a tad).

Until very recently you were content to argue that ev was flawed because it could not evolve a gene fast enough. Now you seem to be suggesting that even if the selection mechanism were modify to make ev work fast enough, this wouldn't satisfy you, because your new position is that the gene must evolve without anything more than completely random selection.

Please explain why a a genome cannot have a selective advantage to an organism at a relatively simple stage of its evolution, which is substantially different from the selective advantage present at some relatively later and more complex point.

As you have already conceded, ev is very fast for short genomes, so there would be no barrier to a quick evolution without selection to some very simple selective advantage, followed by more environmentally channeled selection speeding the evolutionary process toward a more complex advantage.

[Unnamed]

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

I just got this result:
65536, 32 mutations/generation (should be 128), 827 generations to perfect creature.

The difference is just too big, so I am posting a screenshot of the options dialog.

[Paul C. Anagnostopoulos]

That modification that Unnamed appears to be changing much more than the threshold.
He explained what he did:

What I did was, for each mistake, to add the distance between the valuation and threshold, and use the result as the sorting order. This is a finer measure than the raw number of mistakes, but it still goes to zero when mistakes = 0, so it converges to the same place.

~~ Paul

[Paul C. Anagnostopoulos]

I just got this result:
65536, 32 mutations/generation (should be 128), 827 generations to perfect creature.
Whoa, Nelly! Is that possible?


The difference is just too big, so I am posting a screenshot of the options dialog.
You have an old version of Evj that doesn't let you set the mutations per base. Can you grab the latest code and make your changes again, then run with the parameters I specified? We're now on version 2.38.

~~ Paul