Annoying creationists

[kleinman]

Annoying Creationists

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]

Annoying Creationists

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.

 

[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