Haldane's Dilemma

JOHN PAUL

Some things to consider before thinking that comparing the chimp & human genomes as a possible falsification of Walter ReMine’s premise (quick thoughts after a weekend away):

1. It assumes humans & chimps evolved from a common ancestor. “In order to analyze which amino acid replacements have occurred during the evolution of humans and apes, the evolutionary relationships among the species being studied must be inferred.”
2. Walter does not make that assumption . As far as I can tell he takes an observed point B, an alleged evolutionary point A and says you can’t get here from there, in the timeframe and mechanisms claimed.

Is it logical to assume an event happened when you are trying to figure out if it could have happened? That is what is being done using the comparison method.

3. The comparison method, using the declared & above (see also the Chimp & Human thread) assumptions, shows how many mutations would have to had accrue and at what rate, since the alleged split from that common ancestor to evolve into what we observe today.
4. Walter’s method shows the number of beneficial mutations (single nucleotide substitutions) that can accrue in a given time period. His time period appears to be 10 million years:

 

ROBERT RAPIER

First, it may be useful for me to reiterate my position on this matter. My position has never been that 1667 beneficial mutations are clearly sufficient to account for the differences. I have always maintained that until we work through the problem, it is not a very scientific approach to just assume that they are not. Both John Paul and I have worked through the problem, and both of us showed that 1667 beneficial mutations are in the range of what sequencing data have to date indicated. This has been the primary criticism of Mr. ReMine – that he did not establish this fundamental premise before launching into an attack on the proposed solutions for Haldane’s Dilemma.

However, the key point here is that Mr. ReMine is arguing for numbers of mutations orders of magnitude higher than this. If the argument is now whether 1667 beneficial substitutions are allowed when the true number is 1903 or even 3000, you have already conceded that Mr. ReMine’s assumption was well off the mark and he was unjustified in dismissing 1667 outright. This then brings into question the assumptions in the model. As someone who uses mathematical models daily, I have a very good understanding of their practicality. The numbers obtained from a mathematical model are not set in stone; they are assumption dependent, and those assumptions depend upon our knowledge of the system under study. Remember, we are talking about a 45-year old mathematical model developed without the aid of sequencing data. Since sequencing data have already surprised us with respect to 1) The high degree of DNA similarity between humans and chimps, and 2) The small percentage of coding DNA; would it be surprising that the assumptions in this 45-year old model may be subject to change? But that ventures past the fundamental premise, and I am content to let the experts hash out whether or not Haldane’s model has been modified by any discoveries in biology since 1957.

Now, on to your post:

Regarding the Fred Williams’ quote, Fred is referring to another common ancestry argument and not to Haldane’s Dilemma. His quote is not at all relevant to our discussion.

I must admit that the logic of this question is baffling to me. If you assume that it didn’t happen, there is no need to try to figure out whether it could have happened. Consider the following:

Assumption 1: No common ancestry. That’s it. No need to even develop an argument with respect to Haldane’s Dilemma. Of course Mr. ReMine assumed the possibility of common ancestry to build his argument. (That doesn’t mean he believed in common ancestry). Haldane assumed common ancestry in formulating his original hypothesis, so in using Haldane’s results Mr. ReMine has by default done the same.

Think about it another way. When you are arguing about design, is it logical to do so without first establishing that a Designer exists? If you want to be held to this standard, the entire field of ID can be thrown out the window. When we make arguments of this sort, of course we make certain assumptions. These assumptions are allowed so the argument may be developed and evaluated. Otherwise, there is really nothing to debate.

Actually that was not your conclusion. Your conclusion was:

You proposed a range of 1425-2000, and I worked out conclusions from that estimate. Based on your statements, I could have just pointed out that 1667 is within the range of the estimate you provided. But I did the math to show the probability of multiple substitutions per gene. I also pointed out the logical error you made with respect to assuming that each change had to consist of a single nucleotide substitution.

I don’t think it, you and I both demonstrated it. I would add that it is pretty good for a 45-year old mathematical model established before sequencing data was available. I am actually quite impressed.

You are misreading him, or reading more into it than what he said. I asked him at OCW if 1667 referred to 1667 single substitutions, and he said “No, not necessarily”. Many of them may be point substitutions, but it is not a requirement. The following is what Mr. ReMine says about the issue on his Web page. He is discussing a debate that he had with Prof. Massimo Pigliucci:

While Mr. ReMine provides no basis for his numbers, but let’s go with them. The Human Genome Project estimates that the average gene consists of 3000 base pairs. Just taking Mr. ReMine’s assumed 60 gene duplications, this would provide for 180,000 new base pairs not present in the common ancestor. Average those over 40,000 genes, and you get 4.5 base pairs per gene from just this one mechanism. Average them over the (at most) 2000 genes estimated to be undergoing positive selection, and you would get an average of nearly 1000 base pairs per gene. Note that this obviously does not imply that each gene would get 1000 base pairs via this mechanism; this is just the average. The actual number of base pair differences in the genes undergoing positive selection was much lower than this in the paper John Paul cited. And we still have 1607 mutations to consider (1667 minus the 60 we just considered).

Some Creationists have confused the issue by contrasting 1667 beneficial substitutions to the millions of total base pair differences between humans and chimps. This approach demonstrates a faulty understanding of the argument.

Upon what basis did you make this determination? Please elaborate on this point. If you read the paper to which you linked, you saw that the genes differ by very few nucleotides. How is a 5 base pair difference in a gene of 1050 base pairs caused by “complex genetic movements”? Copying errors would easily account for that. You do acknowledge that gene duplication, insertions, deletions, etc. occur, don’t you?

This point is unimportant, though, as it does not change the order of magnitude of the number of changes. It was merely an observation.

As pointed out, key differences do not have to be single nucleotide substitutions.

What would those differences in protein structure be? I nominate cytochrome C if you want to compare a protein between humans and chimps (don’t forget to split the difference). Also note: http://www.eurekalert.org/pub_releases/2002-04/aaft-uoa040402.php

From the link, we learn: “The differences between humans and their closest relatives are more a matter of quantity than quality, according to the report. Differences in the amount of gene and protein expression, rather than differences in the structure of the genes or proteins themselves, distinguish the two species.”

Next, let’s look at what your article has to say. One of the genes under consideration in the paper to which you linked had 1050 base pairs, and they determined that the difference between humans and chimps was 5 base pairs. This would translate to 2-3 base pair differences between humans and the common ancestor.

However, they don’t indicate whether those base pairs were together or were scattered throughout the gene. If they were consecutive, it would suggest a single event was responsible for the 2-3 base pair difference. If they were scattered, it would argue for 2-3 single nucleotide substitutions. Either way, this gene was determined to be under strong selective pressure even though there were only 5 total base pair differences between humans and chimps. Considering that it is likely that not every substitution was beneficial (due to the rarity of beneficial substitutions), the answer to your question above is an emphatic “Yes”.

It doesn’t matter what ARN, David Plaisted, or some biotech companies estimate the total number of genes to be. Several groups have various reasons for wanting or needing the number of genes to be higher. The biotech company in the link has a vested financial interest in seeing the number go up, so do you really want to put your faith in them? The two groups who sequenced the genome are presently the authorities on the matter, and they say 30-40,000. When they say 40-50,000, then I will listen. Also, I would think that Creationists would be very cautious in using articles that imply that there might be in excess of 100,000 genes. I would have thought they would have learned when they were burned by their (too high) estimates of the amount of coding DNA in humans and then again by their (too high) estimates of the DNA differences between humans and chimps.

The discussion may continue, but my goal was to demonstrate that Mr. ReMine’s fundamental premise was not sound. This goal has been accomplished, even by your analysis.

[Administrator: the following email was received as an addendum to the above post]

One correction needs to be made to my last post. I mentioned dividing 180,000 base pairs into 2000 genes undergoing positive selection to get almost 1000 base pairs per gene. That should have read almost 100. (That’s what I get for doing the whole exercise without my calculator). I realized it when I reread my post, and knew that 1000 sounded really high. The real number would be about 90 base pairs per gene, still well above the average number of base pair differences per gene found in the study.

The base pair differences in the study ranged from 5 base pairs up to 39 base pairs. The latter was for the BRCA 1 gene, consisting of 5592 total base pairs. If you split the difference, you can infer that at most humans accumulated new 20 base pairs (in the genes under study) since the divergence. Some small fraction of these would have been beneficial.

The 4.5 base pair difference averaged over 40,000 genes is correct, but probably not the best way to illustrate the issue. It might mislead a person into thinking that one gene got 40 base pairs via gene duplication, another got 100, some got 0, etc. for an average of 4.5. In reality, entire new sections of DNA would have been created with an average of 3000 new base pairs (per duplication) not found in the ancestor. Sorry if that was confusing. Hopefully this will more clearly illustrate the issue, and explain why 1667 beneficial mutations lead to A LOT of base pair changes.

[ July 30, 2002, 04:29 PM: Message edited by: Administrator ]

 

JOHN PAUL

Robert:
I must admit that the logic of this question is baffling to me. If you assume that it didn’t happen, there is no need to try to figure out whether it could have happened. Consider the following:

John Paul:
Yes I can understand how it would be. If you assume that it did happen there is no need to figure out if it could. That’s the theory of evolution for ya in a nutshell. Tell everyone it did occur often enough and no one will question if it could.

Once you assume we did evolve from some common ancestor all the math will give you is how many changes occurred. Then you can speculate how they were divvied up from there. It won’t tell us if those changes actually happened (already assumed), could happen (already assumed) or even if those DNA differences can actually effect the observed differences (already assumed).

Robert:
Think about it another way. When you are arguing about design, is it logical to do so without first establishing that a Designer exists?

John Paul:
Absolutely. There is no need to know who or what the designer is/ was in order to detect design. Once deliberate design is inferred, the design then implies a designer. No need to know anything about the designer to observe and study the design in hopes of understanding it so it can be maintained. Once you establish a designer exists there is no longer a need to infer design. It will be a given (the Law of Life- designed by…).

SETI is a prime example of not having to establish a designer exists in order to detect design. Or have we already established that and SETI is a cover-up? (pretend to look for something we already have been in contact with)

[ July 31, 2002, 08:03 PM: Message edited by: Administrator ]

 

FRED WILLIAMS

Robert has made some fundamental errors in his analysis that I would like to address.

Here Robert makes the false assumption that functional genome = exons only (coding DNA). Ironically his mentor (Scott Page) corrected me when I made this same false correlation a few years ago. I wonder why Scott has not pointed this out to Robert?

So, we know Robert’s 1.1% parameter is wrong, which alone invalidates his entire argument. The study he cited did not give a functional estimate, but obviously it will be some number greater than 1.1%. We know that mutations to introns can be deleterious. Just do a search of PubMed and many examples will pop up, ie:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list _uids=12144818&dopt=Abstract

To give you an idea how far off Robert could be, if all introns are functionally important, then from Robert’s citation the functional % shoots
to 25%, which yields ~10 million base pair differences, not 432K. We are not even considering the flanking segments and scaffolding where some mutations have also shown to be functionally important.

It is also worth noting here that ALL fixed differences between chimp and humans have to go from few to many in the allotted time, not just the beneficial mutations in the functional genome. This means that (using Robert ’s 1.24% difference between chimps/man) ~40 million base pairs must become fixed within the allotted time, not 432K. Using Robert’s 50% adjustment (this assumption has problems but for argument’s sake I will accept it) yields 20 million mutations that need to become fixed in the chimp line, and 20 million in the human line. The neutral theory is supposed to come to the rescue and lessen the burden of such neutral mutations. But it requires 1) a very high % of mutations that are neutral, and 2) a very high mutation rate to give it a fighting chance. But there is a problem - as they raise the mutation rate they raise the cost of harmful mutation within the functional area. Robert completely glossed over this very important fact. It is also addressed in Remine’s book (it is very clear to me Robert has not even seen Remine's book, which is unfortunate because it would only seem fair that if you are going to claim you refuted someone's argument, you should at least hear the argument in its entirety and not just in bits & pieces found on the internet; Remine addressed many of Robert's complaints in his book, including an entire chapter dedicated to the neutral theory and why it falls short in solving Haldane's Dilemma).

Robert then writes: “The vast majority of the mutations are neutral”
Here is another bold assumption by Robert. He needs to provide evidence that the debate is over on the validity of the neutral theory. This is news to me, as I’m sure it is to many others here. How does Robert know the “vast majority” of mutations are neutral? According to Futuyma, the widespread belief is that the vast majority are “nearly neutral”, or better stated, slightly harmful;, not “neutral”. See this graph:

http://www.evolutionfairytale.com/images/mutation_dist.jpg

This is crucial. Why? How does Robert expect us to believe upward evolution can occur when the vast majority of these fixation events, 20 million of them in chimps and 20 million in humans, are slightly harmful? “Evolution”
is amazing, isn’t it!

To conclude, Robert’s 216K number is clearly bogus. It assumes that only the exons are functionally important, which scientists have shown overwhelmingly to be false. This alone refutes Robert’s argument. Robert needs to return to square one.

[ July 31, 2002, 08:04 PM: Message edited by: Administrator ]

 

ROBERT RAPIER

Why didn’t you just use this argument in your first reply? You could have said, “I refuse to assume common ancestry as a part of this argument”. Then you wouldn’t have had to address any of the issues. I can understand that you might want to take this position now, as the substantive issues have been laid to waste. But what you fail to understand is that what Mr. ReMine has done is propose a falsification test for shared ancestry. This falsification test requires the assumption of common ancestry in order to present the arguments required to falsify it. As has been pointed out, using your numbers or my numbers, Mr. ReMine’s falsification test has failed. That doesn’t “prove” common ancestry, but it does demonstrate that what we observe is consistent with common descent. If you want to argue that it is consistent with a common creator, please provide a falsification test. But I implore you in the future if you have difficulty in addressing the substantive issues, please don’t wait until the end of the debate to say that you reject the entire argument because you reject common ancestry. That smacks of sour grapes.

Note that I didn’t say that the identity of the designer would be required. I just said that if a designer can’t be proven to exist, then what you infer as design may be illusory. This approach utilizes the same logic that you use in the paragraph above.

If you have anything to add with respect to Haldane’s Dilemma, I would certainly be glad to discuss it. However, this most recent post from you was not remotely related to Haldane’s Dilemma. I would respectfully request that if you have other unrelated issues to discuss, you do so in another thread. I will respond as time allows.

Now, back to Haldane’s Dilemma:

Hello, Fred. It’s been a while. I have been expecting you. As you shall see, the errors, as well as misrepresentations and red herrings, belong to you.

That is false, and a clear misrepresentation of my position. I calculated the number of base pairs in coding regions. I never said or implied that this was the only “functional” region. But you seem to have been tripped up once again by the word “functional” as it applies to DNA. As you pointed out above, Dr. Page corrected you on this error before. I am surprised to see this issue confuse you again, as I never mentioned the word functional. I calculated the numbers for coding regions only because I don’t believe anyone would suggest that noncoding regions take precedence over coding regions when doing interspecies comparisons. Informed scientists know that exons are where the changes of interest are to be found; that’s why they look there when doing interspecies comparisons.

But before we lose people, let’s define terms. Exon sequences are the portion of the gene that actually codes for proteins. This is synonymous with the 1.1% coding region that I mentioned above. Intron sequences are base pair segments that are found within genes, but which do not code for proteins. Intron sequences have been referred to as “junk” DNA, but it has been reported that they may play a role in gene expression.

See above. The 1.1% parameter is not wrong, as this term was clearly defined. Perhaps a retraction from you would be appropriate? 1.1% refers to coding DNA, which informed scientists will tell you is the region primarily responsible for expressed differences between species. There may be some affect from introns, but you grossly exaggerate the issue. In order to impact my treatment of the argument, you are going to have to demonstrate that the majority of the expressed differences are due to introns (as you have implied). Good luck finding support for that.

Besides that, it is a logical error to assume that if the 1.1% parameter is wrong then the whole argument fails. As I point out throughout, in your hasty attempt to engage in damage control, you have made a number of statements that are in error. Using your logic, this means your entire rebuttal is invalidated.

Isn’t that like saying, “if the earth is flat”, or “if the moon is made of green cheese”? It is merely a baseless assertion for the purpose of exaggerating the numbers. Please prove me wrong by supplying some references indicating that anyone believes this. You can assert anything you like, but I would ask that you support these assertions with references. Maybe I misunderstand what you mean by functionally important. Are you saying that we should expect a large portion of the allowed beneficial mutations (1667) to occur in introns, and that these affect the expressed differences between chimps and humans? Because that appears to be what you are implying. Mr. ReMine certainly did not say or imply that. Reread the paragraph I posted above where he is assigning the mutations. If you are able to support that assertion, I am prepared to take on the argument. But don’t forget, we are talking about expressed differences here.

This is a BIG red herring, but let me allow Mr. ReMine to clear up your confusion on this one. From the OCW board, on Jan. 12, 2002:

And:

Emphasis by Mr. ReMine in each case. That should clear up the issue for you. I can point out at least 2 more errors in your above analysis if you are interested, but it really is beside the point. Remember, the issue of neutral mutations arose because Creationists were having a difficult time explaining how two different species of chimpanzee could accrue millions of fixed differences, when you were arguing that Haldane’s Dilemma prevented it in humans. You have acknowledged the issue as a problem for Creationists in previous discussions, so I am surprised you brought it up. I can provide more information if you like, but as Mr. ReMine has said, it is a nonstarter with respect to Haldane’s Dilemma.

I request an apology from Fred after he removes his foot from his mouth. I most certainly have seen Mr. Remine’s book. I have borrowed the book and have been in possession of it for some time. I have no interest in reading the entire book, because I am only interested in Haldane’s Dilemma (which starts on page 208 with a quote from Gould and concludes on page 236 with a short summary by Mr. ReMine. If you stick to the topic, then I have read all of the sections that pertain to this discussion. Which by the way is almost nothing, as most of the section addresses proposed solutions to the dilemma without first establishing that a dilemma exists.

With respect to solutions for Haldane’s Dilemma (including neutral theory), perhaps you should go back and read the posts I have contributed in this thread. I am not really interested in the proposed solutions until it can be established that a dilemma exists. I have not proposed neutral theory, or any other solution to the dilemma because it has become quite clear that there is no dilemma. There is no reason for me to spend time trying to solve a dilemma that doesn’t exist. Your insistence that Mr. ReMine addresses complaints in his book, that I have never made (e.g., regarding neutral theory) is bizarre, but may be attributable to your not having read all the posts in the thread.

Once again, see Mr. ReMine’s comments from OCW. If that doesn’t clear up the matter for you, I would be happy to elaborate. Actually, I am pretty sure that I have some archived quotes from you stating the same thing when confronted with millions of differences between chimpanzees and bonobos. I can try to dig those up if you like. But I think you are confusing my position again. I am not proposing neutral theory as a solution to Haldane’s Dilemma. Common sense says that a solution isn’t required if the dilemma can’t be shown to exist. If you object to my conclusions because some small fraction of introns may play a part, then see John Paul’s treatment of the issue. He came to the same conclusion using a different approach and different sources.

More red herrings, but I can’t resist this one. Please, everyone, take a look at Fred’s graph. Note the first 2 sentences in the caption: “A possible frequency distribution of the effects on fitness of newly arisen mutation. (The real frequency distribution is unknown).” LOL! What was the point, Fred?

It is going to take more than baseless assertions to refute my arguments. Please find an informed scientist who believes that a majority of the expressed differences between humans and chimps will be found in introns and I will grant you the point. Introns were not considered in my treatment because nobody (I bet including Mr. ReMine) would propose that they take precedence over exons in this debate. If you followed the math closely, you can see that it would require an expressed effect from a tremendous number of introns before the argument is affected. You may support this line of argumentation at any time, but I think you are going to have a difficult time finding references.

You raised a lot of red herrings in your response, and I am sorry that I didn’t touch on each one. I would ask that you review my last few posts so you understand the position I have taken and so you won’t misrepresent it so badly in future responses. You seem to be under the impression that I am proposing solutions to Haldane’s Dilemma, when I am merely demonstrating that no dilemma exists.

 

[Administrator: Robert Rapier evidently posted his response above on another message board as well and so John Paul's response to that came in the same email group that Robert Rapier's post above came. So here is John Paul's response to Rapier's post above]

JOHN PAUL

Robert:
Why didn’t you just use this argument in your first reply?

John Paul:
I thought it was clear that the claims made by Walter ReMine are not my claims and Haldane’s Dilemma is not my argument. Aren’t you the one who posted :

Isn’t it odd that you would then turn around and want me to substantiate a claim I never made?

You were the one that wanted to play number games all the while thinking I was incompetent to play such games. Well I played but I was able to see the fruitless nature of such a thing.

Robert:
You could have said, “I refuse to assume common ancestry as a part of this argument”. Then you wouldn’t have had to address any of the issues.

John Paul:
Being a Creationist it should be obvious that I don’t accept common ancestry so why would I want to assume it? For the record: The only reason I even attempted the number game was because Robert didn’t think I could do it. It had nothing to do with my thinking the argument was valid or not. If I would have said the argument wasn’t valid and didn’t post the math Robert would have taken that for evidence that I could not do it.

Robert:
I can understand that you might want to take this position now, as the substantive issues have been laid to waste.

John Paul:
As a Creationist I have taken that position for years. BTW the substantive issues haven’t even been discussed. One such substantive issue would be how to objectively test the premise that humans & chimps do in fact share a common ancestor. Any time you or any evolutionist would like to address that aspect please join us in the Questions for evolutionists thread.

Robert:
But what you fail to understand is that what Mr. ReMine has done is propose a falsification test for shared ancestry.

John Paul:
Like I said, it wasn’t MY claim. I was under the impression that Walter proposed a test that falsified the alleged evolution of modern humans from some primitive ancestor, not necessarily the one common to chimps & humans.

Robert:
This falsification test requires the assumption of common ancestry in order to present the arguments required to falsify it.

John Paul:
Tell us something Robert- Have you read the Biotic Message?

Robert:
Note that I didn’t say that the identity of the designer would be required. I just said that if a designer can’t be proven to exist, then what you infer as design may be illusory. This approach utilizes the same logic that you use in the paragraph above.

John Paul:
SETI- Searching for designers by looking for design. Science isn’t about proof, Robert. And yes scientists know that anything they propose (ID) could be incorrect, but there isn’t any evidence that would lead an objective person to infer purely natural processes can account for life. Again, the design implies the designer so no need to prove the designer’s existence.

 

ROBERT RAPIER

Because my last reply was long and technical, I wanted to provide a short and compact summary for those not interested in the technical details. I realize that many readers have no interest in reading a long technical treatise. This is a brief summary of the arguments:
</font>

1. There are some 3 billion base pairs in the human genome, but a very small fraction of them are pertinent to Haldane’s Dilemma. In my analysis, I calculated the base pair differences in coding regions. These are the regions of DNA that actually code for proteins.</font>
2. Fred’s point is that I have neglected to consider so called “junk” DNA. He stated that scientists have proven its importance.</font>
3. Whether it is necessary is not the issue. The issue is whether it is relevant to the number of fixed, beneficial mutations, by definition expressed, that separate humans and chimps. If not, then it is not relevant to Haldane’s Dilemma. Since junk DNA has been shown to be under little selective pressure, Fred’s point fails.</font>
4. Fred could have made a similar argument by just assuming that the entire genome of 3 billion base pairs is relevant to the argument. But that misses the point: A very small subset of the genome is relevant, and Fred made an unsupported assertion to try to increase the size of that subset.</font>
5. Fred brought up neutral theory and said that 40 million mutations must actually become fixed in the allotted time. </font>
6. I used Mr. ReMine’s own words to refute Fred and demonstrate that this issue was not relevant to Haldane’s dilemma. It was merely another failed attempt to expand the subset in the argument. </font>
7. I now await Fred’s references to demonstrate that “junk” DNA is under selective pressure. This would imply that it had benefited from beneficial mutations, and would support his argument.</font>

Now, I will briefly address John Paul’s post.

Nobody ever stated that those were your claims. But you chose to defend his argument. In doing so, you are taking up his position. Now you choose to distance yourself from his argument, which is understandable considering that his falsification has been falsified.

I wanted you to play the numbers game for 2 reasons. The first is that I figured you would give it a try and would make some mistakes and then I would nudge you toward the answer. However, you did a very good job with the argument. (The only thing that is absolutely incorrect is the 1.5% of coding DNA; that paper was written before the Human Genome Project published their figure of 1.1%). Which brings me to my 2nd reason. If you did the numbers correctly, I knew that you would see the fundamental weakness in Mr. ReMine’s premise. I could tell you until I was blue in the face, but until you worked the numbers out for yourself you would not have seen the problem. But, this should not be taken as a complete indictment against Creationism. It merely demonstrates that this one specific argument is faulty.

For the same reason that anyone takes this position in these debates. You would take that position in order to attempt to falsify it. I take this position all the time. I might assume a global flood, or that the earth is less than 10,000 years old in order to draw conclusions from this. It doesn’t mean that I believe it. I take this position in order to present a falsification argument. This is just basic science John Paul. You should understand that I know you don’t (and will never) accept common ancestry, no matter what the evidence indicates. You always rationalize the evidence away by saying (without providing a falsification test) “Common Creator”. By your logic, all anyone ever has to do is to say “I reject the underlying assumptions needed to develop the argument”. At that point, the debate truly is over and there is nothing else left to discuss. You say “black”, I say “white”, and neither ever assumes the other position in order to attempt a falsification. Science could not function under this type of system.

Yet it wasn’t relevant in the discussion of Haldane’s Dilemma. Nobody forced you to defend Mr. ReMine; you did that of your own free will.

Think about the logic of your statement. Unless the ancestor he is referring to is very recent, it has to be common to humans and chimps since they diverged an estimated 5-7 million years ago. If you had read his book, you would know what he has to say on that matter.

See above response to Fred. For the record, I have the book in my possession. I have read all sections pertinent to Haldane’s Dilemma, including those made in the appendix. The book was loaned to me before I made my first post in this thread. The person who loaned me the book is a well-known name in these debates (but it is not Dr. Page). What is ironic is that it is clear from your statements that you have not read the book, but you still chose to respond to my argument. Note that until now I have not criticized you once for this, and I do so now only in response to your question.

As one of my undergraduate degrees is in chemistry, I have spent a lot of time doing scientific research, and I am currently in charge of a research lab for one of the largest corporations in the U.S., it is not necessary for you to explain to me what science is about. I have first hand knowledge. Once more you don’t seem to follow the logic. In the argument above, we assumed common ancestry to test a hypothesis. When that hypothesis was shown to support common descent, you took the position that you don’t accept common ancestry; therefore the entire argument is null and void. By the very same logic, I can say to you that I reject a designer; therefore all of your arguments for design are null and void. What you see as design is merely illusory. Is that really so difficult to understand? I am just using your logic to come to this conclusion.

* * * *

second email, same day

ROBERT RAPIER

Fred,

I was doing a little research on Haldane’s Dilemma this evening, and decided to visit your Web site. In the following article, you have made a very serious mathematical/logical error in the article Monkey-Man Hypothesis Thwarted by Mutation Rates which may be found at http://www.evolutionfairytale.com. In the article, in the section on Haldane’s Dilemma you write:

The serious error is that 1667 beneficial mutations is far, far greater than 0.001% difference between human and chimp genomes. In fact, 1667 is 0.001% of the number 166.7 million, so I am not sure where you came up with 0.001%. To make matters worse, you have obviously confused 1667 beneficial mutations with 1667 single nucleotide substitutions, or you would not be comparing 1667 to 166.7 million. As demonstrated in this thread, 1667 beneficial mutations yield far more than 1667 single nucleotide substitutions.

Using Mr. ReMine’s hypothetical allotments, we see that 60 gene duplications alone will give us 180,000 nucleotide differences. He also “allows” for 100 mutations for repositioning genes (inversions, etc.). Once again, this can add a few hundred thousand differences. It is not too hard to see that 1667 beneficial mutations can easily equate to 500,000 nucleotide differences or more! This is over twice the total coding difference calculated for human and common ancestor. This amounts to 1.27% of the 39.25 million base pair difference between human and chimp genomes. Your 0.001% is off by a factor of at least 1270, Fred!

Next, split the difference between humans and chimps to arrive at a 19.62 million total base pair difference from our common ancestor. That gives at least 500,000 nucleotides available (solely from beneficial mutations) out of a total of 19.62 million to account for the differences between humans and common ancestor. This doesn’t even include expressed neutral mutations. Again I ask, where’s the dilemma? Someone, anyone, please show me mathematically where the dilemma is. WHERE’S THE HARD EVIDENCE? Any way you want to slice it Fred, any way you want to work the problem out, it is clear that there is no dilemma. Sequencing data have put this argument to rest.

But a more serious issue, Fred, is that your error was pointed out to you, on several occasions, more than a year ago. (I can supply the relevant archives and jog your memory if you don’t remember). I wonder why it is still in your article. Perhaps you forgot about it. Are you willing to now acknowledge the error and correct it? I understand that contrasting a number like 1667 against 90 million is much more impressive from the Creationist perspective, but it is absolutely incorrect. It will give those who read your article a false impression.

By the way, remember earlier when you said “So, we know Robert’s 1.1% parameter is wrong, which alone invalidates his entire argument”? There was actually nothing at all wrong with my number, but based on your logic I assume we can invalidate your entire article based on your serious mistake identified above?

But let’s cut to the chase and address this issue head on. No games, misdirection, or change of subject. Let’s focus on Haldane’s Dilemma until it is resolved. I challenge you or Mr. ReMine to demonstrate once and for all that he was justified in assuming that 1667 beneficial mutations can’t account for the differences between modern man and a hypothetical ancestor shared with the chimpanzee. Work out the math any way you want, make any assumptions you want, but provide support for your assumptions. I think you will end up with the same answers that John Paul got. (But first please address the error in your article).

[ August 02, 2002, 12:37 PM: Message edited by: Administrator ]

 

FRED WILLIAMS

Robert, this is not even remotely a misrepresentation of what you wrote. If a base pair has functional importance it must be considered. You say no, which is the equivalent of saying “functional genome = exons only” under the context of your argument. Whether or not you specifically stated functional or “expressed” is semantics hairsplitting. You are *assuming* that the only portion of the genome that matters when comparing chimps to humans is the coding region. You have admitted this openly. This is a false assumption, and I provided you with one of many citations to show you why. Here are three more:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12148094&dopt=Abstract

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12138283&dopt=Abstract

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12124994&dopt=Abstract

Robert, you simply cannot spin your way out of this one. You attempted to pack the genome into a tight little area consisting of exons only, and this is unquestionably an erroneous assumption that invalidates your entire argument. Please start over.

So now its primarily responsible? If it’s not completely responsible, then how can you justify, using your own logic, that 1.1% is a valid parameter when you know and just implicitly admitted 1.1% is the bottom limit and the true value must actually be higher? Your own logic refutes your argument.

No, I sought to merely illustrate one possible range of your error. I actually ignored a large portion of the genome that may also be functional (such as scaffolding) and only focused on introns, which alone showed that your 1.1% parameter really could be anywhere between 1.1% and 25%. Is it any surprise that you chose 1.1%? Evolutionists invariably are forced to choose the assumption most favorable to their argument, they have no choice.

No, I am saying that any base pair with functional importance must be considered, as common sense would dictate, not brushed aside as you attempted to do.

You totally misunderstood my point, which I honestly attribute to the deficiencies of internet exchanges and nothing intentional. Read the paragraph in its entirety and then comment; don’t insert your response half-way through it. I am noting how evolutionists (esp. Kimura) worked to lessen Haldane’s dilemma, by getting most of the substitutions with little reproductive cost via a very high neutral mutation rate. My conclusion in the paragraph is what I would like you to comment on: “But there is a problem - as they raise the mutation rate they raise the cost of harmful mutation within the functional area. Robert completely glossed over this very important fact.”

Regarding your citations from Walter, I am well aware of what he has written on this, and agree that there is not much of a speed impediment going downhill, much like dropping a ball in contrast to the work needed to throw it upward. The whole idea of intense selection is anti-evolutionary, and is why Haldane essentially rejected it (Haldane p 521). As you mentioned, I did indeed believe some time ago that Haldane’s Dilemma seemed to also be a problem for YECs (as did Kurt Wise and others), noting though that at least there were tenable, yet unproven, YEC solutions including bottlenecks-subsequent drift, and/or non-random mutation. I was not convinced of the former, but in the last 6 months I am beginning to envision scenarios that could bring about high fixation differences between related species. But the only way, as Walter mentioned, is via *anti-evolutionary* mechanisms, such as radiating a population.

Being “in possession” of book does not mean you read it. You just implicitly admitted you did not read the chapter on the Neutral Theory, which is an integral piece in the Haldane debate. This chapter addressed your current attempt to confine the functional part of the genome (or “expressed”, as you want to call it) into a tiny little box. I don’t have the page number because I loaned the book out, but I’m certain this was addressed in the “Neutral Theory” chapter. If you had read this, you would have perhaps not brazenly claimed your analysis refuted ReMine’s claims. Walter’s chapter on the Neutral Theory is very much tied to the Haldane chapter. Please read this chapter.

Your mentor also used this strawman when I posted the graph. I never said this *is* the frequency distribution, I said the graph clearly shows Futuyma’s depiction of the widespread *belief* that the vast majority of mutations are between harmful and slightly harmful, NOT precisely neutral. Do you agree, or disagree with this? Yes or No. There is a reason I had to add that vertical line to the graph (your mentor claimed to a previous audience that the Y-axis went through the middle of the curve’s apex, not to the right of the apex). I happen to be part of the “widespread belief” crowd who think most mutations are slightly neutral or worse. The only part of the graph I would dispute is the area to the right of the line! (surprised? )

LOL! Robert, it turns out your “demonstration that no dilemma exists” is awfully close to Kimura’s ‘solution to Haldane’s dilemma’. If you want to try to portray it as something other than a “proposed solution”, feel free. It’s silly, if you ask me.

From a previous post, that I couldn’t get to earlier:

It is completely relevant to the discussion. An auxiliary (if you will) of Haldane’s dilemma is the cost of harmful mutations. As the cost of harmful mutations increases, the cost of beneficial substitution increases because there is less reproductive excess available to move a beneficial mutation to fixation. While the cost of mutation that my article addresses need not rely on the validity of Haldane’s model, conversely Haldane’s model does rely on the cost of mutation, and it needs the rate to be low. His model assumes 10% reproductive excess. If we ignore other types of genetic deaths (such as rock falling on head, or being a prude) and only focus on genetic death due to harmful mutation, then you need the harmful mutation rate to be ln(10/2) = 1.6 or less. This is clearly relevant to our discussion, since an increasing mutation rate has a proportionally negative impact on Haldane’s substitution rate.

Finally:

 

ROBERT RAPIER

Fred seems to have misunderstood my argument completely, because he wants to discuss solutions to Haldane’s Dilemma. Before Fred’s next reply, it might be helpful if he reads my earlier posts. Then he might not keep confusing my position. My argument is that if there is no dilemma, then no solution is necessary. Walter ReMine has never attempted to mathematically defend the basis for his claim that 1667 beneficial mutations can’t turn a common ancestor into a man. For the record, Haldane never made this claim. Mr. ReMine, using Haldane’s work, made this claim. Also, as I pointed out, Fred tries to contrast this number to the millions of total substitutions separating humans from chimps. This is completely incorrect, and has been pointed out to him for well over a year.

I will briefly address some of Fred’s comments. As many of them deal with solutions to Haldane’s Dilemma, they are really of no concern to me as I first expect the dilemma to be established as such. In future responses, I respectfully request that Fred stay on topic until we can establish that Mr. ReMine’s fundamental premise is sound.

Not true. It has to be a result of a beneficial mutation if we are to consider it. The word functional continues to give you a problem, Fred. Functional can mean structural. Are you going to tell me that a functional section of the genome, functional in the sense that at least X number of any random nucleotides are needed to separate two sections of a gene, is relevant to Haldane’s Dilemma? You know the dilemma, the one in which only 1667 beneficial substitutions could have accrued between man and common ancestor. Since junk DNA has been shown to be under little (note that I don’t say zero) selective pressure, its contribution would be minimal. The links you provided don’t say anything to contradict that!

Once again, you are incorrect. I am not assuming that the only region that matters is the coding region; I am assuming that this region will predominate. There are plenty of mutations, ranging from very deleterious all the way up through very beneficial that are relevant. A small fraction of these may be found outside coding regions. Of these, a small fraction will consist of beneficial mutations. So the number of differences outside coding regions that impact Haldane’s Dilemma is small and I am justified in ignoring them. You keep asserting that this is not true; please quantify it and I will address the argument.

No need for me to spin, Fred. I am not the one who has never once attempted to support the assertion that 1667 is not enough to account for the differences. My exercise was merely to show that it is certainly within the range of possibility. You may need to go back and look at the math, especially considering how many base pair substitutions that 1667 beneficial mutations will provide. Then you will see why your whole exon argument is moot.

Again incorrect. You are an engineer, correct? If I am doing an engineering calculation, and some of the numbers I know with relative certainty, and other numbers I don’t know with absolute certainty, but I have evidence that they are not enough to significantly impact the bottom line, I am completely justified in doing the calculation with the numbers I have. That is, unless it can be demonstrated that the error in doing so makes a significant impact on the answer. Sure, the answer might have been 1.3% instead of 1.1%. At that point you have to determine whether or not it makes a big difference. You assert, Fred, but you do not quantify your assertion. Nobody disputes that introns may affect the differences between species, but the effect is small. It is not quantifiable. Therefore I performed the calculation using knowns, instead of throwing in small unknowns. If you wish to quantify the impact of introns, be my guest. As I said, I will address the argument at that point.

But the bottom line is that your exon exercise is just a diversion. You are just saying that because we don’t know everything, Robert’s entire argument is invalid. I showed above, in my critique of your article, that even using all the base pair differences between man and common ancestor, it is still not unreasonable to assume that 1667 can account for the differences. Please demonstrate otherwise. I am pleading with you to mathematically support your argument.

Challenge to Fred: Please make any assumptions you like and demonstrate that Mr. ReMine is justified in dismissing 1667 beneficial mutations as being able to account for the differences between common ancestor and modern man. Support your assumptions.

No, I didn’t misunderstand the point at all. My argument is whether or not Mr. ReMine is justified in presuming that 1667 beneficial mutations are not nearly sufficient to account for human evolution, and you launched into neutral theory. But it is completely irrelevant to discuss solutions to a dilemma that has not been shown to exist. That is what you are attempting to do, and until you demonstrate the dilemma, there is really no point in discussing solutions. Heck, all the solutions in the world may be unable to solve the dilemma. That is not the point of my argument. If the dilemma is shown to not really be a dilemma, no solutions are needed.

Then what was the point of your stating “This means that (using Robert ’s 1.24% difference between chimps/man) ~40 million base pairs must become fixed within the allotted time, not 432K”? You are trying to throw neutral mutations into the mix when we are talking about fixed, beneficial mutations that relate to Haldane’s Dilemma. As the 40 million do not refer to fixed, beneficial mutations, I merely used Mr. ReMine’s words to show that you were flat wrong to confuse the issue. He has told others in the past that they were flat wrong to confuse the issues. You are merely trying to confuse the reader into thinking that 40 million is a number relevant to establishing whether there is a dilemma, when it clearly is not.

Once again, Fred, you stuck your foot in your mouth. I can help you out with the page numbers; pp. 237-253, as I have read the Neutral Theory chapter. As I said, I read the sections that dealt with Haldane’s dilemma, including “The Neutral Theory of Evolution”. I just refuse to discuss the solutions to an alleged problem that has yet to be established as a real problem. (I guess you still don’t think you owe me an apology for stating “it is very clear to me Robert has not even seen Remine's book…”). That was flat out wrong, and not only do you not offer to retract it, you compound your errors.

Also, you again fail to understand my argument. My brazen claim, unrefuted to this day, is that Walter ReMine has no scientific justification for claiming that 1667 beneficial mutations can’t account for human evolution from a common ancestor. If you choose to refute anything in this post, refute that!

Also, I am not trying to “solve” the dilemma by confining the genome to a tiny section. If you have evidence to the contrary, that beneficial substitutions arise from outside coding regions, now might be a good time to present it.

Do you think you can dispense with the snide remarks and just address the issues? Another word about terminology, Fred. A strawman would imply that I misrepresented your position. Since you attempted to use the graph to try and support your contention that most mutations are at least slightly harmful, it was quite proper to point out the caption: A possible frequency distribution of the effects on fitness of newly arisen mutation. (The real frequency distribution is unknown). That just demolishes the point you were trying to make.

Now why in the world would I be surprised that you would accept as absolute truth the opinion of a scientist when it appears to support your belief, and then reject the opinion of that same scientist as garbage when it goes against your belief? You have been doing this for years, so no, I am not surprised. This is the reason Creationism persists; because of this cafeteria-style approach to science.

Once more, Fred, you demonstrate that you do not understand my argument. I am not offering up a solution to Haldane’s Dilemma. For the umpteenth time, my position is that Mr. ReMine has failed to establish that the dilemma exists as he applied it to human ancestry. I say that no dilemma exists because there are relatively few beneficial differences that separate us from the common ancestor. Recent sequencing data back me up. Or do you think that the closer than expected genetic similarity between humans and chimps supports Mr. Remine’s argument?

Please demonstrate how your quote is relevant to the point John Paul was making. You were specifically addressing the high deleterious mutation rate when you made that quote. That is not Haldane’s Dilemma, despite your attempt to link them. John Paul used your quote as if it somehow supported his argument. It was clearly irrelevant. If you now want to take the stance that your quote shows that Haldane was wrong, that the substitution rate was lower, and the allowed mutations are less than 1667, well that’s a brand new argument. But enough diversions for now, OK? Try to stick to the point.

My pleasure. Sequencing data have shown that humans and chimps are much more closely related than was previously believed. This means it is much more likely that 1667 beneficial mutations (remember, that’s 500,000 or more nucleotide substitutions) can explain human evolution from a common ancestor. If there had been a large genetic difference, then there would have been a stronger case that a dilemma was indeed present. Sequencing data have merely demonstrated that what was believed to be a dilemma is not. Mr. ReMine, as well as Fred Williams, clearly believed that the differences between humans and chimps would be much greater than they have turned out to be. They were both wrong.

 

FRED WILLIAMS

(1667*2)/3 bil = .0001%. I doubled the 1667 as a favorable assumption for evolution by assuming the maximum substitution rate along each clade. My only “error” was I left out a zero, which was less favorable to my argument, not the other way around as you claimed. Such a “serious” error indeed!

I have not confused this, I simply used the same assumptions as the Nature study (Keightley, et al) that was the emphasis of my article. You are engaging in a double-standard.

Robert, do you know what a “hypothetical” is? Walter used it to illustrate a point, and you twisted it into reality. I am not aware of even one known fixed duplicated gene in either chimp or man that is not in the other. It is common practice to assume point mutations because they are by far the most common mutation. Are you prepared to challenge Keightley et al that their Nature study is flawed because they only considered point mutations?

You know you’ve won an argument when your opponent shifts to “alterative” tactics. Robert has made an unsubstantiated accusation and unless he can “supply the relevant archives and jog my memory” I deserve a retraction. The only thing “pointed out” to me at that time was the new data regarding gene count that came out after I wrote the article. At some time I do plan on writing a “2nd edition” of my article to use current data. But the gene count (nor Robert’s specific complaint, see below) does not detract from the point of my article one iota, and in fact recent data (in part thanks to Scott Page, unwitting as it was) shows the problem is actually worse for evolution. It’s to your advantage I *don’t* update the article!

Though I again emphasize I was using the same assumptions as evolutionists use in their models (and the same assumption of Walkter/Keightley in the study I cited), I grant your point that it could be a bit misleading without some sort of qualifier. I will expand on this when I write another edition of the article. However, I deny that this complaint was “pointed out to me before”. It’s actually quite trivial, and does not impact the core argument of my article a single iota. I again find it sheer desperation on your part to shift attention to something not related to the argument I refuted in this thread (your false assumption that only exons are functionally important).

[Note to Robert: No one here wants to be bored with “the relevant archives to jog my memory”. If you can prove you pointed this out to me before, I will state so here. You can email me at [email protected]. If you can’t substantiate your claim, I expect a simple retraction. Deal?]

Now let’s see if you are willing to alleviate your double-standard. The Walker/Keightley U=1.6 number was based on point mutations only and only within exons. Contrast this to Crow’s adjusted U=3 in his follow-up letter to the editor, where he accounted for other mutations. Crow’s adjustment has far greater implications to the problem than the side-comment in my article that had nothing to do with my core argument. Are you prepared to write Walker/Keightley and ask them to include in their next abstract a more representative number that accounts for both non-exon and non-point mutations?

Perhaps you would like to attempt use real data and show 1667 is enough. We already know you’ve tried this by twisting a hypothetical into reality. Use data Robert, not hypotheticals. Remine used a hypothetical merely to illustrate a point, not as “evidence” for something.

As I have also pointed out to Robert many times before, this is not just a problem for the evolution of man. It is a problem for all species, especially vertebrates with a low zygote count and long reproductive cycles. Can Robert demonstrate that so few mutations can account the evolution of all animals from some distant ancestor? The 1667 number is but one of many to illustrate to anyone with common sense just how untenable evolution is, given that only one substitution on average can occur every 300 generations in any clade. Hippos & whales? Elephants and who knows what? (a brief search of the internet and I couldn’t even find an alleged hypothetical ancestor of the elephants other than Mammoths). The bottom line is, you need to either hypothesize that the vast majority of the information was already in the genome before this vast amount of evolution occurred, or you guys need to make the earth older by orders of magnitude, and fast! Come on, the earth gets older by millions of years every decade or so, aren’t you guys due for another adjustment?

To conclude, Robert’s post was largely a red-herring intended to detract from his clearly false illusion that exons are the only functionally significant part of the genome. Does Robert still believe this, or is he prepared to acknowledge his error (which was the core of his argument) and start over?

Robert’s next post…

LOL! But you unwittingly DID NOT ignore them! Why did you apply gene duplications to your analysis?!!! Do you realize that this requires a) an expansion of the coding region, and 2) inclusion of inter-dispersed introns within your 3k bp gene? (over half!) But Robert’s magic wand turned ALL 3000 base pairs of the gene, including all the introns, into base pair differences! But wait, he says he’s “justified in ignoring them [introns]”. Huh? Apparently Robert is “justified in ignorning them” only when it serves his purpose!

I have provided evidence that your excluding all but exons likely does significantly impact the bottom line. You have provided no evidence that it does not. Yes, I am an engineer. I would reject your analysis and tell you to start over, and try to justify your number with evidence and then make a reasonable estimate based on all available data. You and I both know your estimate is absolute bottom, which makes it a ridiculous number to use. You did not qualify this fact, which by your own standards makes it misleading. Then, to make matters worse, you went and included introns when it served your purpose by expanding 60 duplicate genes into 180k bp differences, yet more than half of these would have been introns - which you claim we should ignore!

Robert, please get Haldane’s paper, it is plainly obvious you don’t have it. No current sequence data I know of overturns Haldane’s substitution rate of 1 per 300 generations. The 1667 number merely uses Haldane’s rate to illustrate what can accumulate in the human/chimp lineage. If you want to believe 1667 is enough, go right ahead. But this does nothing to refute or impact Haldane’s substitution rate of 1 beneficial mutation per 300 generations. That is what I asked you. I did not ask you if you think 1667 is enough to account for human evolution from a poo-throwin’ ancestor. What I did ask, and will again ask, how does recent sequence data impact Haldane’s mathematical model? How are his numbers affected? What parameters or assumptions are impacted? Please get his paper before you respond. You can find it at any major university library.

 

ROBERT RAPIER

First, I want to repeat the challenge that Fred has ignored: Challenge to Fred: Please make any assumptions you like and demonstrate that Mr. ReMine is justified in dismissing 1667 beneficial mutations as being able to account for the differences between common ancestor and modern man. Support your assumptions.

If you don’t read anything else, ask yourself why Fred will not take this challenge if he is so sure that he is right. Is it maybe because he can’t support the assertion? Yes, it is.

In an effort to get to the bottom of this issue, I am going to bite my tongue (a little) in my response. I have gotten feedback that people are getting confused. Fred has used a shotgun approach to throw a lot of irrelevant minutiae into the debate. If I substantively address each point he made, my reply will be over 10 pages long. But since Fred is unwilling to concede a point even when he is shown to be 100% wrong (e.g., false accusations regarding Mr. ReMine’s book), I believe there is zero chance that he will concede on other points where he is clearly in error. Therefore, the point and counterpoint goes on forever with no end in sight. But I want to get to the bottom of the matter. This issue is really not that complicated. Fred has tried to make it complicated. All you really need to know is the following:

Is Walter ReMine justified in stating that 1667 beneficial mutations can’t account for the differences between an unidentified common ancestor and man? Is there any scientific evidence to support him? Did he put the cart before the horse in making this assumption? Mr. ReMine has asserted that it is absurd to think that 1667 is enough, and as I pointed out, Fred has echoed this sentiment. To this day, including in this thread, Fred has not tried to support this argument at all. Not once! His argument always boils down to “It just can’t be”. Here are a few quotes from each to make clear their feelings on the matter:

And a couple where Mr. ReMine is discussing his book (Note that I took these from Mr. ReMine’s website instead of directly from his book, as I can’t just cut and paste from the book. This also makes it easier for the reader to confirm the quotes. Mr. Remine’s exact wording in the book is only slightly different):

Note that the last reference refers to the number of allowed expressed neutral mutations. Mr. ReMine seems to be guilty of the same thing Fred did when he used the number of mutations as a percentage of the total number of base pairs. This is analogous to claiming that 1 bunch of bananas is equivalent to 1% of 100 bananas. This is obviously absurd, as we are comparing a bunch, in which the quantity of individuals has not been unidentified, to an known quantity. Yet that is exactly what Fred has done, and it appears that Mr. ReMine did the same in his book (note Mr. ReMine’s reference to 1,667 beneficial nucleotides).
My theory is that this is precisely why this issue has persisted. I believe that when Mr. ReMine wrote his book, he made this comparison and came to the conclusion that there was a vast gulf between the number of allowed beneficial substitutions, which he believed to be single nucleotide substitutions, and the total number estimated to separate chimps and humans. After publication of his book, it appears that someone pointed out to him that 1667 refers to beneficial mutations and not single nucleotide substitutions. Mutations can include inversions, insertions, deletions, gene duplications, etc. Suddenly 1667 beneficial mutations got a LOT bigger in terms of nucleotide substitutions, but this fact has been “confused, garbled, and brushed aside”. In fact, Fred continues to gloss over it in his reply.
Based on their quotes, both have made their feelings plain on the matter in the past. But what is interesting to note is that neither then nor now has Fred attempted to defend this assertion. You would think if 1667 “is not in the ballpark”, Fred would have no trouble defending the assertion.

Now, to address a few gems from Fred’s post:

First of all, even you admit that you were off by a factor of 10. But you quickly gloss over your careless error like it’s no big deal. On the other hand, you don’t like my assumption (which has evidence to back it up) so you call it a fundamental error. But you did make a fundamental error, and it is more serious. As I pointed out, what you are doing is analogous to claiming that 1 bunch of bananas is equivalent to 1% of 100 bananas.

LOL! So your error is Dr. Keightley’s fault? In the Keightly article, they sampled 41,471 DNA bases from coding regions. In my analysis, I simply used the same type of assumptions that they did in their study; that coding regions would be where the significant differences could be found. Dr. Crow says that the mutation rate may be somewhat higher do to some deleterious mutations in coding regions, but he based his estimate of 3 on his assumption (pre-Human Genome Project) that there would be far in excess of 60,000 genes.

But the kicker is that Fred is mixing apples and bananas. Haldane’s Dilemma is not addressed in Keightley’s paper. Fred mixes the two to try and give support for his arguments. Nobody, except for Creationists, ever claimed that 1667 beneficial mutations couldn’t account for a human evolution. Haldane never claimed it, Keightley doesn’t discuss it, and it is not being discussed in the literature.

Once again you misrepresent me. I didn’t say Mr. ReMine’s analysis is exact. Nobody knows what the real breakdown of beneficial mutations between humans and chimps is, which is precisely why neither you nor Mr. ReMine even have an argument. I merely used Mr. ReMine’s hypothetical to show just how unrealistic equating 1667 beneficial mutations to 1667 single nucleotide substitutions is. Heck, ReMine assumed that 1500 out of the 1667 (90%) were point mutations. Where’s the justification for that assumption?

See above. Are you prepared to acknowledge that Dr. Crow’s higher estimate of the mutation rate is based on the assumption that the human gene count is well in excess of 60,000? But once again you imply that Keightley is addressing Haldane’s Dilemma. Apples and bananas, Fred.

Are you acknowledging a mistake?

So am I to assume then that I have won because you have shifted to this shotgun approach?

Fred, you should know me well enough to know that I would never make such an accusation if I couldn’t back it up. See below.

I guess you believe that if you repeat something enough times, people will believe it (only exons are functionally important). I addressed your mistake in your Haldane’s Dilemma piece. As pointed out above, I believe this type of mistake is exactly why this argument persists. How is that irrelevant? I also wanted to point out what a true fundamental error looked like, instead of the strawman version of a fundamental error that you presented. Finally, I wanted to point out your flawed logic in assuming that if any part of the argument is in error, the entire argument fails. If we apply this criterion, your entire article fails. You acknowledged an order of magnitude error in your article, so how can we trust any of the numbers in the article?

No deal.. I prefer to put it out there and let the reader decide whether or not you were told about this before. Deal?

But it is the only problem relevant to this debate, whether or not 1667 beneficial mutations can account for human evolution. ReMine made this argument and applied it to human evolution. If you apply it to other species, 1667 is no longer your number. So focus on this issue please.

Evidence? You provided some links saying that certain changes outside exons might have a deleterious effect. I don’t dispute this, and wouldn’t have before this debate began. But since ReMine’s argument concerns beneficial mutations, you have provided not one shred of evidence to support your argument. But again, see the Keightley article.

This tactic is called moving the goalposts. That is not what this debate is about. It is not necessary for me to demonstrate this, as I am not the one who made claims that 1667 is not nearly enough. I said I don’t know, but have tried to put some numbers to the argument to show that 1667 is certainly in the ballpark. You have never once tried to justify your argument that 1667 can’t account for the difference. You just assert it over and over. How about putting up some evidence?

I never said or implied that exons are the only functionally significant part of the genome. Remember, that was your mistake that Dr. Page previously corrected. What I said was that with respect to this debate (whether or not 1667 beneficial mutations can account for human evolution) it is the one that matters. Apparently Keightley agrees with me. I am still waiting for you to present evidence that beneficial mutations are found outside coding regions.

First of all, the evidence is in that introns are under little selective pressure. I am sure you are aware of this. This justifies my assumption that they would make little to no contribution to the problem. Keightley’s approach also validates my approach, unless you know something he doesn’t. But, you make another mistake in assuming that my analysis was a minimum. I calculated the total number of coding base pairs between species. In order for my analysis to be rock bottom, you are saying that each change in a coding region must have the potential to make some contribution toward a beneficial mutation. Do you think that? Have you ever heard of synonymous substitutions? Expressed neutral mutations? Deleterious mutations? That alone invalidates your point that my analysis was rock bottom. I could have gone on to say, of the 216,000 base pairs in coding regions, only a fraction have the potential to be involved in a beneficial mutation. (According to your logic, I have just invalidated your entire argument).

You are very confused here Fred. The 60 duplicate genes would contribute toward the total difference between species. We are no longer considering just coding regions in this case. It doesn’t matter what the function or makeup of the gene is in that case. You compared 1667 to some 90 million total base pair differences between species, and I showed you just how far off you were by showing you how many base pairs 60 gene duplicates alone would generate. This is in no way relevant to my calculation of how many coding base pairs differ between the two species, and you show your confusion by mixing the issues.

The issue is not Haldane, and never has been. For the purpose of this argument, I accept that Haldane was correct. The issue is ReMine’s assertions regarding human evolution. Haldane’s analysis could be spot on, and it doesn’t affect the matter of whether ReMine’s fundamental premise is sound.

Fred, I don’t know if 1667 is enough. But if you want to play scientist, you are going to have to offer up some evidence for your claim other than your say so. This debate has been running between us for probably 2 years or more, and you always avoid the question: What is the evidence that 1667 beneficial mutations can’t account for human evolution? You can end this debate by putting your cards on the table. I think it is becoming clear to everyone that you are holding no cards, so you have no choice but to bluff and misdirect.

In an upcoming post I will provide the proof that the error in your article was pointed out to you over a year ago. I did not want to add it here and make this post any longer. This will likely be my last lengthy post, unless Fred makes an attempt to justify his assertion.

 

ROBERT RAPIER

I want to tie up a couple of loose ends from my last post. First, Fred made another error above that I almost overlooked. In the correction of his error above, Fred said:

Why in the world have you divided by 3 billion? In your article, you write that 1667 is “only a 0.001% difference between human and chimp genomes”. The difference between human and chimp genomes is not 3 billion, so your correction is still wrong. I don’t understand why you would throw 3 billion into the mix, since about 99% of the genomes are identical. Perhaps you can clear that up. If you had written (1667*2)/40 million or so, then you reduce your errors to a single error. Now the single error is equating 1667 beneficial mutations to 1667 single nucleotide substitutions.

Second, Fred asked about elephant evolution. There are lots of fossils from elephant precursors available. Just go to Google and type in “elephant evolution”. You will find lots of good information. The Houston Zoo recently had an exhibit on elephant evolution, and they displayed a number of the fossils, as well as life-sized replicas of mammoths. I think I enjoyed the exhibit as much as my kids did.

Next, I pulled up more information regarding Dr. Crow’s adjusted estimate of the mutation rate that Fred touts above. What Dr. Crow based that on was an assumption that the total number of genes would be in excess of 60,000. He wrote his letter before the results of the Human Genome Project were released, so his estimate of the mutation rate would certainly be reduced by the new estimates of gene numbers. He also mentions that some regions outside coding regions are expected to be subject to selection, which is the point that Fred has been harping on. My point is that the overall contribution will be small, based on graphs showing a much higher rate of evolution in noncoding regions. Also note Dr. Crow’s statement from a 1995 abstract:

[/quote]James Crow: The mutation rate is an order of magnitude higher in males than females, due presumably to the greater number of cell divisions in the male germ line, and increases more than linearly with paternal age. It is likely that a large fraction of these mutations are in unimportant 'junk' DNA, but if even 2% of the mutations are selected, this means two new deleterious mutations per generation.[/quote]

Source: Crow, J. F. 1995. Spontaneous mutation as a risk factor. Exp Clin Immunogenet 12:121-8

But the entire exercise is a diversion, because even if I grant the most optimistic scenario Fred can imagine, it still doesn’t help his argument a bit. If I assume that every single coding difference is subject to Haldane’s Dilemma (it’s not), and then double the number under consideration (which implies that non-coding regions have just as significant an impact as coding regions), the probabilities look like this: We now have 432,000 base pairs to consider. Of these, Mr. ReMine says we can have 1667 beneficial mutations and 25,000 expressed neutral mutations. Even if 90% of the 1667 beneficial mutations consist of point mutations, we can easily get 500,000 base pair changes before we even begin to consider the neutral mutations. That’s why Fred’s point fails. It doesn’t matter if I look at large sections of non-coding DNA. I can consider every single base pair difference between human and common ancestor, and Fred’s argument fails. That is why I have said that it is just a diversion. Maybe Fred didn’t understand the point I was making; maybe I wasn’t clear. Hopefully, it will now be clear.

* * *

[Administrator: Robert Rapier had two responses in one email. The following is the second response.]

ROBERT RAPIER

Fred states:

I want to be clear that I would never make an unsubstantiated accusation. It is very important for me to demonstrate that this is not the case. I present this to demonstrate just how unwilling Fred is to acknowledge his errors. (It is also highly relevant to our discussion). In this thread alone when dealing with his errors, he has blamed the communication medium, other people, he has glossed over them, or he has merely ignored them. At the same time, he seized on an assumption in my argument and tried to play it up like it was a fundamental error. (Wasn’t he complaining about double standards?) The fact is that even without the assumption, the core issue is unaffected. I can do the same exercise and consider not just every coding difference between the species, but every difference. This analysis still shows that the ReMine/Williams assumption that 1667 is not enough is not supported.

Below is just one of the relevant exchanges. Note that the exchange is about Mr. ReMine’s treatment of Haldane’s Dilemma. I have kept a large collection of archives related to Haldane’s Dilemma because I find the problem very interesting. As you can see, Fred’s error was clearly pointed out to him in the exchange. I also have archives where the error was pointed out to Fred by others (including myself), but they are longer and interspersed with more irrelevant details. If requested, I can send the archived Web page(s) to a 3rd party of his choosing for verification. I can also supply additional quotes, but I think the following will establish my point.

This exchange occurred over the course of several days in April of 2001 on the old OCW board. Fred was debating several people, including a poster known as “Sumac”, who is still actively debating today. Sumac is addressing the portion of Fred’s article that I posted above and declared it to be in error. Pay particular attention to the portions in bold. Here is the relevant exchange:

Sumac follow-up comments:

Another exchange:

Sumac follow-up comments:

The emphasis in bold is mine. While Fred continued to address arguments in this thread, he did not answer Sumac’s follow-up. (Except he did later acknowledge that “1000 trillion years” is an exaggeration). As I said, I have other archives related to this matter, but this should suffice.

I have nothing else further to say with respect to Fred’s error, unless Fred requests that I address it in more detail. In my next reply, I will attempt to summarize my arguments.

 

FRED WILLIAMS

[After mentioning that it was probably time to "wrap this up", Williams continues:] Regardless of what one believes regarding Haldane’s Dilemma, my reason for popping in here was to correct several errors and unsubstantiated claims Robert made involving an analysis where he attempted to justify that 1667 beneficial mutations may be enough to account for human evolution over the last 10 million years. These errors led him to prematurely declare the “dilemma” to be non-existent. I doubt there is an objective person who would not be able to see that Robert’s invalid assumptions and obvious misunderstanding of Haldane’s Dilemma clearly rendered his argument moot. Here is a quick summary of these errors:

1) Failed to recognize that “Haldane’s Dilemma” is 1 substitution on average over an entire population per 300 generations. The 1667 number merely illustrates what this rate means to the human clade. It puts the 300 rate in perspective. Even if Robert had made a case that 1667 is a reasonable number to account for human evolution, he would still be mistaken to claim that this rendered Haldane’s 1 per 300 generation number moot. In Robert’s latest posts, he failed to acknowledge this error. Even if he chooses not to admit this error publicly, I hope that he will stop claiming that “1667 may be enough” renders Haldane’s model moot and removes the dilemma. This is a false statement, and shows a confusion of the issue. Even if it were established that man and chimps are related, this would not impact Haldane’s number one iota.

2) In his analysis that attempts to show 1667 may be enough, he assumed “expressed differences” lie solely in the exon areas of the genome. He completely dismisses the remaining 99% of the genome. I provided hard evidence showing Robert’s assumption is highly questionable. Robert provided no evidence to defend his claim, other than his opinion that only “a small fraction” of mutations outside the 1.1% exon range would be beneficial.

3) Considers 1667 as bunches, and extrapolates this to as many as 500,000 bp differences! This particular error now seems to be Robert’s focal point. This magic wand of his is quite amazing! I will address this in more detail below.

4) (there were other minor errors that were not as crucial because they were not focal to Robert’s argument, such as his unsubstantiated claim that the “vast majority of mutations are neutral”).

Now for some quick elaboration on error #1, then I’ll address some of Robert’s recent comments, especially those related to error #3.

I have provided evidence that we know that some unknown percentage of introns (which represent 25% of the genome) plays a functionally significant role, which means they too likely impact “expressed differences”. I have not even considered the large portion of the genome used for flanking and scaffolding. Here is just one citation showing the functional significance of flanking:

http://www.sciencedaily.com/releases/2002/04/020422072647.htm

The fact that mutations to introns or flanking regions impact health demonstrates that they are functionally significant. How did such functionally important sections of DNA arise? It would be absurd to claim they arose by random chance alone, yet this is precisely what Robert is arguing! (unwittingly?). Robert writes “I am still waiting for you to present evidence that beneficial mutations are found outside coding regions.” Question for Robert: Accept for a moment that the intron examples I cited indeed have functional significance. Did they arise under positive selection, or by pure random chance?

I suspect even Robert will now admit that for evolution to be true, positive selection got them there.But I bet he will still stick to his claim that there is only a “tiny fraction” of them, despite evidence to the contrary (he later confuses the issue by saying they are “under little selective pressure now”; those that are functionally important would obviously be under negative selective pressure upon mutation, as my citations showed.)

(I’ll remind the reader that this is a pseudo-red herring on Robert’s part, as it detracts from our debate regarding the errors I claim Robert made while trying to justify 1667 as enough.)

Robert makes this challenge because he was unable to do the opposite, to demonstrate that 1667 is a reasonable number to account for human evolution. Robert claims that he has asked me the above challenge over and over again for two years and was never given an answer. A minor note is that it is only in the last year that I recall Robert capitulating to this position that is shared by Robert Williams and Scott Page (a position that is not supported in any scientific journal, I might add). Regardless, I can’t count the times I have answered this, so here I go again.

I cannot conclusively prove that 1667 isn’t enough because there is not enough sequence information available for both chimps & humans (even if there was, it would still not be provable because we cannot obtain a sequence from the alleged 10-million-year-ago ancestor). But common sense alone suggests that 1667 beneficial changes is way too low given that there are at least 30 million bp differences separating us from chimps (more on this below). Yes, many of these may be neutral differences, but only 1667 beneficial? I don’t think so. I think it’s a pipe-dream to believe otherwise, but I cannot prove it and never claimed I could. Regardless, the onus is on the evolutionist to demonstrate 1667 is a viable number. To claim 1667 may be enough is a complete capitulation of the issue. Does such a claim appear anywhere in the evolutionist’ science journals? I recommend Robert (or someone qualified) take such a position to the evolutionist journals and allow an open discussion on it.

Is contrasting 1667 to 30 million bp differences (ranging from deleterious to beneficial) between human and chimp a valid comparison? I say yes, despite Robert’s protests otherwise. It forces the evolutionists to postulate that the vast majority of these mutations are neutral (indeed this was Kimura’s approach).

When I acknowledged to Robert that such a comparison may be a bit misleading without me adding a qualifier, it was not an admission that 1667 represents “bunches” instead of base pairs. My intent in the future is to add a qualifier (footnote) that Haldane’s model deals with beneficial substituted alleles, and that it is possible, though highly unlikely, that a new alelle may represent more than one base pair change. It is incredibly trivial to my core argument in the article, but I nevertheless will add it in a subsequent article.

Now to the heart of Robert’s protest. Robert believes it is highly likely the 1667 number represents “bunches”, and thus it’s not fair and misleading to make a comparison of 1667 to 30 million. Specifically, Robert wrote that 1667 new beneficial alleles could easily represent 500,000 bp substitutions!

This is merely Robert’s opinion. Robert again has provided absolutely NO evidence to support this claim, other than to twist a hypothetical Mr Remine wrote to illustrate a point. Let’s explore this further. Robert arrives at his estimate primarily via duplicated genes. As I pointed out to Robert in a previous post, there is are many problems with his argument:
1) There is no concrete evidence of a duplicated gene mutation that has ever improved an the evolved type over the wild-type.
2) There is no evidence of even a single duplicated gene that exists in humans that does not exist in chimps. Robert arrives at his number by assuming 60 of these! How convenient! Moreover, even if a duplicated gene is found in humans that does not exist in chimps, Robert would need to make a reasonable case that the gene is a “beneficial” substitution and not a harmful or neutral mistake.

There are more reasons to reject non-point mutations as playing much of a role in beneficial substitutions. Frame-shift mutations caused by inserts or deletions are almost always harmful. Transposons give all the appearances of non-randomness and thus do not offer a compelling example of a random beneficial “mutation”. Inversions are also often harmful (BTW, Hemophilia A is caused by an intron inversion).

Another thing for the reader to consider. If Robert were correct that it is reasonable to make such an incredible extrapolation, why have no other noted evolutionists since Haldane (Kimura, Crow, Maynard Smith, GC Williams, etc) latched on to this argument?. There is a good reason evolutionist scientists have not come up with this particular magic wand. It’s an argument with absolutely no merit and will not see the light of day other than from laymen on internet discussion boards.

I could not help but respond to this. I only asked this *after* YOU MOVED THE GOALPOSTS! It is YOU who issued the red-herring, goal-post moving challenge to show that 1667 isn’t enough!!!

Yes, you did and continue to imply this by only considering exons in your analysis. And this is not the mistake I made several years ago. On several occasions I wrote functional where I should have written genic. I never claimed that exons where the only functionally significant part of the genome.

Not so. Hard data, actual, direct sequence comparisons, currently provide solid evidence that chimps and humans do not share a common ancestor. The hard data is showing that there are far too many bp differences to account for a shared common ancestor. It has little to do with Haldane’s 1 in 300 substitution rate. We don’t even get to the point to consider this rate, it doesn’t even have a chance to get out of the gate. It has *everything* to do with the cost of harmful mutations (one of several auxiliaries within Haldane’s model). Studies that do actual sequence comparisons continue to yield a mutation rates that are far too high for human/simian ancestry to be true. This is the core argument of my article. Your attempts to hairsplit and to find trivial, unrelated typos and errors in the article do absolutely nothing to refute the hard data. Let me also note that since Crow’s number that assumed a gene count of 60k, several studies since the more recent estimate of 30k moved the rate even higher. See article for details.

[A second email added the following.]

The following post answers several charges Robert has made. By and large I think the following is a waste of time for the reader as it has nothing to do with our current debate, though I do think in the very least it provides a strong and clear signal that the debater making the allegations can no longer effectively defend their position being debated.

Yes, I stand corrected. After thinking about this some more it finally occurred to me how I arrived at .001%. When I first wrote the article, there was a report (I think from Celera) that produced a genome size of 4bil. I then took 3% of this (120 mil), then took 1667/120 mil) = .001%. When it became clear that 4 bil was an overestimate, I changed the article but forgot to change the % number. The correct number should be .002 to .005% (30 – 90 million).

I will again note that this is an incredibly trivial error, no worse than Robert’s trivial errors in this thread. I could remove the entire paragraph on Haldane’s Dilemma from my article and it would not impact my core argument one iota. If Robert’s only recourse is to nit-pick trivial errors in the article, it’s a solid commentary that he cannot argue against my article’s key claims, particularly that the assumption of chimp/man ancestry must be flawed because sequence comparisons are yielding mutation rates that are unrealistically too high.

Next, Robert protests that I haven’t apologized after being shown with “100%” certainty that he read the appropriate parts of Remine’s book. I would like to ask Robert how he expects me to think otherwise once we examine what transpired:

1) Robert argues for a small percentage of the genome that is functionally significant (his 1.1% exon number).
2) I mention that Remine dealt with this in his book, and claim Robert should have known this if he had read the book.
3) Robert claims to have read the relevant portion of the book: He writes: “I have no interest in reading the entire book, because I am only interested in Haldane’s Dilemma (which starts on page 208 with a quote from Gould and concludes on page 236 with a short summary by Mr. ReMine.
4) I then point out to Robert that the item in question was dealt with in the following chapter on the Neutral theory. I mention that I didn’t have a page number because my copy was loaned out.
5) Robert then responds: “Once again, Fred, you stuck your foot in your mouth. I can help you out with the page numbers; pp. 237-253, as I have read the Neutral Theory chapter. As I said, I read the sections that dealt with Haldane’s dilemma, including “The Neutral Theory of Evolution”.

So there you have it. I would hope that Robert could see why I am completely justified in being skeptical that he read the Neutral Theory chapter. It was only after I pointed out to him *where* Remine had dealt with his claim did these new page numbers pop up that suddenly now include the Neutral Theory chapter! My other question is, why didn’t Robert acknowledge that Remine dealt with it in his book during the time he was making the argument? Even if Robert disagreed with Remine’s handling of the argument, I would have expected him to mention that Remine dealt with it. That is why I originally became skeptical Robert read the book, then later became even more skeptical after Robert came up with the additional page numbers after I mentioned where it was handled. I grant that Robert may have read the appropriate chapters and simply forgot Remine handled it, or perhaps he knew Remine handled it but did not feel it was worth mentioning. I can accept either of these. Hopefully Robert can now see, based on the sequence of events, why I was justified in my skepticism.

Now to Robert’s claim that the “serious error” in my article was pointed out to me several times in the past. I recall quite well my exchange with Sumac. Now I know why Robert refused to email me this. His claim remains completely unsubstantiated and I expect a retraction. I would like to ask Robert where, in that entire sequence of posts that he copied here (I’m quite flattered you save my posts), that mutations within the 1667 number may include multiple bp substitutions (or “bunches” as you call them), such as duplicate genes, inversions, etc. THAT WAS THE CONTEXT OF YOUR CLAIM!!! Go back and read it (August 02, 2002 12:28 PM). This is what I thought you were referring to, and what I agreed to add a footnote for elaboration. DO YOU DENY THAT THE 1667 != BP SUBSTIUTION WAS THE CONTEXT OF YOUR CLAIM?

[ August 09, 2002, 08:52 PM: Message edited by: Administrator ]

 

From the ADMINISTRATORS:

This thread has turned into a personal fight between two people. Therefore each will be given one more post to summarize his position and then the thread will be locked and archived.

 

WALTER ReMINE

The issues in the present thread are simple. Yet the to-and-fro between other participants here has become unreadable to outsiders. Such highly entangled, unreadable discussions occur far too often on the Internet. (Where one side stands to gain from entangling, diluting, garbling, and generally making useless, the communication of the opposing side.) The administrator here is wisely calling an end to it. I hope I may interject some brief closing comments, for benefit of future readers.

In this thread, Robert Rapier happens to casually misquote me on several occasions. He uses quotes for purposes plainly not allowed by the original context. (His mis-use of “60 gene duplications” is an example.) Also, conversely, he allots to me things I did not actually say. Therefore, I urge readers to use caution. **

Robert Rapier’s suggestion – that “most biologists never considered it [i.e. the 1667 figure] to be a problem” (July 26, 2002) – is a bluff, a grotesque distortion of history, and unsupported anywhere in ink.

Comparisons between modern chimps and modern humans may be useful for tutorial purposes (and a few creationists have done so) to build perspective and interest in Haldane’s Dilemma, but such comparisons have never been part of my argument. Evolutionists pretend to rebut my argument, when they are merely misrepresenting it. Let me say again. If you focus on comparing modern chimps and modern humans, then you are misrepresenting my argument. My argument is about the limited number of beneficial substitutions – (nominally 1667 beneficial nucleotides, according to Haldane’s figures) – available to explain the origin of all human adaptations since ten million years ago. My book focused the argument that way for specific reasons – largely to exclude the just-so evolutionary storytelling exemplified (explicitly and implicitly) in this thread by Robert Rapier. I will be discussing that more (see below).

I have decided to have my future postings of general interest carried at my publisher’s website (St. Paul Science at http://www1.minn.net/~science), where these may be conveniently found and enjoyed by anyone seeking them. This step is taken to be more time-productive for my readers and me.

**Administrator: in a following email, Robert Rapier took strong exception to ReMine's charge here saying he could verify everything. We urge interested participants to continue the debate on another board or with ReMine directly on the website he has given the URL for.

[ August 11, 2002, 09:53 AM: Message edited by: Administrator ]

 

ROBERT RAPIER

I agree that it is time to wrap this up. This is my final post in this thread. I am going to have three parts to my response. The first is the super-short summary. The second is a longer and more comprehensive (but not too technical) summary. The third part deals specifically with Fred’s most recent post.

SUPER-SHORT SUMMARY

That’s really all you need to know. If this admission had been made in Fred’s first reply, I wouldn’t have had anything else to argue about. My biggest complaint over this issue is that Fred and Mr. ReMine have repeatedly made claims that 1667 beneficial mutations can’t turn a common ancestor into a human. They take this as a fact, and then base arguments off of this fact. In the extraordinary admission above, Fred acknowledges that this claim has zero scientific basis; it is an argument of disbelief. Therefore, Mr. ReMine has no scientific justification for his basic premise in his treatment of Haldane’s Dilemma. As I said, his treatment of Haldane could be 100% accurate, but the premise that he bases it on is not scientifically supported. Therefore, this is not remotely a scientific argument.

SUMMARY

If we ever had an audience during this debate, we have probably lost most of it by getting bogged down in technical details. Therefore, I am going to try and summarize my arguments here, and do so with as little technical detail as possible. My summary will also be unique in that these points are non-controversial. In other words, I don’t think Fred can dispute any of them. If you haven’t followed the argument to this point, this summary will tell you everything you need to know about the problem.

What Walter ReMine has done is effectively provide a falsification test for human/chimpanzee common ancestry. If his argument is completely correct, it proves that humans and chimpanzees did not share a common ancestor. However, if he is incorrect, that obviously does not prove common ancestry by default, nor is it an indictment against Creationism in general. It just demonstrates that his argument is invalid, and therefore deserves a place among the refuted Creationist arguments. A brief summary of the relevant issues:

1). Walter ReMine wrote a book, The Biotic Message. In this book he addressed the subject of Haldane’s Dilemma, which highlights the difficulty of getting beneficial mutations established throughout a population. His conclusion is that any hypothetical common ancestor to both modern humans and chimpanzees could have only accrued 1667 beneficial mutations over the course of 10 million years.

2). Various solutions to Haldane’s Dilemma have been proposed since Haldane wrote his 1957 paper. In Mr. ReMine’s book, he attacks the proposed solutions, but spends absolutely zero time pondering the obvious questions: Are 1667 beneficial mutations enough to account for the differences? How many should there be? Without addressing these questions, Mr. ReMine’s point fails because he has not established that there is actually a dilemma. This is like prosecuting a crime before first establishing that a crime has been committed. If, for example, it is determined in the future that 854 beneficial mutations are estimated to have accrued between common ancestor and man, Mr. ReMine’s entire argument fails.

3). Mr. ReMine also wrote that Motoo Kimura showed that 25,000 expressed neutral mutations could also have accrued over the same 10 million year period. By expressed, that means that the mutation makes some kind of detectable difference in the organism. This may be as simple as a single amino acid modification in a protein.

4). Fred Williams and Walter ReMine have both been engaged repeatedly on this matter, but both have consistently refused to put forward an argument that 1667 beneficial mutations and 25,000 expressed neutral mutations can’t account for human evolution. They just assert it over and over. This is not science.

5). In science, the person making the claim is expected to provide the evidence. Claims are not accepted as true unless proven false. If this was the way science operated, then science would be placed in the position of having to refute any claim from anyone: alien abductions, perpetual motions machines, bigfoot, etc. It seems quite obvious that if I claim to have encountered bigfoot, that it is not up to science to disprove my claim. If I really want to convince people, then I need to bring some pretty convincing evidence. Yet Mr. ReMine and Fred Williams seem to believe that no evidence other than their statements of disbelief are required to show that 1667 beneficial mutations can’t account for human evolution. Fred only makes statements like “If you want to believe 1667 is enough, go right ahead”. This is not remotely scientific.

6). While the burden of proof is not on me, I made an attempt to show that 1667 is not “out of the ballpark”, as Fred once claimed. I looked at the coding differences between man and common ancestor. The coding area of the genome is the area responsible for producing the proteins that build an organism’s brain, heart, skin, muscles, etc. In other words, this is the region that builds a human, a chimpanzee, or a common ancestor. The difference between human and common ancestor in this region is estimated to be 216,000 base pairs.

7). Fred protested that I had only included coding regions and he pointed out that non-coding areas have been implicated in diseases. He tried to expand the area under consideration to some 10 million base pairs (5 million for the human/common ancestor comparison). Fred’s statement may have some merit, but there are a couple of problems with it. The first is that Haldane’s Dilemma is only concerned with beneficial mutations, and the only references Fred provided were related to disease. The second is that by all accounts, the vast majority of mutations are either neutral or harmful. So, even if we greatly expand the area under consideration, only a small fraction of the mutations would be beneficial, and therefore relevant to the problem. This is why Fred’s argument, while potentially interesting, doesn’t really help his case.

8). I demonstrated that 1667 beneficial mutations and 25,000 neutral expressed mutations can easily equate to several hundred thousand or even several million base pair differences between species. This does not even count neutral mutations that aren’t expressed, and harmful mutations, which Fred has indicated are the most predominant.

9). Conclusion: Neither Walter ReMine nor Fred Williams even attempt to meet the burden of proof in establishing that 1667 beneficial mutations and 25,000 neutral expressed mutations can’t account for human evolution. The major weaknesses in their case are: 1). The ancestor has not been identified, therefore the required adaptations are unknown. 2). If the ancestor had been identified, it is still unknown how many beneficial mutations are required for various adaptations. 3). Comparisons between human and chimp genomes have indicated that the genetic similarities are closer than previous estimates had indicated. This significantly weakens the ReMine/Williams argument.

10). Unless Fred or Walter ReMine are ready to step forward and present evidence that 1667 beneficial mutations and 25,000 neutral expressed mutations can’t account for human evolution, you may consider their argument refuted. ReMine’s discussion of Haldane’s Dilemma is moot, as he failed to establish that there is a dilemma as it pertains to human evolution.

REGARDING FRED’S LATEST POST

I have to truly wonder if Fred is skipping over large sections of my post, because much of what he wrote is irrelevant. He also clearly misinterpreted parts of my post, and in doing so wrongly declared them to be in error. I have stated multiple times that my argument is not whether or not Haldane’s assumptions were correct. I indicated that they might not be, (in fact many biologists argue that they are not) but I accepted for the purpose of this argument that they are. Therefore, 2/3 of Fred’s response is moot, because it dealt with Haldane’s assumptions, neutral theory, etc. None of these are relevant to my argument, which I have repeated numerous times: Are Walter ReMine and Fred Williams justified in presuming that 1667 beneficial mutations can’t turn a common ancestor into a modern human. There is no reason for me to address these moot parts of Fred’s response.

Misrepresentation. You clearly demonstrate a misunderstanding of my position. If 1667 is a reasonable number, it means that there is no dilemma with respect to human evolution. It has nothing to do with 1 substitution every 300 generations, and I never stated otherwise. In fact, I stated that with respect to this discussion, I accept Haldane’s assumptions. It is just common sense that if 1667 is a reasonable number, then there is no dilemma in the case of human evolution. Therefore, ReMine’s entire discussion on Haldane is moot as far as human evolution is concerned.

Uh, Fred, since 99% of the respective genomes are identical, I am perfectly justified in dismissing 99%. It is the remaining 1%, in which the differences lie, that is relevant to our discussion. Perhaps you just misstated the point you were attempting to make. As it stands, I don’t see how looking at identical portions of the genome are relevant.

Exaggeration/misrepresentation. I only considered that a mere 10% consist of “bunches, using ReMine’s own hypothetical. Are you saying that Mr. ReMine just pulled these numbers out of thin air with absolutely no basis for this hypothetical? I would be shocked if this were the case.

And I countered Fred’s assertions in two ways. The first is that all of your references related to disease. Haldane’s Dilemma is concerned with beneficial mutations, therefore it can correctly be pointed out that you have provided no evidence relevant to Haldane’s Dilemma. Second, I pointed out that even if I consider all the differences (some 20 million base pair differences between human and common ancestor) your argument still fails the burden of proof required to be considered scientific.

Unless you are making the claim that beneficial mutations make up a significant fraction of total mutations, then I am easily justified in stating that only a tiny fraction are relevant to Haldane’s Dilemma. After all, Creationists continually stress the rarity of beneficial mutations. Therefore, a tiny fraction of regions outside coding regions would be beneficial, and therefore relevant. The only way to counter this is to assume that beneficial mutations are not rare.

I will remind the reader that the core of my argument is that Fred’s and Mr. ReMine’s claim is not scientifically supported. This is why I asked Fred to read my previous posts; so that he would understand my position. Clearly he did not read my earlier posts, and therefore misrepresents my position.

Not true. I made the challenge because the burden of proof is on he who asserts. You and Mr. ReMine asserted; I did not. I said I don’t know, but it is not scientific to assert without evidence.

Actually, you again show your misunderstanding of my position. I said that I don’t know if 1667 is enough, so how could I have capitulated to a position. The burden of proof is on you for making the assertion, and you seem to have capitulated to the position of “it just can’t possibly be enough”. In addition, Mr. ReMine did not make his claims in a scientific journal, so why would they have been addressed? Note that I am not saying that Haldane’s Dilemma is not discussed in the literature, I am talking about Mr. ReMine’s claim that 1667 is not enough for human evolution. Finally, the position that I (and others) have taken, that the burden of proof is on you, has been taken every time Mr. ReMine posts on a board to defend the issue. Following is in an exchange that occurred just last week, on August 3rd. A poster (“Steven J.”) on the newsgroup alt.talk.creationism posed the following questions to Mr. ReMine who had dropped in:

Note that Mr. ReMine did not even attempt to address the question, except with evasive qualitative arguments. He also tried to evade the only scientific possibility of addressing this question by downplaying human-chimp comparisons. If he is unwilling to address the question in this manner, then he has absolutely zero ground left to stand on with respect to this issue. Note also his reference to “nominally 1667 beneficial nucleotides”. I have discussed the particular wording of this statement in the past with Mr. ReMine. Apparently Mr. ReMine considers that if 90% of the mutations are point mutations, as in his hypothetical, the final product is somewhere in the neighborhood of 1667 beneficial nucleotides. I have demonstrated that this is not remotely true.

Without knowing how many base pairs 1667 beneficial mutations equate to, this is an invalid comparison. Also, how rare are beneficial mutations? You say they are exceedingly rare, which supports my argument in this case. Let’s compare human to modern ancestor, and assume that every mutation is a point mutation. This is a very generous assumption for your case. Then we have 1667 beneficial mutations out of 20 million total base pair differences. What is the ratio of beneficial mutations to the total? ReMine states that a population of 100,000 is not likely to see one every generation. 1667 out of 20 million is equal to 1 beneficial mutation per 12,000 total mutations. This probability is increased as soon as more realistic assumptions are used (e.g., not every mutation is a point mutation). Again, even with the most optimistic assumptions, your argument fails.

This is also the position that Mr. ReMine has taken, which is quite unusual since the ReMine/Williams claim has not been made in any science journals. So why would anyone address it there? To use a familiar analogy, no one in the science journals has refuted the claim that the moon is made of green cheese. The reason is that no such claim has been made in a science journal. If you or Mr. ReMine wish to make claims in science journals, they will be addressed.

Once again, as I have pointed out (and Sumac and others pointed out over a year ago) without knowing how many base pair substitutions 1667 mutations provide, this is an invalid comparison.

False. It presumed that only 3.6% of the total consisted of duplicated genes. This is a far cry from “primarily”. I was also using Mr. ReMine’s hypothetical, and merely applied the math (no twisting required) to demonstrate the trouble his hypothetical provides for his own (and your) argument. Do you believe that he completely made these numbers up, or do you think he had some kind of basis for his hypothetical?

Convenient? No. I just used Mr. Remine’s hypothetical to illustrate the point. But that brings up another point that I should have addressed earlier. What evidence do you have of any beneficial mutations existing in us that don’t exist in chimpanzees? I am sure you have some that you can share? The only significant difference I am aware of is the one that John Paul and I discussed earlier, the sialic acid mutation. But that involves a 92 base pair deletion, so would more likely fall into the category of deleterious mutation for humans. But note that it is not a point mutation. Therefore, the only evidence we have for an expressed difference between humans and chimps involves a 92 base pair event. If you wish to counter, you need to come up with some expressed differences due to point mutations. To be completely relevant, they should be of the beneficial variety.

Because Mr. ReMine’s claims are not made in a scientific journal. To confuse Mr. ReMine’s claims (that 1667 is not enough) with discussions made in the literature on Haldane’s Dilemma is ludicrous.

More evidence that you have not been reading my posts. This is the absolute crux of my argument; how can it possibly be a red herring? I have stated this in every post I have made.

False. If your claims were true, geneticists would support them. Can you point me to a scientific journal where anyone is suggesting that sequence comparisons imply that chimps and humans don’t share a common ancestor? If not, it is once more mere assertion on your part. Assertion is not evidence.

I think it is very important to note how you deal with your errors. In every single case you deflected responsibility for them. In this particular case, you acknowledged the error, stated that it was trivial, and then “corrected” it. However, your correction was also in error, so you had to make a second correction (changing the number by an order of magnitude!), once again calling it trivial. My point in highlighting this is to demonstrate that with such poor attention to detail, how are your articles supposed to instill confidence that you are doing quality work? Your numbers were all over the map in this case, and yet according to you the errors were trivial.

I agree with this, which is why I could never understand why it was in the article in the first place. But note that I did not attack your article in general, I attacked the small section on Haldane’s Dilemma, which is completely relevant to our debate. The rest of the article is not relevant to our debate, and I did not attempt to address it here.

First of all, as I mentioned I have an archive of Haldane’s Dilemma posts. It has nothing to do with you personally, so no reason to feel flattered. Second, I have no idea why you expect a retraction. In fact, this was precisely the reason that I wanted to put the posts out there and let the reader decide. I said that you compared 1667 substitutions to millions of base pair differences as if they were equivalent. I pointed out that 1667 substitutions can equal a lot more than 1667 single nucleotide substitutions. I stated that this had been pointed out to your before, and you denied it. A quick reading of Sumac’s posts, particularly the parts in bold, demonstrate that you were told before that your approach is incorrect. In fact, you acknowledge that you remember the exchange well, so you can’t claim you didn’t see it. Note Sumac’s statements:

Given the above statements, which clearly indicate that you were incorrectly equating beneficial mutations with base pairs (which was exactly what I said), it is bewildering to me why you think a retraction is in order. On the contrary, I was expecting an acknowledgement of error from you. But again, that’s the reason I put the statements out there. The reader can decide whether or not your error was pointed out to you over a year ago.

In conclusion, I reiterate the position I have maintained throughout this debate: My position has never been that 1667 beneficial mutations are clearly sufficient to account for the differences. I have always maintained that until we work through the problem, it is not a very scientific approach to just assume that they are not. This has been the primary criticism of Mr. ReMine – that he did not establish this fundamental premise before launching into an attack on the proposed solutions for Haldane’s Dilemma. They key question is: Are Mr. ReMine and Fred justified in asserting that 1667 beneficial mutations can’t account for human evolution from a primitive ancestor?

Fred answered this question in his latest post, which effectively puts an end to this debate, by establishing that they were not justified in making the assumption:

To use a final analogy, despite the ability of Johnnie Cochran to confuse the jury, O.J. Simpson was certainly guilty of the crime with which he was charged. The core issue was pretty simple to resolve, but Mr. Cochran took a long detoured approach which confused the jury to the point that they didn’t know what to believe.

 

JOHN PAUL

John Paul:
It was easy to substantiate Walter’s assumptions on language, speech and upright posture. Our current knowledge pertaining to those topics show his assumptions are good (under the evolutionary scenario). That is what I found from Internet searches and have provided links to. No one knows how, when or why these adaptations came to be. All we have is speculation based upon the assumption they did. Hopefully in the foreseeable future we will have such an understanding of genomes that we will be able to make the determination if in fact changes to the DNA can effect the changes required by the ToE.
I have yet to see anything posted, nor have I found anything via the Internet, that would give us any reason to doubt those assumptions. If someone knows of such information please post it.

Choosing to play the numbers game does not equal the premise I was trying to defend Walter’s argument pertaining to Haldane’s Dilemma. Even Walter can see it doesn’t.

You don’t get to choose the mutations. In this method the criterion for selection is a long-range goal when in direct contrast the criterion for natural selection must be short-range. Even when something looks good on paper there still comes a time when you must consider if it is indicative of reality. I would concede your falsification to be valid only if reality was an intelligently guided designed process. That is the only way I see 1667 mutations as being enough- if it was meant to and had no other choice. But then again in that scenario Haldane’s Dilemma wouldn’t be.

Like I tried to tell you earlier- The only thing this method can give us is the number of mutations there were since the split (divergence) assuming all the assumptions & estimations are correct. This method can’t tell us if those mutations were possible, what they were, if they occurred, if they could accrue, why they were selected, if they were random, what the sequence was or if they could lead to the changes necessary.

Your falsification is based on several unsubstantiated assumptions, estimations, a mechanism not indicative of the theory of evolution and has as much chance of passing muster as a house of cards has surviving a nor’easter.

Making an assumption for argument’s sake is one thing but it appears you have assumed yourself right into Intelligent Design.

 

FRED WILLIAMS

Robert’s conclusion greatly exaggerates the significance of my statement. My statement above should be no surprise since 1) I have told evolutionists this before, and 2) it’s common sense that I cannot conclusively prove that 1667 isn’t enough. I also cannot “conclusively prove” that the moon’s impact craters are the result of meteorites, even though deductive reasoning based on observable characteristics of the craters strongly suggest they are. Robert then erroneously claims I have always treated Haldane’s substitution rate as “fact”. I have never claimed Haldane’s Dilemma is a “fact”, in fact I have said many times it could be wrong. I wrote this on Percy’s board July 6: “I've stated before that I don't really emphasize Haldane's problem that much. It's an interesting model that could be wrong (though I have yet to see a convincing argument that it is).” Even in this thread 6 months ago I said I don’t emphasize Haldane’s Dilemma much as evidence against chimp/human ancestry (Feb 26). I instead focus on the cost of mutation problem (a piece of Haldane’s model) because I think it’s easier to grasp and because recent scientific data amplify the problem. But even this argument is not conclusive proof that chimp/man do not share a common ancestor, as I have also stated in the past. Is Robert going to now latch onto this statement and declare the mutation problem a “non-issue”? “Strong evidence” and “conclusive proof” are two different things.

Again, I did not pop back in to this thread to defend Haldane’s Dilemma as a nail in the coffin argument against creation (nor was it my motive 6 months ago when I rebutted Scott Page’s original claims that initiated this thread). I came here to correct some errors Robert made that led him to prematurely declare that it is “quite clear that there is no dilemma.” I did notice something in Robert’s last post. He now qualifies dilemma with “as it pertains to human evolution.” He did this three times! This is an implicit admission on his part, which is good enough for me, that he was wrong to declare the Dilemma null and void (as he did many times in this thread), not realizing that Haldane’s substitution rate does not go away even if he had made a case that 1667 beneficial mutations could account for human evolution in the last 10 million years.

This is a shell game. When you compared chimps to humans, you took the estimated differences (1%) and placed all of them within the exon portion of the genome, which is estimated to be 1.4% of the total genome. Thus you were able to get a much reduced number for your analysis (1.4% of 1% of 3 bil). You effectively ignored 99% of the genome. I showed that this is an invalid assumption. Your next two statements relate to this:

This is a continuation of the shell game. Obviously creationists do not believe beneficial mutations are prevalent (in fact I argue that there are no solid examples of any mutation that added new information to the genome). But for evolution to be true, almost all of the coding exons, and many of those non-exon base pairs (such as introns) had to get there by positive selection at some time in the past. Since mutating introns often results in negative selection, it only follows that, for evolution to be true, they must have been under positive selection in the past to get to the point where mutating them does the opposite. You could of course assume no selection for the 99% of the genome you ignored and attribute their arrival to pure random chance, but I suspect this is a position you would rather not try to defend.

Here Robert continues to show his misunderstanding of Haldane’s Dilemma, since harmful mutations are very much relevant as their presence aggravates Haldane’s substitution rate. For example, if reproductive excess is based only on harmful mutation and the mutation rate is U=3, this yields a reproductive excess of 1/ (2*e^U) = .025. That means Haldane’s speed limit for beneficial mutations slows from 300 to 30/.025 = 1200! (this would lower the 1667 number to 417). Robert is therefore very much mistaken to claim Haldane’s dilemma is only concerned with beneficial mutations (see Haldane, 1957, p520-521; Remine p228). While it calculates the rate of substitution for beneficial alleles, this rate is very much dependent on the reproductive excess available to drive it to fixation. Since reproductive excess is dependent on the level of harmful mutations; Haldane’s dilemma is therefore also dependent on the level of harmful mutations.

SUMMARY

To conclude, Robert made some errors and unreasonable assumptions that led him to prematurely declare Haldane’s Dilemma null & void. He also failed to offer a convincing argument to dismiss the dilemma “as it pertains to human evolution”. The originator of this thread, Scott Page, also failed to make his case. His two citations proved to be either irrelevant (Rice et al) or detrimental (Wu et al) to Haldane’s Dilemma.

Does this mean Haldane’s number is accurate? I believe his number is likely too low because he arrived at it using favorable assumptions for evolution. But I am not closed on the subject, and realize there may be some argument that comes down the pike that renders the dilemma moot. But I have yet to see such an argument that is convincing. It remains a dilemma, one of a myriad of stumbling blocks for evolution.

[Regarding Sumac’s comments, I suggest you email him and ask him if he was arguing that one beneficial mutation could be represented by multiple base-pair substitutions; It is not obvious at all from my exchange with him that he was arguing this, and this was the basis of your objection. It is clear to me that Sumac was objecting because I was comparing beneficial substitutions to a number that encapsulates harmful, neutral, and beneficial substitutions. He then exercised the same fallacy as you did by expecting me to use the percentage of beneficial mutations creationists expect, within the context of an evolutionary scenario that requires a much larger percentage of beneficial mutations].

 

This thread is now closed.