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Haldane’s Dilemma and peer-review

J.B.S. Haldane first described the ‘cost of substitution’ and its limitation on the speed of evolution. That gave rise to a problem (see, for example, Dodson), known today as Haldane’s Dilemma. The problem is more severe in organisms with low reproduction rate and long generation time, such as the higher vertebrates: elephants, whales, apes and humans, etc. Evolutionary geneticists saw this as a compelling issue. Maynard-Smith and Kimura each cited it as the main reason for their revolutionary new views of evolutionary process.

Yet the fundamental cost concept fell into long-lived confusion, which limited its deployment. Today, most commentators say the problem is solved, but exhibit little agreement as to why. One modern authority, George C. Williams, asserted, ‘the [Haldane’s Dilemma]
problem was never solved, by Wallace or anyone else’. This paper will show the problem cannot be solved so long as confusion prevails over the fundamentals.
…..
I share with Haldane and Kimura and Crow the belief that quantitative cost arguments ‘should play a part in all future discussions of evolution’. I also agree with George C. Williams that ‘the time has come for renewed discussion and experimental attack on Haldane’s Dilemma’.

Walter ReMine

Walter ReMine is a former fellow at the Discovery Institute. His book, Biotic Message is available at ARN, and one will see his name in the acknowledgement section of Bill Dembski’s Design Inference.

I tracked the saga of Walter’s attempt at getting his peer-reviewed paper published. He had prestigious reviewers like Warren Ewens and James Crow reviewing his paper and who acknowledge ReMine was correct.

I think ReMine’s paper on Haldane’s Dilemma is worthy of consideration whether one agrees with him or not. I think he makes a devastating case against the efficacy of Darwinian evolution based on first principles of population genetics in his book Biotic Message and shows how the Darwinian community has obfuscated the real problems into oblivion.

Having faced numerous rejections, and documenting the rejections, ReMine was finally forced to publish his paper as a last resort in a (gasp) creationist journal. If one reads his paper, there is not one reference to God, Intelligent Design, or any theological issue, simply pure science.

He makes well-reasoned arguments from population genetics, and I hope readers will realize the great value of his mathematical contributions to the field. I think his work was not welcome because it hit too close to home for some. But that is my opinion, I will let interested readers decide for themselves.

Cost Theory and the cost of Substitution

and

Evolutionist peer-review & Haldane’s Dilemma

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26 Responses to Haldane’s Dilemma and peer-review

  1. Hmmm, wasn’t there some chatter either here or on telic thoughts where one of the proNDEs was saying, “show me any work which has been rejected…”. Well, here is a work that has clearly been rejected. Though it is floating right over my head at the moment, I certainly am enjoying the general concepts expressed.

  2. He should post the reviews so that readers could see the points that the reviewers were making first hand. He could still keep them anonymous.

  3. I enjoyed the paper (though I have not read it in-depth yet), but there are a few things to keep in mind. Mostly that a lot of the math and arguments only apply to neo-Darwinistic evolution. For example:

    It is assumed that a given mutation isn’t likely to occur more than once in a population. If mutations are directed, then this is no longer true.

    It is assumed that, with fewer members of a population, the rate of new mutations generated must slow down by the same factor that the population is reduced. Again, if mutations are directed, this is no longer true.

    (note that these assumptions are not ones invented by ReMine — they are ones used by Haldane and pretty much anyone else who works with population genetics under the Modern Synthesis)

    Also, I don’t believe ReMine has yet jumped into Haldane’s dilemma yet. This paper focused on the substitution cost of a single allele. Multiple alleles have more mathematical complications which were alluded to, but not expounded upon.

    I did think that his reworking of the concepts made it a much better conception of the whole picture. I liked the fact that he tied it much more closely to physical concepts than the original Haldane paper. He also explained it very well.

  4. Here’s an easier to understand summary of Haldane’s dilemna by ReMine: http://ourworld.compuserve.com.....aldane.htm

  5. russ –

    That’s an excellent summary of the problem.

  6. I went to the Amazon listing for his book, and found a review by Scott L. Page. I’ve “quote mined” the review here:
    —————–
    “And, more importantly, one should wonder why ReMine’s amazing ‘theory’ can only be read about in his vanity press book? Why has he not written up manuscripts to be critiqued by his fellow scientists? The answer? Creationists prefer writing in a medium wherein they receive only praise from like-minded individuals, such as ‘John Woodmorappe’, not where those that know better would demolish his flimsy, evidence-less claims.

    This book belongs on the scrap heap of egomaniacal creationist rants.”
    —————-

    This review is pretty funny when you consider ReMine’s struggle to get peer-reviewed, with two committees rejecting his paper because his theory was “wrong”, and a third rejecting it because it was “correct”, but scientists have known all that stuff for years!

  7. I remember trying to dig up info on the “cost of substitution” during my early genetics/molecular evolution studies. The modern literature, as mentioned above, is remarkably silent on the matter. Kimura et al did bring us part way to a solution by introducing the concept of neutral substitutions. There are other nuances in population genetics that also help alleviate the magnitude of the problem. Why has no one systematically addressed the issue in the mainstream literature? I have yet to find a satisfactory explanation. If the issue was formally put to rest somewhere, I would seem to have missed that publication or series of publications. Definitely a good topic for discussion.

  8. I read the Biotic message online sometime ago and enjoyed it immensely as a first look into this ongoing debate. Thanks for bringing this up Salvador. I had forgotten about his struggles in peer-review. The one rejection was just pathetic. It is straight forward, logical and still unsolved imho.

    Now, lets see, about those non-coded regions again…

    OT, re: age of earth, geologic columns, crust, etc.,
    if MMadigan happens by, check out the following article:
    http://service.spiegel.de/cach.....47,00.html

    Excellent photos, shows a 345 mile long rift splitting the crust as deep as 345ft in less than a year. Predictions by OE geologist are the Horn of Africa will split and form an ocean in 10 million years. I wonder what Creationist predict? It seems like good fodder for the YE/OE debate.

  9. Thanks Russ for the link. I was having trouble wading throught the official article.

    I am a bit baffled by this delemma, however. I’ve just played a few population games myself. Rather than a 100,000 population picking up 1 mutaton per genration, consider 1000 villages, each with 100 people. Now each of these villages gets the lucky mutation, which spreads like wildfire through the population. Now in the number of generations that it takes to spread through the system, you have 1000 natural selection tested mutations within the species. Does that address Heldane’s dilemma? If not, why not.

    Further, Remine says, “He calculated that the higher vertebrates (such as mammals) have only enough reproductive capacity to sustain an average rate of 300 generations per substitution.” What does this mean? Can anyone help translate.

  10. Bringing up Haldane’s dilemma reminds me of another evolutionary conundrum I’ve often wondered about: why did the Passenger Pigeon go extinct? Here we had a bird that was once considered the most common bird in the world, with vast flocks that blotted out the sun. Europeans started to hunt it with modern weapons, putting it under huge evolutionary pressure, and within 300 years it was totally extinct. One can understand birds like the Dodo, which were limited to small island populations, wouldn’t have the ability to adapt in time to avoid extinction, but if a species made up of billions of members, reproducing every few years, that ranged over a continent couldn’t succesfully evolve enough iover a few centuries to avoid extinction, why are we convinced that other species can magically adapt to abrupt changes it their environments through evolutionary transformation?

  11. russ -

    It looked like Scott Page has also dismissed this paper out-of-hand:

    http://all-too-common-dissent......again.html

    He apparently had access to ReMine’s paper before it was published. Here is Scott’s comments on ReMine’s paper:

    “Actually, the paper that you refer to is of substandard quality AND it says nothing new. I have read it. It was standard ReMine. Lots of finger pointing and sophomoric prose, very little of substance. Of course, ReMine’s paper did not address his baseless claims re: Haldane’s dilemma, so what we have is yet another red herring from Crevo.”

    (quoted from http://all-too-common-dissent......onist.html )

  12. bFast:

    Let’s look at your scenario. I think the separating out into villages actually makes the cost tougher, not easier.

    Let’s say I have a village with 100 people. If I introduce a new allele, what is the minimum time it takes to spread to that 100 people? Well, in order to maintain the population, even if everyone without the allele died off in a single generation, it would take 3 generations of having 5 children each to return to the original population. However, in most scenarios, the old-type doesn’t die off immediately. In addition, in order to get it to each village, it would require an additional 5 generations in the _best_ case scenario. However, with a segregated population, it is much less likely that the allele would make it to all the villages.

    Now, let’s think about two beneficial alleles, one arising in one village, and one arising in another village. Let’s say they each become fixed within their village. How does it now become fixed within the population? You now have _competing_ alleles. Some will combine, some will not. But to get the alleles _fixed_ (100%) you have to have enough reproductive excess to combine the alleles and propogate their combination. This is a much more difficult problem.

    You can read Haldane’s original paper here:

    http://www.blackwellpublishing.....ldane2.pdf

    There is another group that has verified Haldane’s thesis with a few proposed modifications here:

    http://www.sekj.org/PDF/anz40-free/anz40-185.pdf

  13. jonnyb: “Now, let’s think about two beneficial alleles, one arising in one village, and one arising in another village. Let’s say they each become fixed within their village. How does it now become fixed within the population? You now have _competing_ alleles. Some will combine, some will not. But to get the alleles _fixed_ (100%) you have to have enough reproductive excess to combine the alleles and propogate their combination. This is a much more difficult problem.”

    Why would this be a much more difficult problem. With the 30,000 genes that make up a man, one would think that the allele developed in village 1 would be an allele of a different gene than the allele developed in village 2. Both would most likely be operating on two areas of the organism that don’t have any meaningful crosstalk.

    Ps, thanks for the link to Haldane’s original work. It is often great to check out the root source.

  14. bFast — the issue isn’t crosstalk, it’s sexual reproduction. If a man is from village 1 and a woman is from village 2, and they have four children, only ONE of those four children is going to have both alleles. One of their children won’t have ANY of the alleles. Two of them will continue to have one or the other. If you think about it, sexual reproduction significantly increases the cost of replacement, especially for multiple alleles — they are competing for space (the group with one good allele will also be carrying one of the bad ones — it takes many generations to resolve this).

  15. “If my mental processes are determined wholly by the motions of atoms in my brain, I have no reason to suppose that my beliefs are true and hence I have no reason for supposing my brain to be composed of atoms.”

    My favorite Haldane quote. It comes from his book, Possible Worlds, and is referenced by C.S. Lewis in his book, Miracles.

  16. JohnnyB: I skimmed Scott Page’s blog at your link, and it doesn’t sound like he’s actually refuting anything of substance. What’s your take?

  17. Johnnyb: “If you think about it, sexual reproduction significantly increases the cost of replacement, especially for multiple alleles — they are competing for space.”

    The joy of alleles is that a bunch of ‘em float around in a population, there is no need for a particular one to dominate the population, it only needs to be part of the population. I still think that the fact that multiple sub-populations each can develop their own alleles challenges the simple view of the problem as presented in ReMine’s summary as presented by Russ (comment 4 above). That said, summaries are summaries. I hardly understand Haldene’s dilemma sufficiently to suggest that it is full of it.

  18. Oh, and, the “there’s lots of alleles floating around” bit, if I understand punctuated equilibrium theory correctly, plays a significant role when very small groups assemble. Those groups have a very small subset of alleles between them. If a few good mutations happen within that group, it can lock in that subset of alleles as a permanent feature of the new species — or so says the punctuated equilibrium “inbreeding is the solution” theory.

  19. bFast:

    “The joy of alleles is that a bunch of ‘em float around in a population, there is no need for a particular one to dominate the population, it only needs to be part of the population.”

    I think that this is where you are confused. The cost that is being counted is the cost of _fixation_. Fixation only happens when the allele is in 100% of the population.

    The problem with Punc Eq is that when you reduce the population size, you either (a) lower the mutation rate to non-existance, or (b) have so many mutations that you suffer from error catastrophe. Likewise, you eventually have to get back to your real population size eventually. So the population has to be (a) small enough to fixate genes quickly, (b) large enough to not die out, (c) have mutations happen at just the right rate so as to not kill the animal who is getting the beneficial mutation, and (d) be able to come back to the “typical” population size at the end of such a journey. Again, for large numbers of beneficial mutations, this is simply not possible.

    russ –

    If I remember correctly, Scott’s primary arguments are:

    1) how do you know that 1,667 * 2 mutations is not enough to separate humans from chimps?
    2) experimental evidence shows that the mutation rate is much faster.

    #1 is fairly obvious to me. Scott thinks that the existance of mutations that cause major problems in numerous systems is evidence that a mutation could cause just as many benefits in multiple systems. Having done lots of design modifications myself, I find that completely contrary to experience. Scott also requires that I list specifically which mutations are needed in order to validate my point. I don’t think that this is explicitly necessary, though I have pointed to which systems I thought were the most important, and several journal papers describing multiple genes with multiple differences between humans and chimps.

    #2 is simply circular reasoning. The paper he points to simply takes the number of differences between humans and chimps at certain spots and divides by the number of years between our supposed divergence. In case you didn’t notice, this math only works if the assumption that we are separated from chimps is correct (note that the people who wrote the paper are NOT engaged in circular reasoning, because they are not using their data as evidence for the split — just extrapolating from the [IMO incorrect] assumption).

    He also always wants to know exactly what the common ancestor looked like. I find this amusing. If he can’t characterize the common ancestor, what makes him so sure there was one? I think he is trying to get me to characterize a common ancestor and then use my characterization as evidence that there was one. I point out that most evolutionary literature would have such an ancestor be more chimp-like than human-like, but there is no real evidence for its existance. I also point out that Haldane’s dilemma wouldn’t actually be a problem if chimps were merely degenerative humans, but that I don’t know any evolutionary biologist who would hold to that.

  20. Walter Remine: “Imagine a population of 100,000 of those organisms quietly evolving their way to humanity… One per generation — or 500,000 nucleotides.

    In fact, each of those 100,000 mammals probably has at least one mutation. So that’s 100,000 mutations per generation, or 50 billion mutations over 500,000 generations. That’s plenty of mutations to turn a wolf into a poodle in just a few thousand years.

    But they’re both still dogs with not a single novel new feature. The only changes are in scale and cosmetics. No one has ever observed or charted a path where random mutation plus natural selection caused the emergence of a novel cell type, tissue type, organ, or body plan. That’s the bottom line. The ability of chance and neccessity to create these things is pure unadulterated speculation. A narrative. A fabrication. A fantasy. -ds

  21. Kimura and Ohta cited Haldane’s dilemma as part of their justification for the exploration of neutral theory. What ReMine points out in his book is that there are also fatal flaws in Kimura’s neutral theory. Denton points out that advocates of selectionist and neutralist theories find fatal flaws in each others theories. I suppose we call it Mutually Assured Destruction (MAD) of each competing theory.

    It has been presumed that population genetics is supportive of large scale naturalistic evolution, much like OOL researchers suppose chemistry is supportive of OOL. However, upon serious contemplation, quite the opposite is true.

  22. Jonnyb:
    If multiple parallel experiments can all be implemented at once, independant of how long each experiment takes, one cannot analyse volume based upon how long one experiment takes. That the allele experiments can quite happily operate in parallel, and even in mass parallel is my case against Haldane’s dilemma.

    Looking at it another way, you hear reports that such and such an assembly line puts out 15 cars per shift. That doesn’t mean that each car only took 1/2 hour to build, front to back.

    As far as punctuated equilibrium theory goes, it is a core component of NDE. There is something obserd about the view, in light of inbreeding realities, but it is an assumption of NDE that speciation all but requires PE.

    There is another phenomenon of nature, however, that I think would assist in allele fixation. Animals tend to be racist, which is to say, animals tend to bunch together into “like groups” even within one species. (Consider, for instance, that the wolf and the coyote are still one biological species, but are pretty determined to stick to their own.) As the traits that create “like groups” are the alleles that we are talking about, this phenomenon would assist in the fixating of those alleles within each group, would it not?

  23. Over at ARN, one of the most recent objections was that the DI never actually funded any science. Walter clearly credits the DI for funding. I guess all that’s left is to claim that Walter’s paper is not scientific. Too bad it wasn’t rejected on those grounds, rather than on the specious and contradictory grounds upon which it actually was rejected. I mean come on now, if it was funded, either in whole or in part by the DI, doesn’t that make it a creationist tract, a trojan horse attempting to smuggle God into the classroom, and religion violating the non-existent separation of church and state clause of the Constitution?

    Sheesh, I know this is OT, but now i’m stirred up, lol. How did a free exercise clause evolve into a thou shalt not clause?

  24. Having faced numerous rejections, and documenting the rejections, ReMine was finally forced to publish his paper as a last resort in a (gasp) creationist journal. If one reads his paper, there is not one reference to God, Intelligent Design, or any theological issue, simply pure science.

    Well, if you read Walter’s book there are some rather unflattering mentions of Dr. Crow in it, lol. I wonder if Crow was aware of them.

    I think there are at least two important points here.

    1. Walter’s scientific paper was rejected on contradictory grounds.

    A. It’s wrong.
    B. It’s correct.

    2. Walter’s paper was rejected as unnecessary.

    Walter documented the vacuousness of the second objection in a 50 page thread over at ARN.

    In that thread the cries of put up or shut up were loud and often. One can understand why Walter didn’t make his paper available to those critics at the time, as he was still trying to get it published. But now that it has been published, what is the explanation for the uniform silence of his critics?

  25. Rather than a 100,000 population picking up 1 mutaton per genration, consider 1000 villages, each with 100 people. Now each of these villages gets the lucky mutation, which spreads like wildfire through the population. Now in the number of generations that it takes to spread through the system, you have 1000 natural selection tested mutations within the species. Does that address Haldane’s dilemma? If not, why not.

    One of Walter’s points about the dilemma is that for evolutionists to get around it they must propose unrealistic evolutionary scenarios. That’s why it is a dilemma. Your hypothetical may get around the dilemma, but in what way is it realistic?

    Why split the population into 1000 sub-populations? Why not just assert that the mutation starts out at a high frequency in the original population? Actually, I think that’s what Haldane did.

    Why would this mutation “spread like wildfire” through each of the villages? Wouldn’t there be a good chance that in each village the mutation would be lost in the very first generation?

  26. [...] drew heavily from the work of Motoo Kimura, James Crow, and Walter ReMine. He featured a lot of data I had never seen, and he applied the concept of signal-to-noise ratios [...]

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