Recently, while reading a post by Professor Larry Moran over at his Sandwalk blog, I stumbled across a lively discussion of Haldane’s dilemma in the comments section. Not being a geneticist, I hadn’t really paid much attention to the dilemma, until now.
For those who are interested in following up the matter, I’m going to post a few links to relevant articles arguing that Haldane’s dilemma remains unsolved (with asterisks placed in front of what I think are the best ones), plus some of the best responses to the dilemma that I’ve seen by evolutionists, before throwing the discussion open to readers.
Articles arguing that Haldane’s dilemma is a real problem for evolution
A Dilemma for Haldane by PaV at Uncommon Descent (2013).
Walter ReMine on Haldane’s Dilemma by Bob Enyart (August 3, 2012).
*** Haldane’s dilemma – the trade secret of evolutionary genetics by Walter ReMine (August 21, 2007).
Haldane’s view of Haldane’s dilemma by Walter ReMine (August 2007).
*** Haldane’s dilemma. Article in CreationWiki.
More Precise Calculations of the Cost of Substitution by Walter ReMine (CRS Quarterly, Vol 43 No 2 pp 111-120 September 2006).
Cost theory and the cost of substitution — a clarification by Walter ReMine (TJ 19(1) 2005, pp. 113-125).
*** Haldane’s dilemma has not been solved by Dr. Don Batten at creation.com.
The Biotic Message: Evolution versus Message Theory by Walter James ReMine reviewed by Dr. Don Batten at creation.com.
Haldane’s dilemma by Laurence D. Smart.
*** Answering Evolutionist Attempts to Dismiss “Haldane’s Dilemma” by Fred Williams (October 2000; updated subsequently).
Articles arguing that Haldane’s dilemma is not a real problem for evolution
*** Haldane’s dilemma. Wikipedia article.
*** Haldane’s non-dilemma (July 1, 2007) and ReMine strikes back (January 27, 2008), by Ian Musgrave at Panda’s Thumb.
*** How fast can evolution work? by Mike Dunford (January 25, 2007)
*** Walter ReMine and Haldane’s Dilemma. Article in EvoWiki.
Claim CB121: Haldane’s dilemma by Mark Isaak at TalkOrigins, 2006.
*** Haldane’s Dilemma by Robert Williams.
- Haldane, J.B.S., “The Cost of Natural Selection“, J. Genet. 55:511–524, 1957.
- Van Valen, Leigh, “Haldane’s Dilemma, evolutionary rates, and heterosis”, Amer. Nat. 47:185–190, 1963.
- Grant, Verne & Flake, Robert, “Solutions to the Cost-of-Selection Dilemma“, Proc Natl Acad Sci U S A. 71(10): 3863–3865, Oct. 1974.
- Nunney, Leonard, “The cost of natural selection revisited“, Ann. Zool. Fennici. 40:185–194, 2003. (This paper describes computer simulations of small populations with variations in mutation rate and other factors, and produces results that are dramatically different than Haldane’s low substitution limit except in certain limited situations).
The debate in a nutshell
Here’s an excerpt from ReMine’s August 2007 article:
What is Haldane’s Dilemma?
Briefly. Haldane’s Dilemma establishes a limit of 1,667 beneficial substitutions (where a substitution is almost always one nucleotide) over the past ten million years of the lineage leading to humans. The origin of all the uniquely human adaptations would have to be explained within that limit.(1) That is a serious problem.
The famous evolutionary geneticist, J.B.S. Haldane, showed that for higher vertebrates (species with low reproduction rates), the long-term rate of beneficial substitution cannot plausibly be faster than one substitution per 300 generations.(2)
Ten million years for the evolution of humans from some ape-humanoid ancestor. (This amount of time is a factor of two or three times the alleged split between chimps and humans. Though that date seems to be getting revised recently.)
A 20 year effective generation time. (This is approximately the age of parents when they give births, averaged over all births that reach mid-parenthood.) My book documents that figure from several evolutionists.
According to evolutionists the substitutions are almost always a single nucleotide (called a point mutation).(3)
All the key data, assumptions, models, and calculations are taken from evolutionists, and put a limit on the rate of beneficial evolution. I call it the “Haldane limit,” or the “1,667 limit.”(4) Since my book came out, there has been no serious dispute that Haldane’s analysis (if correct) places a 1,667 limit on human evolution.
My book identifies many factors further reducing that figure by orders of magnitude.(5) In other words, Haldane’s estimate is overly optimistic in favor of evolution. Yet I focus on the 1,667 limit because it derives directly from Haldane – so evolutionists cannot evade the issue by blaming it on me.
All those matters were known to evolutionary geneticists in 1957 when Haldane published his argument. Yet despite it being interesting, important, and easy to communicate, they did not inform the public. No, there was no conspiracy. But it was a staggering bit of negligence. Haldane’s Dilemma is not just the problem itself, but also the evolutionists’ negligence for not communicating it to the public…
(1) Haldane’s Dilemma puts a limit on the rate of beneficial evolution. It does not limit the rate of neutral or harmful evolution, which can be far more rapid. However, my book also contributes a style of argument previously unheard of – a serious limit on the rate of expressed neutral substitutions. The argument involves something routinely left out of evolutionary discussions – error catastrophe. By seeing the connection between error catastrophe and plausible substitution rates, I was able to create a new type of argument.
(2) Haldane’s calculations included the possibility of many substitutions overlapping in time. His argument did not require single substitutions tacked end-to-end.
(3) Sometimes the ‘thing’ being substituted into the population might be larger than a nucleotide, such as: insertion, deletion, gene inversion, gene duplication, or the relative order of genes on a chromosome. Each of these would count as a substitution, and the argument puts a limit on the total number of substitutions.
(4) The math is easy: 1,667 substitutions = 10,000,000 / (20 * 300)
Substitutions = (Years) / [(Years / Generation) * (Generations / Substitution)]
(5) As discussed in my book, several factors could reduce the 1,667 limit significantly. For example, according to Eldredge and Gould’s evolutionary theory, punctuated equilibria, species are in statis at least 99 % of the time, and Gould claimed punc-eq applies to human evolution. According to Gould (in his last book, The Structure of Evolutionary Theory) genetic change would typically cease during statis. If correct, this factor alone could reduce the Haldane limit by a factor of about 100, to a limit of 17 substitutions. I was the first to bring up this relationship between punc-eq and Haldane’s Dilemma. Evolutionists should have seen this relationship, but if they did, they did not publicize it.
And here’s an excerpt from Musgrave’s July 2007 article:
What the real problem is: One of the consequences of Haldane’s calculation is that it sets an upper limit to the amount of allelic variation (heterozygosity) in the genome. Under Haldanes’s assumptions, if different alleles of genes represent deleterious variants being selected against, too much variation means that the organisms fitness fall below survivable levels. When the variation in the genomes of several organisms was measured, it was way above the limits that would be survivable if Haldane’s assumptions held. The problem is not that evolution is too slow; the problem is that it is much faster than Haldane’s limit.
Let’s restate that, the amount of measured variation in the genome meant that if Haldane’s assumptions were right, all vertebrates would be dead. So we know that Haldane was wrong. Exactly where he was wrong occupied many pages of journal articles in the 60’s and 70’s. Kimura (Kimura, 1968) used the heterozygosity problem to advance the neutral theory. In neutral theory, most mutations are neutral with respect to fitness, and neutral alleles are fixed by drift. Since the alleles have no effect on fitness, a very large number of allelic variants can be in the population and not reduce its fitness, thus solving the heterozygosity problem.
Several others proposed selectionist explanations using different assumptions to Haldane’s that could drive more substitutions. The technical details need not concern us here, suffice it to say there were a number of models which could exceed Haldane’s “speed limit” (soft selection, truncation selection and gene hitchhiking for example. All of which have some experimental and observation evidence, see Ewens, 1969, Grant and Flake 1974, Smith, 1968 and many others in the reference list). The discussions over Haldane’s dilemma rapidly got subsumed into the larger neutralist vs adaptionist debate. In the end, the evidence came down on the side of the neutralists, and it is accepted that the majority of variation in genomes is due to neutral mutations .
How many benefical mutations? While the majority of variation is neutral, the question remains exactly how much variation is due to selection, and does it break Haldane’s “speed limit”. Recent comparisons of Human and Chimp genomes, using the Macaque as an out group, have given us a good idea of how many genes have been fixed since the last common ancestor of chimps and humans (Bakewell, 2007).
Actually, that’s 154 of 13,888 genes. Given that we have around 22,000 genes  in our genome (http://www.ensembl.org/Homo_sapiens/index.html), then if the same percentage of beneficial mutations holds for the rest of the genome, no more than 238 fixed beneficial mutations is what separates us from the last common ancestor of chimps and humans.
You are probably sitting there astonished that we are around 240 genes away from our last common ancestor with the chimp and saying “this can’t be right” (how much did the guess you wrote down differ from the real thing?). However, this result agrees with previous estimates of the number of positively selected genes (Arbiza, 2006, Yu 2006). You can argue until the cows come home about whether you can get around Haldane’s assumptions using truncation selection, soft selection or whatever, the plain fact is that humans and the last common ancestor of humans and chimps are separated by far fewer fixed beneficial mutations than even Haldane’s limit allows.
Now, it’s likely that the above values is an underestimate, and the some weakly selected genes have been missed, but it is in accord with previous studies using smaller gene sets (Arbiza, 2006, Yu 2006). Even if you say we missed half of the genes that underwent selection (very unlikely), the number of beneficial genes fixed by natural selection would be around 480, and the real number is certainly less (Arbiza, 2006).
The above study only covered protein coding genes, not regulatory sequences, and most biologists expect that changes in regulatory sequences played an important role in evolution. Getting at the number of beneficial mutations in regulatory genes that have been fixed by natural selection is a lot harder, but it seems like around 100 regulatory genes may have been selected (Donaldson & Gottgens 2006, Kehrer-Sawatzki & Cooper 2007). Again, even if we set the number of regulatory genes that have been selected as the same number as the most wildly optimistic estimate of protein coding genes fixed by natural selection, then we end up with 960 fixed beneficial mutations, below ReMine’s calculation of Haldane’s limit . This means Haldane’s dilemma is irrelevant to human evolution.
Conclusion: Haldane’s dilemma has never been a problem for evolution, but the technical nature of the arguments involved made it difficult to clearly demonstrate anti-evolutionists misuse of the “dilemma”. Also, the difficulty in getting the original papers meant that the distortion of Haldane’s work by anti-evolutionists was not obvious.
Now Walter ReMine’s claim that 1667 beneficial mutations is too few to generate a philosopher poet from the common ancestor of chimps and humans is shown to be trivially false from comparison of the human and chimp genome. As this claim was the keystone of ReMine’s argument, Haldane’s dilemma should disappear as an anti-evolutionist claim.
Excerpt from Wikipedia:
Haldane stated at the time of publication “I am quite aware that my conclusions will probably need drastic revision”, and subsequent corrected calculations found that the cost disappears. He had made an invalid simplifying assumption which negated his assumption of constant population size, and had also incorrectly assumed that two mutations would take twice as long to reach fixation as one, while sexual recombination means that two can be selected simultaneously so that both reach fixation more quickly.
Excerpt from a recent MedicalXpress article (Fate of new genes cannot be predicted, September 13, 2013):
…[T]he research team addressed the probability of fixation of a beneficial allele in the population, i.e., to have all individuals of the population carrying the new allele. They repeated the competition experiments between the two same lines of C. elegans, but this time used an initial higher number of invading individuals, to mimic a population in which the beneficial allele was already established. The researchers observed that the adaptive value of each allele, i.e., whether it behaves as beneficial or deleterious, depended on its frequency in the population. If its frequency was higher than 5% (when more than five different individuals in a population of 100 individuals), the allele was perceived as deleterious and it started to be eliminated by natural selection. But when the frequency was less than 5%, the allele was beneficial. The result of these complex dynamics is that genetic diversity could be maintained indefinitely, without one allele or the other ever being fixed in the population…
Henrique Teotónio adds: “To our knowledge, this is the first time anyone was able to directly test Haldane’s theory. We have proved it correct for the initial stages, when a new allele appears in a population. But our results show that further empirical work and more theoretical models are required to accurately predict the fate of that allele over long time spans”.
Well, that’s what I’ve dug up. I invite everyone to put in their two cents’ worth. Is Haldane’s dilemma a real one for evolutionists?