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Haldane's dilemma is a limit on the speed of beneficial evolution, first calculated by J. B. S. Haldane in 1957, and clarified further by later commentators. Creationists, and proponents of intelligent design in particular, claim it remains unresolved. Today, Haldane's Dilemma is raised mostly by creationists opposed to evolution, who claim it is evidence against large-scale evolution, and a supposed example of negligence on the part of the scientific community.
Though the scientific community in general no longer regards Haldane's Dilemma as a problem, there remains little clarity as to how it became dismissed, and as recently as 1992 the issue was still regarded as a challenge by evolutionary biologists. 
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.
In the introduction to The Cost of Natural Selection Haldane writes that it is difficult for breeders to simultaneously select all the desired qualities, partly because the required genes may not be found together in the stock; but, writes Haldane (p. 511),
especially in slowly breeding animals such as cattle, one cannot cull even half the females, even though only one in a hundred of them combines the various qualities desired.
That is, the problem for the cattle breeder is that keeping only the specimens with the desired qualities will lower the reproductive capability too much to keep a useful breeding stock.
Haldane states that this same problem arises with respect to natural selection. Characters that are positively correlated at one time may be negatively correlated at a later time, so simultaneous optimisation of more than one character is a problem also in nature. And, as Haldane writes (loc. cit.)
[i]n this paper I shall try to make quantitative the fairly obvious statement that natural selection cannot occur with great intensity for a number of characters at once unless they happen to be controlled by the same genes.
In faster breeding species there is less of a problem. Haldane mentions (loc. cit.) the peppered moth, Biston betularia, whose variation in pigmentation is determined by several alleles at a single gene. One of these alleles, "C", is dominant to all the others, and any CC or Cx moths are dark (where "x" is any other allele). Another allele, "c", is recessive to all the others, and cc moths are light. Against the originally pale lichens the darker moths were easier for birds to pick out, but in areas, where pollution has darkened the lichens, the cc moths had become rare. Haldane mentions that in a single day the frequency of cc moths might be halved.
Another potential problem is that if "ten other independently inherited characters had been subject to selection of the same intensity as that for colour, only , or one in 1024, of the original genotype would have survived." The species would most likely have become extinct; but it might well survive ten other selective periods of comparable selectivity, if they happened in different centuries.
Haldane proceeds to define (op. cit. p. 512) the intensity of selection regarding "juvenile survival" (that is, survival to reproductive age) as , where is the quotient of those with the optimal genotype (or genotype) that survive to reproduce, and is the quotient for the entire population. The quotient of deaths for the entire population would have been , if all genotypes had survived as well as the optimal, hence is the quotient of deaths due to selection. As Haldane mentions, if , then – since ln(1) = 0.
At p. 514 Haldane writes
I shall investigate the following case mathematically. A population is in equilibrium under selection and mutation. One or more genes are rare because their appearance by mutation is balanced by natural selection. A sudden change occurs in the environment, for example, pollution by smoke, a change of climate, the introduction of a new food source, predator, or pathogen, and above all migration to a new habitat. It will be shown later that the general conclusions are not affected if the change is slow. The species is less adapted to the new environment, and its reproductive capacity is lowered. It is gradually improved as a result of natural selection. But meanwhile, a number of deaths, or their equivalents in lowered fertility, have occurred. If selection at the selected locus is responsible for of these deaths in any generation the reproductive capacity of the species will be of that of the optimal genotype, or nearly, if every is small. Thus the intensity of selection approximates to .
Comparing to the above, we have that , if we say that is the quotient of deaths for the selected locus and is again the quotient of deaths for the entire population.
The problem statement is therefore that the genes (actually alleles) in question are not particularly beneficial under the previous circumstances; but a change in environment favours these genes by natural selection. The individuals without the genes are therefore disfavored, and the favourable genes spread in the population by the death (or lowered fertility) of the individuals without the genes. Note that Haldane's model as stated here allows for more than one gene to move towards fixation at a time; but each such will add to the cost of substitution.
The total cost of substitution of the gene is the sum of all values of over all generations of selection; that is, until fixation of the gene. Haldane states (loc. cit.) that he will show that depends mainly on , the small frequency of the gene in question, as selection begins – that is, at the time that the environmental change occurs (or begins to occur).
A mathematical model of the cost of diploids
Let A and a be two alleles with frequencies and in the generation. Their relative fitness is given by (cf. op. cit. p. 516)
Genotype AA Aa aa Frequency Fitness 1
where 0 ≤ ≤ 1, and 0 ≤ λ ≤ 1.
If λ = 0, then Aa has the same fitness as AA, e.g. if Aa is phenotypically equivalent with AA (A dominant), and if λ = 1, then Aa has the same fitness as aa, e.g. if Aa is phenotypically equivalent with aa (A recessive). In general λ indicates how close in fitness Aa is to aa.
The fraction of selective deaths in the generation then is
and the total number of deaths is the population size multiplied by
Important number 300
Haldane (op. cit. p. 517) approximates the above equation by taking the continuum limit of the above equation. This is done by multiplying and dividing it by dq so that it is in integral form
substituting q=1-p, the cost (given by the total number of deaths, 'D', required to make a substitution) is given by
Assuming λ < 1, this gives
where the last approximation assumes to be small.
If λ = 1, then we have
In his discussion Haldane writes (op. cit. p. 520) that the substitution cost, if it is paid by juvenile deaths, "usually involves a number of deaths equal to about 10 or 20 times the number in a generation" – the minimum being the population size (= "the number in a generation") and rarely being 100 times that number. Haldane assumes 30 to be the mean value.
Assuming substitution of genes to take place slowly, one gene at a time over n generations, the fitness of the species will fall below the optimum (achieved when the substitution is complete) by a factor of about 30/n, so long as this is small – small enough to prevent extinction. Haldane doubts that high intensities – such as in the case of the peppered moth – have occurred frequently and estimates that a value of n = 300 is a probable number of generations. This gives a selection intensity of .
Haldane then continues (op. cit. p. 521):
The number of loci in a vertebrate species has been estimated at about 40,000. 'Good' species, even when closely related, may differ at several thousand loci, even if the differences at most of them are very slight. But it takes as many deaths, or their equivalents, to replace a gene by one producing a barely distinguishable phenotype as by one producing a very different one. If two species differ at 1000 loci, and the mean rate of gene substitution, as has been suggested, is one per 300 generations, it will take 300,000 generations to generate an interspecific difference. It may take a good deal more, for if an allele a1 is replaced by a10, the population may pass through stages where the commonest genotype is a1a1, a2a2, a3a3, and so on, successively, the various alleles in turn giving maximal fitness in the existing environment and the residual environment.
The number 300 of generations is a conservative estimate for a slowly evolving species not at the brink of extinction by Haldane's calculation. For a difference of at least 1,000 genes, 300,000 generations might be needed – maybe more, if some gene runs through more than one optimisation.
Origin of the term "Haldane's Dilemma"
Apparently the first use of the term "Haldane's Dilemma" was by palaeontologist Leigh Van Valen in his 1963 paper "Haldane's Dilemma, Evolutionary Rates, and Heterosis".
At p. 185 Van Valen writes:
Haldane (1957 [= The Cost of Natural Selection]) drew attention to the fact that in the process of the evolutionary substitution of one allele for another, at any intensity of selection and no matter how slight the importance of the locus, a substantial number of individuals would usually be lost because they did not already possess the new allele. Kimura (1960, 1961) has referred to this loss as the substitutional (or evolutional) load, but because it necessarily involves either a completely new mutation or (more usually) previous change in the environment or the genome, I like to think of it as a dilemma for the population: for most organisms, rapid turnover in a few genes precludes rapid turnover in the others. A corollary of this is that, if an environmental change occurs that necessitates the rather rapid replacement of several genes if a population is to survive, the population becomes extinct.
That is, since a high number of deaths are required to fix one gene rapidly, and dead organisms do not reproduce, fixation of more than one gene simultaneously would conflict. Note that Haldane's model assumes independence of genes at different loci; if the selection intensity is 0.1 for each gene moving towards fixation, and there are N such genes, then the reproductive capacity of the species will be lowered to 0.9N times the original capacity. Therefore, if it is necessary for the population to fix more than one gene, it may not have reproductive capacity to counter the deaths.
- Williams, George (July 1993). "Natural selection: Domains, levels and challenges.". American Journal of Physical Anthropology 91 (3): 397–398. doi:10.1002/ajpa.1330910317. Retrieved 20 January 2014.
- "CB121: Haldane's Dilemma". TalkOrigins Archive. Retrieved 3 November 2008.
- Robert Williams. "Haldane's Dilemma". Retrieved 3 November 2008.
- Ian Musgrave. "The Talk.Origins Archive Post of the Month: September 1999". Retrieved 3 November 2008.
- Majerus, M.E.N. (1998) Melanism: Evolution in Action. Oxford University Press, New York.
- 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 from Haldane's low substitution limit except in certain limited situations).