Haldane’s Dilemma

Darwin's Finches

Editors Note: This is an extract from an upcoming project. It has been edited slightly to provide context. The introductory paragraph is not part of the project but is added for readability. 

When considering what natural selection can do, it is important to keep in mind that traits are coded for by alleles which make up the genetic code. However, this code is manifested in the phenotype of an organism.  Natural selection, the driving force behind evolutionary dogma is an external force. It is important to keep this in mind.

Often multiple nucleotide triplets, make up an allele, and sometimes multiple alleles are involved in the expression of a trait.  Natural selection does not select for codons. Nor does it directly select for alleles.  Instead, natural selection can only see the whole organism. In other words, natural selection is blind to the genome[1]. It can only see the outward manifestations of the genome. This means that a recessive allele can only be seen by natural selection if it is expressed.  However, even if a recessive phenotype is expressed, it is not acted upon by selection. The only thing acted upon by selection is the whole organism.

As an analogy, consider a dinosaur/bird example.  Suppose that a theropod dinosaur hatched with a mutation that granted it feathers on its forearms. While the feathers would be useless, evolutionists would view this as a step along the evolutionary pathway to birds and indeed argue for feathered theropods regularly in the literature[2]. Would those feathers be passed on in the theropod population? For this to happen, the theropod would need to reach adulthood, which is not guaranteed. Even today, only 32% of juvenile lizards survive from one year to the next[3].  Assuming that a similar rate applies to juvenile theropods, we can determine the likelihood of our feathered theropod surviving to maturity. Tyrannosaurus rex took eighteen years to reach sexual maturity[4]. Therefore if our feathered theropod had a similar age of maturity, it had a very small chance of reaching maturity. Working the math gives us odds of 1.238×10-9 for our one feathered theropod to survive to maturity. That is less than one-thousandth of one percent.

Even if our feathered theropod were to reach maturity, which is incredibly unlikely, there is an additional problem. Genetics dictates that his gene for feathers is almost guaranteed to be recessive because it is a mutation[5].  This means that even if he passes on his DNA successfully, none of his offspring will exhibit the feathered phenotype. He is the first feathered dinosaur after all. No other theropod has the gene yet. And his offspring must go through the same gauntlet he did to reach maturity. The new gene has a much greater likelihood of simply vanishing from existence due to all its carriers dying off. Selection is blind to the gene for feathers. All it can see is the organisms complete phenotype. When the gene is not manifest, selection ignores it. Even if we give evolution the benefit of the doubt and say that the gene for feathers is slightly beneficial and dominant, only half of our example theropod’s offspring will have it, and they are in no way guaranteed to be as lucky as their forefather. This is what natural selection is conservative. New traits do not tend to fare well in populations, at least in terms of establishing them.

It turns out the example I just presented is incredibly simplistic. The truth is much more complicated.  Most traits are coded for by multiple genes. “Variation in human skin color is clearly a multifactorial trait with a number of major gene determinants, several modifier genes, and environmental influences such as exposure to UV irradiation and gender effects[6].” As another example, at least eleven different genes are involved in hair color[7].  More than a single change is needed to alter a trait.

This feeds into something known as Haldane’s dilemma. Named for the man who formulated it, Haldane’s dilemma refers to something called the “cost of substitution”. What this means is that when a new gene arises as in our feathered theropod example, it must spread into the population for evolution to proceed. This, of course, requires reproduction. The time involved represents the “cost” of “substituting” the new gene for the old ones. For organisms with a rapid reproductive rate, the cost is lower than it is for organisms with a slower reproductive rate.   However, regardless of the reproductive rate, this process will be slow[8]. Haldane wrote: “But even if enough modifiers were available, the selection of, say, ten modifiers which between them caused a previously dominant mutant to become recessive, would involve the death of a number of individuals equal to about 300 generations of the species concerned. Even the geological time scale is too short for such processes to go on in respect of thousands of loci[9].”  This is why Haldane’s dilemma was such a problem: there was not enough time for evolution to work using mutations, which Haldane acknowledged.

The evolutionists insist that Haldane’s Dilemma has been solved. They point to a paper published about a decade later by Kimura which claimed that most molecular evolution is neutral and thus the cost of substitution does not apply[10]. However, even neutral mutations carry costs with them[11]. While they may have no impact on the reproductive success of the organism, neutral mutations still represent a missed opportunity in time for the evolutionary process. This is because evolution does not have an infinite number of mutations available to it. Each mutation takes place in time. If it is neutral or deleterious, it is a missed opportunity to move up the evolutionary tree of life.

Worse, as Dr. John Sanford has shown, selection has multiple costs that must be paid prior to selection and they are additive[12]! Think back to our feathered dinosaur example. Just reaching adulthood is a significant reproductive cost. Only roughly one in three lizard hatchlings makes it from year to year. That means lizards must have many babies just to perpetuate their lineage, let alone have selection act on them. There are other selection costs as well, all of which must be paid upfront before any selection can happen[13].

This is incredibly significant. It puts a timeline on how long natural selection has to work. Further, it puts population size and reproductive rate restrictions on selection.  Natural selection has much less potential to work with than evolutionists seem to believe.

Do you know what’s going to happen when you die? Are you completely sure? If you aren’t, please read this or listen to this. You can know where you will spend eternity. If you have questions, please feel free to contact us, we’d love to talk to you.


[1] John C. Sandford Genetic Entropy New York: Feed My Sheep Publications, 2005.  

[2] Xing Xu et al “Mosaic evolution in an asymmetrically feathered troodontid dinosaur with transitional features.” Nature Communications 8, no. 14972 (2017) https://www.nature.com/articles/ncomms14972?origin=ppub

[3] David A. Pike et al “Estimating Survival Rates of Uncatchable Animals: The Myth of High Juvenile Mortality in Reptiles” Ecology 89. No. 3 (2008) 607-611, https://researchonline.jcu.edu.au/26750/1/Pike_et_al_2008_Ecology.pdf

[4] Andrew H. Lee and Sarah Werning “Sexual maturity in growing dinosaurs does not fit reptilian growth models.” Proceedings of the National Academy of Sciences 105, no. 2 (2008) 582-587, https://www.pnas.org/content/105/2/582

[5] Brian Oliver and Michael Parisi “Battle of the Xs” BioEssays 26 (2004) 543-548, https://onlinelibrary.wiley.com/doi/pdf/10.1002/bies.20034

[6] Richard A. Sturm, Neil F. Box and Michele Ramsay “Human pigmentation genetics: the difference is only skin deep.” BioEssays 20 (1998) 712-721, http://citeseerx.ist.psu.edu/viewdoc/download?doi=

[7]Manfred Kayser et al “Model-Based prediction of human hair color using DNA variants” Human Genetics 129 (2011) 443-454, https://link.springer.com/article/10.1007/s00439-010-0939-8.

[8] Don Batten “Haldane’s dilemma has not been solved.” Journal of Cration 19, no. 1 (2005) 20-21, https://creation.com/haldanes-dilemma-has-not-been-solved.

[9] J.B.S. Haldane “The Cost of Natural Selection” Journal of Genetics 55, (1957) https://www.ias.ac.in/article/fulltext/jgen/055/03/0511-0524

[10] Motoo Kimura “Evolutionary Rate at the Molecular Level” Nature 217 (1968) 624-626, https://authors.library.caltech.edu/5456/1/hrst.mit.edu/hrs/evolution/public/papers/kimura1968/kimura1968.pdf

[11] Walter J. ReMine “Cost theory and the cost of substitution—a clarification.” Journal of Creation 19, no. 1 (2005) 113-125, https://creation.com/images/pdfs/tj/j19_1/j19_1_113-125.pdf.

[12] Sanford, 2005, 65.

[13] I have only scratched the surface here on how damaging this is to evolution. Read Dr. Sanford’s book Genetic Entropy for a fascinating analysis.


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