Fossil Friday: Walking Whales and Why All Critiques of the Waiting Time Problem Fail
Günter Bechly
This Fossil Friday features the reconstructed skeletons of Pakicetus (below) and Ambulocetus (above), which are so-called “walking whales” from the Eocene of Pakistan. These fossils are often celebrated as missing links and a success story for Darwinism. However, they indeed create a fatal problem for neo-Darwinism, which is known as the waiting time problem. The general problem is that the window of time established by the fossil record for the transition from “walking whales” to fully marine whales is orders of magnitude too short to accommodate the waiting times for the origin and spread of the required genetic changes, based on the standard mathematical framework of population genetics. This problem has been elaborated in a popular way in several publications of the ID community (Meyer 2013, Evolution News 2016, LeMaster 2018), and in the Illustra Media documentary Living Waters.
An Ongoing Multidisciplinary Research Project
The waiting time problem is the subject of an ongoing multidisciplinary research project funded by Discovery Institute. We have already published the theoretical ground work in two peer-reviewed papers in mainstream science outlets (Hössjer et al. 2018, 2021). An application on the example of whale origins is forthcoming by Bechly et al. (in prep.).
The waiting time problem has been the target of scornful critique by anti-ID spokesmen (e.g., Moran 2016, Rasmussen 2021, Stern-Cardinale 2022, Farina 2022), who claimed that it is fallacious and fails to challenge Darwinism. We will address this critique in great detail in our forthcoming technical paper, but let me here briefly refute the main points for a lay audience so that you are equipped for eventual debates.
Reviewing the Main Points
1.) Critics often explicitly or implicitly suggest that the waiting time problem is a pseudo-problem invented by evil and stupid creationists. This is a silly and embarrassingly incompetent argument, which only shows that these critics have not only failed to grasp the problem, but also seem to be totally unaware that the waiting time problem has a long history and has been much discussed in mainstream science (especially population genetics). It even plays an important role in cancer research. They should talk to Harvard professor Martin Nowak, who is an evolutionary biologist and expert on the waiting time problem. Here are just a few references of renowned scientists publishing about this “crazy stuff” as Farina (2022) calls it: Bodmer (1970), Karlin (1973), Christiansen et al. (1998), Schweinsberg (2008), Durrett et al. (2009), Behrens et al. (2012), and Chatterjee et al. (2014). It was not before Behe & Snoke (2004, 2005) and Behe (2007, 2009) that the waiting time problem was recognized as an argument for intelligent design. Durrett & Schmidt (2008) attempted to refute Behe but arrived at a prohibitive waiting time of 216 million years for a single coordinated mutation in human evolution, while only about 6 million years are available since the origin of the human lineage from a common ancestor with chimps. Behe arrived at 1015 years by using empirical data about an actual waiting time for a coordinated mutation that conveyed chloroquine drug resistance in malaria. He simply transposed these empirical findings on humans, considering their much lower population size and much longer generation time. Durrett & Schmidt’s result was based on a mathematical model, which of course must make certain simplifications that can introduce errors. When such model calculations conflict with hard empirical data, we should trust the empirical data as pointing closer to the truth. Anyway, both numbers are prohibitive and refute the feasibility of a Darwinian mechanism of macroevolution.
2.) Most critics considered the most powerful objection to be the “Texas sharpshooter fallacy.” They claimed that nature does not go for specific mutations as a target but is totally random. This argument fails because it presupposes the existence of many targets, which is contradicted by the rarity of function in the search space for proteins and by the common phenomenon of convergence. The argument also fails to recognize that life cannot allow for periods of maladaptation only to descend a local peak of the fitness landscape to explore other ones. Instead, life has to further adapt to its local fitness peak, which requires specific solutions for specific problems. It’s not like any beneficial mutation could do. A stem whale would have no use for a mutation that would be beneficial for a stem bird, such as improving skeletal pneumaticity. In the computer models applied in our publications on the waiting time problem we also allowed for alternative targets and fuzzy targets, so not just one pre-specified binding site, which prevents another possible critique.
3.) Some critics failed to grasp the concept of coordinated mutations and even called it meaningless. They suggested that every individual mutation can be selected for. This shows that they did not get the simple point that in coordinated mutations each individual mutation is neutral and thus in principle cannot be selected for. Only the combination of coordinated mutations has a selection value, which is the whole point, and the reason why they were called “coordinated mutations” in the first place.
4.) Some critics claim that the waiting time problem implies that mutations have to occur in a specific sequence. This is simply false and maybe based on a misunderstanding of the technical term “coordinate gene.” The fact is that no ID proponent ever claimed that the waiting time problem only applies for particular sequences of mutations. For any set of reasonable parameters, the waiting times for coordinated mutations (i.e., mutations that have to occur together to have a selection value) will be prohibitive, irrespective of the order of these mutations. What is true is that the waiting time problem gets even worse when such mutations also have to occur in a specific sequence.
5.) Critics also claimed that the waiting time problem ignores recombination, which according to Farina (2022) “baselessly discounts the profound evolutionary benefit” and is “dramatically accelerating the accumulation of beneficial mutations.” This shows how ignorant the critics are of the actual technical literature, because the influence of recombination of the waiting time problem has been studied by Christiansen et al. (1998), who have shown that: “Recombination lowers the waiting time until a new genotypic combination first appears, but the effect is small [my emphasis] compared to that of the mutation rate and population size.” In our papers (Hössjer et al. 2018, 2021, Bechly et al. in prep.) we show that recombination does not affect the waiting time under realistic assumptions for parameters like mutation rates and population sizes.
6.) Critics also claim that the problem is merely theoretical but not realistic in biological terms, e.g., because it does not apply to concrete examples or because coordinated mutations are not necessary. We will address the latter claim very thoroughly in our forthcoming paper, where we do apply the theoretical framework to the concrete example of whale origins. We will also show, based on mainstream evo-devo data, that coordinated mutations indeed are required. This is also suggested by the fact that even simple characters like skin color turned out to be highly polygenic, thus controlled by many different genes. By the way: The waiting time problem has also been applied to the concrete example of human origins by Durrett & Schmidt (2008) and Sanford et al. (2015) with prohibitive results for Darwinian evolution.
And Finally
Last but not least, some critics were puzzled by how papers by ID proponents on the waiting time problem could somehow make it into peer-reviewed journals like the prestigious Journal of Theoretical Biology. Well, that’s easy: because it is good peer-reviewed science and the usual censorship of the Darwinist mafia sometimes fails to sabotage the publication of inconvenient research, even though they always try very hard. It is the height of hypocrisy when the very same people turn around and claim that ID proponents don’t publish their stuff in the peer reviewed literature. Darwinists, as is well known, love to play the game of “Heads I win, tail you lose.”
References
Behrens S, Nicaud C & Nicodéme P 2012. An automaton approach for waiting times in DNA evolution. Journal of Computational Biology 19(5), 550–562. DOI: https://doi.org/10.1089/cmb.2011.0218
Behe MJ 2007. The Edge of Evolution. Free Press, New York (NY), 336 pp.
Behe M 2009. Waiting Longer for Two Mutations. Genetics 181(2), 819–820. DOI: https://doi.org/10.1534/genetics.108.098905
Behe MJ & Snoke DW 2004. Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Science 13(10), 2651–2664. DOI: https://doi.org/10.1110/ps.04802904
Behe MJ & Snoke DW 2005. A response to Michael Lynch. Protein Science 14(9), 2226–2227. DOI: https://doi.org/10.1110/ps.051674105
Bodmer WF 1970. The evolutionary significance of recombination in prokaryotes. Symposium of the Society for General Microbiology 20, 279–294.
Chatterjee K, Pavlogiannis A, Adlam B & Nowak MA 2014. The time scale of evolutionary innovation. PLoS Computional Biology 10(9):d1003818, 1–7. DOI: https://doi.org/10.1371/journal.pcbi.1003818
Christiansen FB, Otto SP, Bergman A & Feldman MW 1998. Waiting with and without Recombination: The Time to Production of a Double Mutant. Theoretical Population Biology53(3), 199–215. DOI: https://doi.org/10.1006/tpbi.1997.1358
Durrett R & Schmidt D 2008. Waiting for two mutations: with applications to regulatory sequence evolution and the limits of Darwinian evolution. Genetics 180(3), 1501–1509. DOI: https://doi.org/10.1534/genetics.107.082610
Durrett R, Schmidt D & Schweinsberg J 2009. A waiting time problem arising from the study of multi-stage carcinogenesis. Annals of Applied Probability 19(2), 676–718. DOI: https://doi.org/10.1214/08-AAP559
Farina D 2022. Exposing the Discovery Institute Part 2: Stephen Meyer. Professor Dave Explains May 13, 2022. https://youtu.be/Akv0TZI985U
Hössjer O, Bechly G & Gauger A 2018. Phase-type distribution approximations of the waiting time until coordinated mutations get fixed in a population. Chapter 12, pp. 245–313 in: Silvestrov S, Malyarenko A & Rancic M (eds). Stochastic Processes and Algebraic Structures – From Theory Towards Applications. Volume 1: Stochastic Processes and Applications. Springer Proceedings in Mathematics and Statistics 271. DOI: 10.1007/978-3-030-02825-1_12
Hössjer O, Bechly G & Gauger A 2021. On the waiting time until coordinated mutations get fixed in regulatory sequences. Journal of Theoretical Biology 524:110657, 1–37. DOI: https://doi.org/10.1016/j.jtbi.2021.110657
Karlin S 1973. Sex and infinity: A mathematical analysis of the advantages and disadvantages of genetic recombination. pp. 155–194 in: Bartlett MS & Hiorns RW (eds). The Mathematical Theory of the Dynamics of Biological Populations. Academic Press, New York (NY), xii+347 pp.
LeMaster JC 2018. Evolution’s waiting-time problem and suggested ways to overcome it—A critical survey. BIO-Complexity 2018(2), 1–9. DOI: https://doi.org/10.5048/BIO-C.2018.2
Meyer SC 2013a. Darwin’s Doubt. HarperOne, New York (NY), viii+498 pp.
Moran L 2016. Targets, arrows, and the lottery fallacy. Sandwalk Jan. 14, 2016. https://sandwalk.blogspot.com/2016/01/targets-arrows-and-lottery-fallacy.html
Rasmussen MN 2021. Waiting Time Problem” and imaginary hurdles for evolution. Pandas Thumb June 12, 2021. https://pandasthumb.org/archives/2021/06/ID-and-imaginary-hurdles.html
Sanford J, Brewer W, Smith F & Baumgardner J 2015. The waiting time problem in a model hominin population. Theoretical Biology and Medical Modelling 12:18, 1–18. DOI: https://doi.org/10.1186/s12976-015-0016-z
Schweinsberg J 2008. The waiting time for m mutations. Electronic Journal of Probability13, 1442–1478. DOI: https://doi.org/10.1214/EJP.v13-540
Stern-Cardinale D 2022. Creation Myth: The “Waiting Time Problem” Creation MythsFebruary 15, 2022. https://youtu.be/F748itCI_es
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