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Mechanism of Evolution?

We know from the fossil record that there has over time been a steady stream of differently shaped animals that evolved over time. When you point out a specific case of a species that transitioned into another, the intelligent design proponent says that this could not have happened naturally without a guiding intelligence:

If you think this species came from that other species, then tell me the exact mechanism that caused a genes to change in this manner.

I find this demand disingenuous for a number of reasons.

Perfect Knowledge or Nothing​

The apologist would like you believe that if knowledge is false unless it is complete down to the molecular level.

When Sherlock Holmes solves a crime, he takes all the clues (evidence) and picks from several available theories the one that best matches all the facts. The suspect left finger prints at the scene of the crime at about the time it was happening, and so on. There may be many more facts about the situation that are unknown: did the suspect wear a hat? or a ski mask? Had he eaten a meal before? Untold mountains of possible facts that we simply don't know. None of that matters, instead what matters is that the available facts all match the theory.

Can Sherlock every change his mind? Of course, a new fact might be discovered and that might make another theory the best fit. That is always the case with science: new data might change the consensus. But we do what we can with the available evidence.

The study of ancient animal species is a lot like a Sherlock Holmes investigation, except that thousands of paleontologiests have compiled millions of piece of evidence all leading to one main conclusion: evolution, along with many detailed aspects that are still being refined.

The apologist here is insisting that if we know that dinosaurs evolved into birds, then we should be able to cite the exact DNA sequence, and exactly what caused it to change. We don't know the exact DNA sequence for dinosaurs because DNA does not survive fossilization. Even if we did, there might be thousands of changes, and we can't say exactly how each change occurred. We are talking about millions of years of evolution, and millions of generations. To map out each exact generation is far beyond our capabilities.

Best Fit is Good Enough​

The apologist says that if knowledge is not perfect, then you are using faith to believe science.

I can tell you that a river flows downhill. We can clearly see this from observations. If I ask you by what mechanism does gravity cause a river flow downhill? There’s no answer for this. By what mechanism does gravity cause a rock to fall to the ground?

I recognize the question is valid on some level: we would like to know more about exactly how this happens. You also well know that we haven’t figured the entire universe out to every micro level. We are far from understanding the complete history of the universe in detail. We can’t even say how the body forms from genes, but we know it does. No matter what answer I give you’ll always be able to ask the question “by what mechanism did that happen?” Eventually, we get to a level that we don’t know and I fully expect your response to be “ah ha, you don’t know!”

Because we may not have figured out the exact mechanism that something happens, that doesn’t mean it doesn’t happen. We don’t currently know why people’s noses come out the way they are. We don’t know the exact mechanism by which a baby is formed with five fingers. We’re quite sure that such a mechanism exists in both cases.

I have explained the competitive pressures that would lead to humans acquiring behavior which we call love. Clearly from the fossil record we can’t look at the genes of people from millions of years ago, and even if we could, we’re not at the technical sophistication to be able to explain what each gene does and what a change in such a gene would bring about.

But ultimately, I find the question disingenuous. Evolution supported by millions and millions of fossils and we know that the process works. We know that something exactly like evolution has brought about the wide variety of animals we see on the planet today. These are the facts. But creationist will ask “what was the mechanism?“ At the same time creationist won’t tell us the mechanism by which God created all of the animals. What mechanism turned a rib into a woman? If I were cynical enough, I would ask the same question of them, but I know they have no answers and it was a waste of time.

Essentialism​

Creationists believe in "essentialism" which is that creatures have a special essence that makes them what they are. Dogs have dog essence in them. Cats have cat essence, and so on. While they understand that dogs vary so much in form that in 1000 years you can breed dogs that look entirely different from each other. But they all have dog essence, and therefor can not be related to cats -- even after 100 million years. That is why they say you can not change from one "type" to another, because each type has an essence.

Empirical Evidence for Evolution​

White, W.T.J., Zhong, B., and Penny, D. (2013). Beyond reasonable doubt: Evolution from DNA sequences. PLoS ONE 8, e69924. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069924

  • Sober, E., and Steel, M. (2015). How probable is common ancestry according to different evolutionary processes? J Theor Biol 373, 111-116. https://www.sciencedirect.com/science/article/abs/pii/S0022519315001216

  • Baum, D.A., Ané, C., Larget, B., Solís-Lemus, C., Ho, L.S.T., Boone, P., Drummond, C.P., Bontrager, M., Hunter, S.J., and Saucier, W. (2016). Statistical evidence for common ancestry: Application to primates. Evolution 70, 1354-1363. https://doi.org/10.1111/evo.12934

  • Bontrager, M., Larget, B., Ané, C., and Baum, D. (2016). Statistical Evidence for Common Ancestry: Testing for Signal in Silent Sites. https://doi.org/10.1101/035915

  • Hug, L., Baker, B., Anantharaman, K. et al. A new view of the tree of life. Nat Microbiol 1, 16048 (2016). https://doi.org/10.1038/nmicrobiol.2016.48

  • Weiss, M. C., Sousa, F. L., Mrnjavac, N., Neukirchen, S., Roettger, M., Nelson-Sathi, S., & Martin, W. F. (2016). The physiology and habitat of the last universal common ancestor. In Nature Microbiology (Vol. 1, Issue 9). Springer Science and Business Media LLC. https://doi.org/10.1038/nmicrobiol.2016.116

  • Weiss, M. C., Preiner, M., Xavier, J. C., Zimorski, V., & Martin, W. F. (2018). The last universal common ancestor between ancient Earth chemistry and the onset of genetics. In M. Achtman (Ed.), PLOS Genetics (Vol. 14, Issue 8, p. e1007518). Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1007518

  • Brink, G. van den, de Ridder, J., & Woudenberg, R. van. (2017). The Epistemic Status of Evolutionary Theory. In Theology and Science (Vol. 15, Issue 4, pp. 454–472). Informa UK Limited. https://doi.org/10.1080/14746700.2017.1369759

  • Pagel, M., O’Donovan, C. & Meade, A. General statistical model shows that macroevolutionary patterns and processes are consistent with Darwinian gradualism. Nat Commun 13, 1113 (2022). https://doi.org/10.1038/s41467-022-28595-z

  • Moody, E.R.R., Álvarez-Carretero, S., Mahendrarajah, T.A. et al. The nature of the last universal common ancestor and its impact on the early Earth system. Nat Ecol Evol 8, 1654–1666 (2024) https://doi.org/10.1038/s41559-024-02461-1

  • S. Wehbi, A. Wheeler, B. Morel, N. Manepalli, B.Q. Minh, D.S. Lauretta, J. Masel, Order of amino acid recruitment into the genetic code resolved by last universal common ancestor’s protein domains, Proc. Natl. Acad. Sci. U.S.A., 121 (52) e2410311121 (2024). https://doi.org/10.1073/pnas.2410311121