Reasons to Believe

Historical Contingency and the Improbability of Protein Evolution, Part 2 (of 2)

A few weeks ago, Kathy Emmons of WORD-FM in Pittsburg interviewed me about the connection between human evolution and human trafficking. During the interview, she asked me if theological or scientific concerns drove my skepticism about human evolution. My answer is both.

I find it difficult to reconcile the idea of human evolution with passages in the Old and New Testaments that address human origins. But I also think that there are significant scientific problems confronting the evolutionary paradigm. A recent study by scientists from the Universities of Oregon and Chicago highlights one of those scientific challenges.1

As described in a previous post, these researchers wanted to develop a better understanding of the role that chance historical events play in evolutionary processes. To do this, they reconstructed what they believe to be the evolutionary pathway that led to the emergence of the cortisol-specific glucocorticoid receptor protein, a key component of the vertebrate endocrine system. Based on their reconstruction, it appears that seven amino acid changes transformed the ancestral receptor protein into one that exclusively binds cortisol. They determined that two of the changes were permissive. That is, these changes do not contribute to the binding specificity of the glucocorticoid receptor but must occur before any of the functional changes took place. Based on their analysis, it appears that the permissive changes were highly improbable, leading the researchers to conclude that historical contingency plays a central role in evolutionary transformations.

According to the researchers:

If evolutionary history could be replayed from the ancestral starting point, the same kind of permissive substitutions would be unlikely to occur. The transition to GR’s [glucocorticoid receptor’s] present form and function would likely be inaccessible, and different outcomes would almost certainly ensue. Cortisol-specific signaling might evolve by a different mechanism in the GR   . . . or the vertebrate endocrine system more generally—would be substantially different.2

Historical Contingency

The concept of historical contingency is the theme of the late Stephen Jay Gould’s book Wonderful Life.3 According to this idea, the evolutionary process consists of an extended sequence of unpredictable, chance events. To help clarify this concept, Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.

Gould envisioned historical contingency as primarily resulting from external events (such as climate change or asteroid impacts). But this latest work indicates that the intrinsic complexity of proteins also contributes to historical contingency because of the necessity and low probability of permissive amino acid substitutions that support functional changes.

How Widespread Is Historical Contingency?

The question then becomes, how widely applicable is this result? The research team from the Universities of Oregon and Chicago expressed uncertainty regarding this point, but other studies indicate that historical contingency must play a prominent role in molecular evolution.

For example, the long-term evolution experiment conducted by Richard Lenski’s group at Michigan State University demonstrated that the emergence of citrate metabolism in E. coli under aerobic conditions was historically contingent, predicated on a sequence of chance molecular events. (For more information, see the articles listed under “Resources.”)

Using simulations to monitor the evolution of a protein dubbed argT, researchers from the University of Pennsylvania showed that genetic mutations selected by the evolutionary process are dependent on previous mutations, and over time it becomes increasingly difficult to reverse mutational transformations.4 In other words, an amino acid substitution that occurs in a protein today and is accepted by the evolutionary process would most likely be deleterious if it occurred in the past (because of the central role permissive substitutions play in evolutionary history). Consequently, this mutational change would be selected against by the evolutionary process. One of the researchers involved in this study, Joshua Plotkin, stated,

There is intrinsically a huge amount of contingency in evolution. Whatever mutations happen to come first set the stage for what other later mutations are permissible. Indeed, history channels evolution down a certain path. Gould’s famous tape of life would be very different if replayed, even more different than Gould might have imagined.5

A Failed Prediction of the Evolutionary Paradigm

Because the evolutionary process is historically contingent, it seems unlikely that evolutionary processes would lead to identical or nearly identical outcomes. Yet, when viewed from an evolutionary standpoint, it appears as if repeated evolutionary outcomes have been a common occurrence throughout life’s history. This phenomenon—referred to as convergence—is widespread. Evolutionary biologists Simon Conway Morris and George McGhee point out in their respective books Life’s Solution and Convergent Evolution that identical evolutionary outcomes are a characteristic feature of the biological realm.6 Scientists see these repeated outcomes at the ecological, organismal, biochemical, and genetic levels. In fact, in my book The Cell’s Design, I describe 100 examples of convergence at the biochemical level.

I regard the widespread occurrence of convergence to be one of evolution’s failed predictions and, as I told Kathy Emmons, a justifiable reason to be skeptical of the claim that evolutionary processes can fully explain the history, diversity, and design of life.

In an upcoming blog post, I will further explore the challenge convergence poses for the evolutionary paradigm.

Stay tuned. . . . (Or set your tape player to “record.”)

Resources

Endnotes

  1. Michael Harms and Joseph Thornton, “Historical Contingency and Its Biophysical Basis in Glucocorticoid Receptor Evolution,” Nature 512 (August 2014): 203–7, doi:10.1038/nature13410.
  2. Ibid., 207.
  3. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton & Company, 1990).
  4. Premal Shah, David McCandlish, and Joshua Plotkin, “Contingency and Entrenchment in Protein Evolution under Purifying Selection,” Proceedings of the National Academy of Sciences, USA  112 (June 2015): E3226–E3235, doi:10.1073/pnas.1412933112
  5. University of Pennsylvania, “Evolution Is Unpredictable and Irreversible, Biologists Show,” Science News (blog), ScienceDaily, June 8, 2015, sciencedaily.com/releases/2015/06/150608213032.htm.
  6. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).

Subjects: Biochemistry, Evolution, Proteins, Molecular Evolution