Bad takes #3. Mutation bias as an independent cause of adaptation.
Unfamiliar ideas are often mis-identified and mis-characterized. It takes time for a new idea to be sufficiently familiar that it can be debated meaningfully. We look forward to those more meaningful debates. Until then, fending off bad takes is the order of the day! See the Bad Takes Index.
Svensson and Berger (2019) begin their opinion piece with a multifarious attack on the theory that mutation bias is “adaptive in its own right” or “an independent force” or something that “can explain the origin of adaptations independently of, or in addition to, natural selection.” They enthusiastically invoke versions of this theory in 5 different places, just on the first page (yellow highlights)!
They associate this theory with the line of argument on mutation bias and adaptation developed in work from my group (e.g., Yampolsky and Stoltzfus, 2001; Stoltzfus, 2006a, 2006b, 2012, 2019), and extended by studies such as:
- Sackman, et al. 2017. Mutation-Driven Parallel Evolution During Viral Adaptation. Mol Biol Evol.
- Storz, et al. 2019. The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function. Philos Trans R Soc Lond B Biol Sci 374:20180238.
- Gomez, et al. 2020. Mutation bias can shape adaptation in large asexual populations experiencing clonal interference. Proc. R. Soc. B. 287:20201503.
- Cano AV, Payne JL. 2020. Mutation bias interacts with composition bias to influence adaptive evolution. PLOS Computational Biology 16:e1008296.
None of these sources promote or assume a theory of mutation bias as an independent cause of adaptation, or a theory of mutation being adaptive in its own right. For instance, in the original twin-peaks model of Yampolsky and Stoltzfus (2001), the peak favored by the higher selection coefficient is accessible only via a lower mutation rate, and vice versa. Stoltzfus and Norris (2015) worked very hard to establish that— contrary to lore— transitions and transversions that change amino acids hardly differ in their fitness effects.
Thus, whereas some other authors have promoted the idea of adaptive mutation (e.g., Cairns, Caporale, Rosenberg), “natural genetic engineering” (Shapiro) or merely some statistical correlations between mutational patterns and fitness effects (Monroe, et al. 2022), the above sources do none of those things. Thus, Svensson and Berger (2019) are illustrating the concept of a strawman argument, criticizing an alternative view by relying on a false representation of that view.
This form of this strawman argument has a long history. Repeatedly, critics of neo-Darwinism have suggested that observed tendencies or directions of evolutionary change cannot be explained solely by selection, but reflect internal aspects of mutation or development, and advocates of neo-Darwinism have responded by accusing these critics of proposing some form of directed mutation or adaptive mutation, or of engaging in mysticism or teleology. Is this simply a case of intellectual dishonesty? Perhaps, but a more sympathetic view is that this is an error in reasoning induced by an ideology that recognizes only one kind of directionality, so that every argument about directions (e.g., in phenotype space) is treated as an argument about intrinsically adaptive directions.
Because Darwin’s followers have used this strawman argument for over a century, we know how the advocates of internalist theories respond:
I take exception here only to the implication that a definite variation tendency must be considered to be teleological because it is not ‘orderless.’ I venture to assert that variation is sometimes orderly and at other times rather disorderly, and that the one is just as free from teleology as the other. In our aversion to the old teleology, so effectually banished from science by Darwin, we should not forget that the world is full of order . . . If a designer sets limits to variation in order to reach a definite end, the direction of events is teleological; but if organization and the laws of development exclude some lines of variation and favor others, there is certainly nothing supernatural in this” (Whitman, 1919: see p. 385 of Gould, 2002)
In general, when we find that false arguments are maintained and nurtured for generations, this is because they are being used, not to resolve substantive scientific questions, but to maintain conformity within a closed ideological system, i.e., advocates of neo-Darwinism use these arguments to help each other avoid thinking any new thoughts, working together to keep the dream alive. Gatekeepers like Svensson and Berger try to discourage new thinking by treating it as bad science and careerism (in this case, with ironic results).
Of course, we must not confuse theories and people, e.g., a theory supported by bad arguments does not become a bad theory for this reason. The theory and its apologetics are two different things. We can define neo-Darwinism clearly in terms of the dichotomy of the potter (selection) and the clay (variation), and this concept stands by itself. Separate from this, there is a culture or a set of rhetorical practices associated with neo-Darwinian apologetics. It is this neo-Darwinian culture or thought-collective that has a sociological aspect and a self-protective urge that gives rise to the same pathologies as any cult or identity-group.
The false accusations of teleology or directed mutation are part of the conceptual immune system of the neo-Darwinian thought-collective (described in a separate post). This kind of strawman is used in two ways. The first line of defense against alternative views is to claim that they are inherently flawed or absurd: they represent mental errors that can be dismissed immediately, not alternative scientific theories that must be evaluated with research. This is what neo-Darwinians teach about history: the neo-Darwinian view is simply the rational evidence-based approach to evolution, whereas critics behave irrationally and hold views with obvious flaws.
Eventually, however, some of the more intellectually rigorous ones begin to sense that scientific theories are supposed to stand for something substantive and risky, and they begin to consider the plausibility of alternative ideas. In this case, the priests of the religion must offer a more sophisticated argument. In this second line of defense, the alternative is granted as a theoretical possibility, but (1) its importance is minimized, and (2) it is described in different language and grounded in the Darwinian faith tradition itself, by reference to obscure passages in the sacred texts. That is, the doubter is shown that the apostles and disciples of olden times, and even the great Lord Darwin himself, also experienced moments of doubt, posed difficult questions, and considered alternative views. The initiate now has a more sophisticated understanding of the faith, which does not demand inner purity, but merely outward piety. In this case, the faith is shown by creating constructive ambiguity that can be used to shift the focus of discussion from new scientific developments backwards to tradition and to the pantheon of heroes.
Svensson and Berger (2019) illustrate both strategies brilliantly. First they attack claims of mutation-biased adaptation by attacking the straw-man of “independent cause of adaptation,” then they present a more reasonable idea based on population genetics— a butchered version of the theory proposed by Yampolsky and Stoltzfus (2001)—, and present this as conventional wisdom. First they state absurdly that the theory is part of the neutral theory— which in their strangely twisted conception of history was somehow swallowed up by the Modern Synthesis— but they cite no source for this, e.g., the theory of Yampolsky and Stoltzfus (2001) appears nowhere in Kimura’s (1983) seminal book on the neutral theory. They also present a derivation of a key equation in Box 1, which gives a short series of mathematical results and names Haldane, Kimura, and Fisher without naming Yampolsky and Stoltzfus, guiding the reader to conclude falsely that the theory comes from famous dead people.
However, at the same that they appropriate the theory on behalf of Fisher, et al., they also purport to undermine it by claiming that it depends on unusual conditions including sign epistasis and drift in small populations (these are not actual requirements, but fabrications intended to make the argument seem more respectable).
For more bad takes on this topic
This is part of a series of posts focusing on bad takes on the topic of biases in the introduction of variation, covering both the theory and the evidence. For more bad takes, see the index to bad takes.
Gould SJ. 2002. The Structure of Evolutionary Theory. Cambridge, Massachusetts: Harvard University Press.