Bad takes #3. Mutation bias as an independent cause of adaptation.
To aid in discussion of mutation-biased adaptation, Svensson and Berger (2019) have compiled a highly entertaining list of bad takes on this topic. Their parody of bad Synthesis apologetics begins with a multifarious attack on the strawman 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 continued in 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.
Of course, 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. 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 transitions and transversions that change amino acids hardly differ in their fitness effects. That is, we typically assume, or try to establish, that the mutational biases are orthogonal to fitness.
Svensson and Berger (2019) use irony to make this point, by first (1) attacking us for assuming that the mutation biases align with what is beneficial (above), then (2) objecting to our actual interpretation (orthogonal effects) by arguing that the mutation biases align with what is beneficial:
transitions could be favored over transversions owing to selection on genomic base composition. Selectively beneficial transitions and selectively beneficial transversions could also have different distributions of fitness effects
Clearly, Erik and David have studied their history, because they are calling on a classic strawman that has worked like catnip on Darwin’s followers for over a century. Repeatedly, internalist critics of neo-Darwinian logic have suggested that the observed tendencies or directions of evolutionary change are not all external in origin, i.e., due to selection, but may arise internally from some aspect of mutation or development. In response, the advocates of neo-Darwinism — who have a tendency to equate evolution with adaptation, and thus to equate direction with adaptive direction — have accused these critics of proposing some form of directed mutation or adaptive mutation, or of engaging in mysticism or teleology.
Because this argument has been used by Darwin’s followers 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 persist for generations, this is because they are being used, not to resolve difficult questions, but to maintain conformity within a closed ideological system, i.e., neo-Darwinians use these arguments to help other neo-Darwinians to avoid thinking any uncomfortable thoughts.
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 new ways of thinking is to claim that they are inherently flawed or patently absurd: they do not represent scientific theories to be considered, but errors to be rejected. This is what neo-Darwinians are taught when they are young: 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 them grow up and see a broader slice of the world, and can no longer be shielded from the plausibility of alternative ideas. In this case, the priests of the religion must offer a more sophisticated argument to keep the faithful from straying. 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, anchored by reference to the sacred texts. That is, the doubting Darwinian 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.
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 (i.e., the theory we proposed), insisting that this version of the idea is already part of the Modern Synthesis, though of course they cannot identify any classic Synthesis sources, because the theory was not formally proposed until 2001. The easter egg in their derivation in Box 1 is that, although they name Haldane, Kimura, and Fisher — giving readers the impression that famous dead people developed the theory —, the crucial mathematical equation (representing mutation-biased adaptation) is introduced with a citation number in brackets that quietly points to the actual source of the theory, a 2001 paper by non-dead, non-famous authors.
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.
- We have long known (Bad Takes #1)
- Mutation pressure (Bad Takes #2)
- Independent cause of adaptation (Bad Takes #3)
- Mutation-driven (Bad Takes #4)
- Contingency (Bad Takes #5)
Gould SJ. 2002. The Structure of Evolutionary Theory. Cambridge, Massachusetts: Harvard University Press.