Bad takes #4. Attacking the phrase “mutation-driven.”
(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 links at the bottom.)
In regard to reports of mutational biases influencing the changes involved in molecular adaptation, Svensson and Berger (2019) write
Despite the importance of mutations in these two studies, we emphasize that selection ultimately drove these adaptive allele frequency changes, rather than evolution being ‘mutation-driven’ as some might claim [1,7,8,13].
Actually the “mutation-driven” language is advocated in reference #1 (Nei’s book), but not in the other 3 sources cited.
The authors object that, whereas the term “drive” refers to a cause that drives an allele to fixation, the changes implicated in the cited studies reflect selective fixation rather than fixation by mutation. The implication is that sources 1, 7, 8 and 13 advocate a theory of population transformation, not by reproductive replacement (via selection or drift), but by mutation pressure, i.e., the cumulative effect of many events of mutational conversion, which is generally a bad idea for reasons pointed out by Kimura (1980), although there are rare cases where it makes sense, e.g., loss of a complex character (for a more thorough explanation of evolution by mutation pressure, see Bad take #2).
But of course, fixation by mutation pressure is not the theory advocated in Nei’s 2013 book Mutation-Driven Evolution, nor the other sources cited, nor sources such as:
One must remember that the piece by Svensson and Berger (2019) is not to be taken seriously, but represents a parody of bad Synthesis apologetics — a Sokal’s hoax for evolutionary biology. Here, the authors are parodying a bad-faith argument that does not address any genuine issue of scientific dispute, but is simply a way to score points with the kind of guileless reader who thinks Masatoshi Nei needs a lesson in basic population genetics from the authors.
If we take away the false pretense that Nei and others are advocating evolution by mutation pressure, the remaining issue is semantic: should we (1) restrict “mutation-driven” only to the case in which mutation is a cause of allele fixation, i.e., the mutation pressure theory of evolution, or (2) allow the meaning of “mutation-driven” intended by Nei and others, which is more explanatory, i.e., evolution is mutation-driven to the extent that the explanation for the character and timing of evolutionary change refers to the character and the probability of the underlying mutations.
Which semantic position is justified? The issue is readily resolved by examining how “drive” is used in evolutionary discourse. Does the literature of evolutionary biology include a meaning of “driven” that would justify the use of “mutation-driven”?
In fact, a generic explanatory meaning for “drive” is well established, e.g., here is just a tiny sample of recent uses from the technical literature:
- “Effective Population Size Drives Model State-Space Selection” (section heading)
- “Epistasis between antibiotic resistance mutations drives the evolution of extensively drug-resistant tuberculosis” (title)
- “Population growth as a driver of initial domestication in Eastern North America.” (title)
- “There is a growing appreciation of the role that the biophysical properties of protein stability, aggregation and degradation have in fitness and disease. Moreover, these properties have been identified as significant factors in many cases of adaptive and compensatory evolution. These properties — and not function — seem to be the forces driving much of protein evolution.” (text from article)
- “Transcription-related mutations and GC content drive variation in nucleotide substitution rates … (title)
Population size is clearly a condition, not a change-making causal process. Therefore, whenever we hear our colleagues talking about population size “driving” something, this indicates an explanatory meaning of “drive.” The non-causal nature is unmistakable in the first example above, because what is being “driven” by population size is model choice, which does not physically exist in the realm of biology, but represents an abstraction in the realm of modeling. A cause X and its direct effect Y must occur in the same place, the locale of causation.
Note that this meaning of “drive” can be used — and often is used — with the concept of selection, i.e., we can talk about selection driving a thing, without that thing being an allele frequency, e.g.,
- “Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes” (title)
More generally, in a purely statistical analysis of patterns, scientists may refer to the predominant explanatory factor as the factor that “drives” the pattern. In this kind of claim, the implied chain of causation may be absent or unclear. As argued by Green and Jones (2016) in regard to “constraints,” scientists sometimes prefer a non-mechanistic or even non-causal language, because this allows them to discuss formal relations applicable to some system, without having to commit to a (potentially problematic) hypothesis for a mechanistic cause.
Again, real scientists doing real, important scientific work sometimes depict formal relations using the language of factors, constraints, drivers, and so on, without implicating a clear causal theory. One of our responsibilities as scientists is to be clear about causation, but sometimes the way to be clear about causes is to say “I’m not sure what are the causes, but here are some rules that the system seems to be following.”
This does not mean that all uses of “drive” are equally welcome. When some authors above write that “These properties — and not function — seem to be the forces driving much of protein evolution” they are literally saying that properties are forces, which is certainly not a clear and careful use of language. I find many of these uses of “drive” to be unhelpful. I would encourage authors to consider using less colorful but more precise language specifying what is being shaped or influenced by a factor, and to what degree.
To summarize, Svensson and Berger, in their satirical exposé of Synthesis sophistry, have crafted a misrepresentation sandwich for us to consume. The meat is a weak semantic argument to the effect that the word “drive” must refer to population-genetic cause in the classic sense, a mass-action pressure that might cause allele fixation. Examples from the research literature demonstrate conclusively that, as much as one wishes for clearer language among evolutionary biologists, the word “drive” simply does not have this restriction. This nutrient-poor semantic filling is sandwiched between two misrepresentations of the cited sources: (1) that they advocate the “mutation-driven” language (this is false for 3 of the 4 sources cited), and (2) that they advocate evolution by mutation pressure (this is false for all 4 sources).
Finally, note that we are having this discussion about language precisely because our customary causal language needs revision. The legacy of neo-Darwinism is that selection is the paradigm of a cause, and any other factor is judged to be causal or not depending on how much it acts like selection. In the shifting-gene-frequencies theory of the Modern Synthesis, evolutionary causes are mass-action pressures (per statistical physics) that may cause allele fixations, e.g., selection and drift are seen as causes because they are potential causes of fixation. When Haldane (1927) and Fisher (1930) addressed the potential for mutation-induced trends, they treated mutation as a cause of fixation and dismissed it as unimportant. Because the introduction process acts nothing like selection, scientists trained in the Darwinian tradition experience great difficulty in comprehending it or accepting it as a causal process in evolution.
The discovery that biases in the introduction process have important effects in evolution prompts the search for precise causal language to describe this cause-effect relationship. In the absence of a widely accepted action language, scientists today are struggling with the issue: this is why they tend to use explanatory language, indirect language, or weak verbs, e.g., we wrote a paper that used weak language to assert (in the title) that mutation biases “influence” adaptation.
Any attempt to introduce causal or even explanatory language with strong active verbs is certain to provoke opposition from the reactionary elements parodied by Svensson and Berger (2019). As I have written elsewhere, this reactionary tendency is cultural, not scientific: it is motivated by allegiance, not to any specific scientific theory, but to tradition and to traditional authorities. The reactionaries will accept saltations (non-infinitesimal changes) and orthogenesis (tendencies due to internal biases) if the evidence demands it, but they will never say the words “saltation,” “internal biases” or “orthogenesis,” because this would reveal a heretical departure from tradition; likewise, they will allow mutation-biased adaptation due to biases in the introduction process, but they will describe such findings using old words while referencing dead authorities, in order to hide the novelty and link the new concepts to tradition (see also Bad Takes #5).
More bad takes on this topic
- 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)
Kimura M. 1980. Average time until fixation of a mutant allele in a finite population under continued mutation pressure: Studies by analytical, numerical, and pseudo-sampling methods. Proc Natl Acad Sci U S A 77:522-526.