Debating philosophers: The difference between genes and alleles

This is my third post on the Lu and Bourrat (2017) paper [Debating philosophers: The Lu and Bourrat paper]. Part of their argument is to establish that modern evolutionary theory is a gene-centric theory. They need to make this connection because they are about to re-define the word "gene" in order to accommodate epigenetics.

In my last post I referred to their defense of the Modern Synthesis and quoted them as saying that the major tenets of the Modern Synthesis (MS) are still the basis of modern evolutionary theory. They go on to say,

One of these tenets, which will be the focus of this paper, is that phenotypic evolution can be explained by changes in gene frequencies in a given environment. This "gene-centric view," relies on genes being the sole heritable material, which, together with the environment, determine the phenotype.

Evolutionary theory has been based on population genetics since the 1920s and 1930s. That's almost 100 years. It's only in that sense that evolutionary theory is "gene-centric." It's more appropriate to refer to it as "genetic."

Calling evolutionary theory "gene-centric" seems to come from Richard Dawkins and his 1976 book The Selfish Gene. I recently pointed out that his view of evolution is not the dominant view among today's evolutionary biologists [The selfish gene vs the lucky allele].

In their discussion of standard evolutionary theory (SET), Lu and Bourrat refer to proponents of a new extended evolutionary synthesis (EES) for their information on what the current view is. They say,

SET, which EES proponents believe retains the core of the MS, has the following three tenets: ‘new variation arises through random genetic mutation; inheritance occurs through DNA; and natural selection is the sole cause of adaptation, the process by which organisms become well-suited to their environment’ (Laland et al. [2014], p. 162).

Now, nobody doubts that variation arises through mutation and that inheritance involves DNA, although very few others would express it that way. The idea that natural selection is the only means of adaptation is debatable but that's not so important. What's important is that there's no mention of non-adaptive evolution and that's a very important part of standard evolution theory in 2017. Furthermore, I would argue that changes in allele frequency in populations is an important part of evolutionary theory.

My major criticism of Lu and Bourrat's paper has to do with their linkage of evolutionary theory and "genes." This is an immportant part of their paper and there will be two other blog posts devoted to their description of the "evolutionary gene" and the "molecular gene." They make their task much more difficult by confusing genes with alleles. This is the same problem I wrote about a few days ago [The selfish gene vs the lucky allele].

Here's an example of the confusion,

Gene selectionism represents a strong version of the gene-centric view of formal evolutionary theory (Hull [2000], p. 422; Laland [2004]). Haig ([2012]) develops the notion of the ‘strategic gene’ in accordance with the common characterization of evolution as ‘changes in gene frequency and phenotypic effects of these changes’. For him, a gene refers to a determinant of difference in the phenotype that correspond to a set of gene tokens, mainly DNA pieces. The crucial point we retain from Haig’s account is that a gene in an evolutionary context is a difference maker. For defending gene selectionism, Haig ([2012], p. 470) regards a gene as ‘a strategist in an evolutionary game played with other strategic genes’, hence his use of the term ‘strategic’.

I don't see any good reason for not using "allele" in the paragraph above. It would be much more accurate, especially when describing the definition of evolution as, "changes in gene frequency."

There are two problems with "gene:"

1. It creates an unnecessary conflict between the definition of the evolutionary gene and the molecular gene. It's not really "gene" frequencies that change; it's allele frequencies where alleles are gene variants that are created by mutation.
2. Not all heritable changes are found in genes but they can all be classified as alleles. For example, variants in regulatory regions are arguably not part of genes but are very important in evolution. Variants in DNA sequences at the sites of centromeres, telomeres, SARs, origins of replication, and even junk DNA can be relevant in evolution and these are not "genes" in any reasonable sense of the word.

There's no reason for these philosophers to ignore the standard use of the word "allele" as in "changes in allele frequency." It's an example of fuzzy thinking. So is referring to current evolutionary theory as "gene-centric."

---

Image Credit: Campbell Biology