This is the forth post on the Lu and Bourrat paper [Debating philosophers: The Lu and Bourrat paper]. The philosophers are attempting to redefine the word "gene" in order to make epigenetics compatible with current evolutionary theory.I define a gene in the following way: "A gene is a DNA sequence that is transcribed to produce a functional product" [What Is a Gene?]. This is a biochemical/molecular definition and it's not the same as the definition used in traditional evolution.
Lu and Bourrat discuss the history of the evolutionary gene and conclude,
Hence we suggest a stripped-down notion of the gene that includes only the minimal requirements for it to play the role in formal evolutionary models. Griffiths and Neumann-Held's (1999) conception of the evolutionary gene fits well with our aim. They define the evolutionary gene as a heritable, atomistic unit that causes a difference in phenotype. This definition corresponds to the manner in which formal evolutionary theory treats genes as one of the determinants of trait variance, and also treats genes as the source of inheritance. According to this definition, any physical structure that causes a heritable variation is what we call a 'materialized evolutionary gene.'Many of you will be puzzled by such a definition but you have to realize that Lu and Bourrat see evolution as synonymous with natural selection. They believe that current "formal evolutionary theory" only recognizes genes that cause a difference in phenotype and that such differences are subject to selection. They don't seem to be aware of neutral or nearly-neutral alleles whose frequency is strongly influenced by random genetic drift. They don't seem to recognize that there are variants in junk DNA that can be fixed or eliminated by evolution. In such cases, it makes little sense to refer to these as evolutionary genes.
As I pointed out in a previous post, Lu and Bourrat tie themselves up in knots trying to make "gene" equivalent to "allele." Here's an example.
Haig (2012), building his notion of phenotypes from the notion of gene, defines a phenotype as 'a gene's effects relative to some alternative', which is not organism-centered, but is coupled to the notion of gene. Two things should be noted. First, as we have mentioned several times, the evolutionary gene is defined by its heritable effects on the phenotype. Hence, to define the phenotype as 'a gene's effects' corresponds well to the concept of evolutionary gene. Second, the requirement of the existence of some alternative seems to mean that if there is no alternative, then there is no phenotype. This is not as problematic as it may first seem to be for three reasons. First, in Johannsen's original definition, phenotypes refer to distinguishable 'types' of organisms, which implicitly assumes a comparison is being made. Second, evolution, as it is classically understood, only occurs when the target population satisfies the condition of variation (Lewontin, 1970). Even in the limit cases where there is no variation in the population at a particular time—because for instance, one variant invaded the population—heritable variations are regularly produced. Finally, under the manipulationist account, causation can only be established when at least two alternatives are compared. Thus, we regard the existence of alternative phenotypes in an evolutionary context as a reasonable assumption.I just don't understand why philosophers put themselves in such a bind by ignoring scientists. Evolution is all about alleles and, by definition, alleles are variants at a certain position in the genome. Evolution is the change in frequency of alleles in a population. If you don't have different alleles then there's no evolution. Alleles are not genes. They are not evolutionary genes nor any other kind of genes. Different alleles at the same locus may or may not produce a difference in phenotype.1 That doesn't make any difference. Evolution will happen regardless of phenotype.
Inspired by Haig's definition, we define the phenotype of an evolutionary gene as everything that the gene makes a difference to when compared to another gene.
This is not rocket science. Philosphers who want to become experts on evolution can start with any undergraduate textbook on evolutionary biology in order to understand that alleles are important and there's more to evolution than natural selection.
Fundamental Principles of Genetic Variation in PopulationsTwo of those causes are random genetic drift (Chapter 10) and Natural Selection (Chapter 11).
We embark now on our study of genetic variation and the factors that influence it—that is, the factors that cause evolution within species. The definitions, concepts, and principles introduced here are absolutely essential for understanding evolutionary theory. We begin with a short description of these ideas, followed by an explanation of a very important formal model.
At any given gene locus, a population may contain two or more alleles that have arisen over time by mutation. Sometimes one allele is by far the most common (and may be called the WILD TYPE), and the others are very rare; sometimes two or more of the alleles are each quite common. The relative commonness or rarity of an allele—its proportion of all gene copies in the population—is called the allele frequency (sometime imprecisely referred to as the "gene frequency")....
An alteration of the genotype frequencies in one generation will usually alter the frequencies of the alleles carried by the population's gametes when reproduction occurs, so the genotype frequencies of the following generation will be altered in turn. Such alteration, from generation to generation, is the central process of evolutionary change. However, the genotype and allele frequencies do not change on their own; something has to change them. The factors that can cause the frequencies to change are the causes of evolution.
I'm not sure that Lu and Bourrat understand current evolutionary theory. But they are philosophers of biology and they are writing a paper about evolutionary theory. They are supposed to be experts.
1. Some colleagues don't like to use the word "alleles" to refer to variants that are not part of genes.