Debating philosophers: The molecular gene

This is my fifth post on the Lu and Bourrat paper [Debating philosophers: The Lu and Bourrat paper]. The authors are attempting to justify the inclusion of epigenetics into current evolutionary theory by re-defining the concept of "gene," specifically the evolutionary gene concept. So far, I've discussed their understanding of current evolutionary theory and why I think it is flawed [Debating philosophers: The Modern Synthesis]. I described their view of "genes" and pointed out the confusion between "genes" and "alleles" and why I think "alleles" is the better term [Debating philosophers: The difference between genes and alleles]. In my last post I discussed their definition of the evolutionary gene and why it is too adaptationist to serve a useful function [Debating philosophers: The evolutionary gene].

The molecular gene doesn't figure prominently in their argument but I'm going to discuss it anyway. Here's how Lu and Bourrat describe the molecular gene in Table 1 of their paper.

A stretch of DNA that contains an open reading frame with a promoter sequence, and functions in transcription and–or translation processes to create a genetic product. (Griffiths and Stotz [2013], p. 73) It is a stereotyped definition of the molecular gene. For more discussions, see Griffiths and Stotz ([2013]) and main text.

The text doesn't really add anything to that definition except to mention that noncoding regions of the gene and alternative splicing create problems with the definition. Nobody who has studied the problem claims to have a definition that covers all possibilities. There are exceptions to every definition of a gene that's ever been proposed.¹ Griffiths and Stotz have done an excellent job of explaining some of the complications in their earlier papers. (I don't have the 2013 book referred to in Lu and Bourrat.)

My preferred definition is [What Is a Gene?]:

A gene is a DNA sequence that is transcribed to produce a functional product.

The functional product is RNA. It may be ribosomal RNA, snRNA, mRNA, tRNA, microRNA or a host of others. The point is that only one of those products is translated to make protein yet we still talk about tRNA genes, snRNA genes etc. The molecular gene is not restricted to just protein-coding genes. This is my main objection to the Giffiths and Stotz definition that Lu and Bourrat use in their paper. Genes do not have to have open reading frames.

There are many scientists who make this same mistake even though they should know better. However, if you are going to write a paper that relies on the correct definition of "gene" then surely you should think about it a little harder than the average scientist who might have been taught incorrectly as a undergraduate?

My preferred definition does not include the promoter and regulatory sequences unless they are transcribed. I prefer to think of regulatory sequences as sequences that control the expression of the gene without being part of the gene. Others may use a different definition of gene. For example, in his evolutionary biology textbook Futuyma (2nd ed. p. 188) describes a genes like this ...

The term gene usually refers to a sequence of DNA that is transcribed into RNA, together with untranscribed regions that play roles in regulating its transcription. The term locus technically refers to the chromosome site occupied by a particular gene, but it is often used to refer to the gene itself. Thousands of genes in the human genome encode ribosomal and transfer RNAs (rRNAs and tRNAs) that are not translated into proteins.

While it may be true that there is no universally correct definition of "gene," it's also true that some definitions are wrong. The Griffiths and Stotz definition is wrong because it excludes all DNA sequences that lack an open reading frame and this means that tRNA genes aren't genes by their definition.

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1. Some genes are made of RNA, for example, and operons consist of several genes even though there's only one transcript.