Of Genes and Species

I straddle the line between being a population biologist and a molecular geneticist. That's a self-congratulatory way of saying that I am an expert in neither field. But existing in the state I do allows me to observe commonalities shared by both. For example, both fields have terminology (or what the uninitiated would call jargon) that lack sufficient definitions.

Amongst my minimal postings from last week were included a couple of riffs on species and speciation (the first, the second) getting at the lack of a coherent definition of species. My conclusion is that there is not, nor will there ever be, a definition of species that performs satisfactorily in every taxon. John Wilkins has studied species concepts much more than I have, and he offered his opinion here. But that's all old news.

What's also old news is the debate over what constitutes a gene. And the debate rages on in the science blog-o-sphere -- PZ Myers, Sandy Porter, Larry Moran, and Greg Laden have all offered their two cents (Moran's subject to an exchange rate, of course). While there is considerable overlap between the definitions, each person offer's his or her unique approach toward defining a gene. Just like species concepts, there is not a single definition of gene that everyone finds satisfactory.

Whether we're arguing species concepts, debating genes, or complaining about any other ephemeral terminology, there is one thing in common: the appropriate definition is not what someone else says it should be, but what fits your research best. A developmental biologist will be interested in how genes function (by exploring the phenotypes of individuals with mutated versions or examining when and where genes are expressed), whereas an evolutionary geneticist will be interested in how sequences (which may or may not be called genes) change over time. Sometimes people will define genes as protein coding sequences, sometimes they'll include introns, other times they'll include cis regulatory regions. You'll also see nontranslated RNAs lumped into the class "gene" if that's appropriate for whatever someone's studying.

The take home message is that this terminology (all terminology?) is not fixed; it depends on context and the person delivering the information. Just as "gene" may refer to a sequence that gets transcribed, a sequence that gets translated, or a sequence with function, "species" may refer to unique gene pools, reproductively isolated populations, or ecologically differentiated populations. You can squabble about what a gene is, what a species is, or even what constitutes "life", but these terms are dynamic, and their definitions are often implied by the context in which they are placed.

Rather than using these poorly defined terms, why not use a more detailed term? If you're talking about protein coding sequences, don't call them genes when you could refer to them as protein coding sequences. The same goes for transcribed sequences or any other sequence that falls into the catchall "gene". That was the point I was trying to get at with my posts on species -- if you're studying reproductive isolation, call it that rather than speciation.