Confession time: one of the main reasons why I chose to study ecology all those years ago was in order to avoid what, to me, were twin peaks of incomprehensibility – biochemistry and genetics. I liked to be able to see what was going on: a plant’s growth, a leaf’s reaction to drought, or stomatal responses to infection were all fine, but when things got subcellular the fog would descend and my mind would wander. So pity my poor chances of comprehending the molecular biology papers that currently abound in the average journal today; sometimes I even struggle to work out whether the author is talking about a gene or a protein… and therein rests my gripe, because there is no reason at all why I should.
OK, conventions do vary a bit from journal to journal, but at a very basic level it seems generally accepted that a gene name should be given in italic type whilst its protein product is given in normal (‘roman’) type. So increased expression of the FLC gene will produce increased amounts of the FLC protein in the cell, a decrease in expression of the MAF2 gene will result in lower amounts of the MAF2 protein. Of course the distinction isn’t needed when the words ‘gene’ and ‘protein’ are present, but clearly you don’t want to repeat them dozens of times in every paragraph – so just use italics instead (and no need to fumble for the ‘italic font’ button: ‘Control + I’ will do the trick in a fraction of the time). And it’s worth being aware that if you don’t make use of italics in your paper then someone else may do so on your behalf: I don’t know of any high-ranking journal that doesn’t carry out some form of editing on accepted papers, and if you don’t make it clear what is a gene and what is a protein then someone else may make a guess on your behalf – and not necessarily get it right, as illustrated by the following sentence that appeared a few years ago in a paper on Arabidopsis: ‘After very long periods of low temperature, however, MAF2 levels decreased and a marked acceleration of flowering occurred’
Now I’m only an ecologist, but I’m not sure the level of a gene can decrease, can it? But am I just being pedantic? In that example it’s pretty clear what is meant, and in terms of the overall effects the gene and the protein are almost synonymous – expression levels of the MAF2 gene decrease so the level of the MAF2 protein in the cell decreases, so what’s the problem? Not much in that simple example, but what about a more complex system where the gene expression increased but some other factor disrupted subsequent production of the protein causing it to decrease, perhaps with several gene/protein systems interacting – would your reader be able to follow it so easily then?
Molecular biology is complicated stuff, so when it comes to clarity every little helps.