Friday, January 29, 2016

What is selfish DNA?

Richard Dawkins’ The Selfish Gene was a landmark book in many ways: the first to lay out for a general audience the gene-centred view of evolution, but also one of the first to re-invigorate (arguably since the 1920s) science popularization as a part of the cultural conversation – and to show how beautifully written it should aspire to be. Dawkins might be divisive today for a variety of reasons, but science popularizers owe him a huge debt.

That’s why it is good and proper to have The Selfish Gene celebrated in Matt Ridley’s nice article in Nature. You can tell that I’m preparing to land a punch, can’t you?

Well, sort of. You see, I can’t help but be frustrated at how Matt turns one of the most problematic aspects of the book into a virtue. He suggests that Dawkins’ viewpoint was the inspiration for the discussions of selfish genes presented in Nature in 1980 by Orgel and Crick and by Doolittle and Sapienza. And it is true that The Selfish Gene is the first citation in both papers.

But both cite the book as one of the most recent discussions of the issue. As Orgel and Crick say, “The idea is not new. We have not attempted to trace it back to its root.” So it is not at all clear that, as Matt says, “a throwaway remark by Dawkins led to an entirely new theory in genomics”.

The problem is not simply one of quibbling about priority, however. Matt points out that this “throwaway remark” concerns the “apparently surplus DNA” – in the hugely problematic later coinage, junk DNA – that populates the genome, and which Dawkins suggested is merely parasitic. Yes indeed, and this is what those two later Nature papers discuss – as Orgel and Crick put it, DNA that “makes no specific contribution to the phenotype”.

But is this what The Selfish Gene is about? Absolutely not, and that’s why Dawkins’ remark was throwaway. His contention was that all genes should be regarded as “selfish”. Orgel, Crick, Doolittle and Sapienza are specifically talking about DNA that is produced and sustained by non-phenotypic selection. This, they say, is what we might regard as truly selfish DNA. Now, one can argue about the word “selfish” even in that context – it perhaps only makes sense if this DNA becomes detrimental to the survival of the organism. But the implication is that the phenotypic DNA is then not selfish, and that the term should be reserved for parasitic DNA. That makes good sense – and it is precisely these waters that Dawkins’ title muddied.

I can’t resist also asking what Matt means by saying that “genes that cause birds and bees to breed survive at the expense of other genes”. (“No other explanation makes sense…”) It seems to me more meaningful to say “genes that cause birds and bees to breed survive while helping other genes to survive.” I don’t exactly mean here to allude to the semantic selfish/cooperative debate (although there are good reasons to have it), but rather, it seems to me that Matt’s statement only makes sense if we replace “genes” with “alleles”. This is not pedantry. Genes do not, in general, compete with each other – at least, that is not the basis of the neodarwinian modern synthesis. Although one might find examples where specific genes do propagate at the expense of others, in general it is surely different variants of the same gene that compete with each other. And when a new allele proves to be more successful, other genes come along for the ride. To fail to make this distinction (which of course Matt recognizes) seems to me to propagate a very common misconception in evolutionary genetics, which is that genes are little pseudo-organisms all competing with one another. That isn’t a helpful or accurate way to present the picture.

Matt understands all this far better than I do. So I am quite prepared for him to tell me I have something wrong here.


Unknown said...

Hi Phil,

I think your comments are not wrong, but nor are they especially game changing, to borrow a phrase I used in the piece. Taking them in turn and briefly:

1. On whether selfish DNA was Dawkins's "discovery": well, I have not found anybody else who stated the idea before him, let alone so clearly, and either Crick or Orgel (memory not perfect) specifically told me it was The Selfish Gene that alerted him to it. The c-value paradox was largely discussed in terms of competing explanations based on function (for the organism) at the time. (Might be worth asking Sapienza.) That paradigm needed challenging. I am sure it is true, as Crick and Orgel hedge their bets by conceding, that somebody may have pre-empted Dawkins somewhere. As you know, history nearly always turns up neglected pioneers of ideas, but Dawkins was probably the first not to be neglected. A point I had to leave on the cutting room floor was the coincidence of timing of this idea and the first computer viruses.

2. On "all genes are selfish", Dawkins and others (such as Austin Burt) have occasionally used "ultra-selfish" as a term for digital parasite elements as opposed to the notion that genes are selected to promote the survival of themselves and copies. But I made clear that selfish DNA is a parenthetical, case in terms of the whole argument, so I am not sure there is much of substance between us here. Burt's work with Wolbachia, transposons and now drive do emphasise that these things are pretty important to evolution, more so than anybody expected in 1980. My discussion of the suggested title "the Immortal Gene" surely does go to the issue your raise about the title being misleading. Incidentally, the almost visceral objection many people have to the phrases "selfish gene" and "junk DNA", as if one was somehow offending somebody by using them, is something I have never understood.

3. Your alternative formulation of my sentence about birds and bees is not an improvement in my mind for the following reason: it implies that genes are selected to help any old "other genes", which we know to be wrong. Genes that promote the survival of their own replicas (to use the word from Dawkins's 1966 lecture notes), whether in an offspring or a relative, tend to survive at the expense of genes that don't. They may do this by causing selfish behaviour, or non-selfish (e.g. parental) behaviour. And while it is true that "allele" is usually the right way of thinking about this -- evolution is the selective survival of alleles, mostly -- it is not exclusively alleles one is talking about. Suppose my brown- or blue-eye gene (I have one of each) is literally identical to yours. And suppose in the context of my body and my lifestyle it has for some reason done a better or worse job of promoting my survival (probably by making me more or less paler skinned and so more or less susceptible to vitamin D deficiency in an ancestral early-farming society in a high latitude, say) then the competition has not been between my two alleles but between my gene and its identical allele in you. We're getting into absurdities, here, of course. but then you started it!! (this meant as a joke, not a criticism.)

4. As for your pseudo-organism remark, well I think that's a good example of Dennett's intentional stance problem, which I raised in my piece. It's a linguistic problem as much as anything else. We just have not got the vocabulary for things that have non-random consequences without having any mind-first intentionality. I don't think the problem is better or worse if you substitute allele for gene.

Thanks for reviewing my review of RD's reviews!!


Unknown said...

Oh that the blogosphere were all like this....