There’s been a slew of “Darwin was wrong” and “Evolution is more complicated” stories in the media lately. It’s nearing Darwin day so simple minded media hacks can be explained as needing to find the requisite “drama” in their “stories”. But the real picture is a lot more nuanced, and ultimately a lot more interesting, than the dichotomies pedalled by what passes for science journalism these days. I am picking up themes also covered by Larry at Sandwalk, Evolutionary Novelties, and Jason at Evolution Blog.
The targets journalists I wish to attack here are those of New Scientist, Newsweek, The Telegraph, and the media release writers for Texas A&M University. And some of the scientists and philosophers whose comments are reported therein are equally guilty. But not wanting to spoil my own nest I shall leave the readers to work out who I mean…
Evolutionary process more detailed than previously believed, study shows
New evidence from a study of yeast cells has resulted in the most detailed picture of an organism’s evolutionary process to date, says a Texas A&M University chemical engineering professor whose findings provide the first direct evidence of aspects, which up until now have remained mostly theory.
Sounds fairly innocuous, doesn’t it? But then it says this:
These adaptations, Kao explained, triggered a competition between these segments, known as “clonal interference.”
It’s the first direct experimental evidence of this phenomenon in eukaryotic cells, or cells with nuclei, and it contrasts the widely accepted classical model of evolution, which doesn’t account for simultaneously developing beneficial adaptations, she said. Instead, that model adopts a linear approach, theorizing that a population acquires such adaptations successively, one after another. Rather than a competition occurring, the model posits a complete replacement of one generation by another better-adapted generation.
That wasn’t the case in Kao’s sample.
I read that and blinked a few times… the classical model of beneficial mutations spreading through a population is Muller’s:
From Wikipedia: This diagram illustrates how sex might create novel genotypes more rapidly. Two advantageous alleles A and B occur at random. The two alleles are recombined rapidly in (a), a sexual population, but in (b), an asexual population, the two alleles must independently arise because of clonal interference.
So, it looked like the writer had just got it wrong. Your not-so-humble correspondent sent of a snarky email to the contact, which he assumed was the media release writer. To his shame, it was the author, who very gently disabused me. But there remains a problem with the media release – it doesn’t say anywhere, unless you know the technical jargon (the key term here is “clonal interference”), that this is a rather elegant experiment done with asexual organisms. If you happen to know that yeast are (mostly) asexual, then you’d get it, but the journo who assisted with the release failed to work that out. Leading to philosophers making idiots of themselves and letting the wider media draw the wrong conclusions. Anyway, here is Kao’s and Sherlock’s figure showing that clonal interference is not so simple as had been expected among asexual organisms. The figure represents an actual count, using flow cytometry, of the various mutants in a single colony.
The caption reads in part: “Experimental population (size of approximately 109 cells) from which adaptive clones marked M1?M5 were isolated and subsequently characterized. The times when putative adaptive subpopulations reach their maxima are marked with arrows. Consistent with previous reports13, these adaptive events occur in the glucose-limited population approximately every 50?100 generations.” So, nice result, challenges some simplifying assumptions in the Muller model, but hardly a disproof of the “established evolutionary model”. But it’s not strictly the authors’ fault – models are often taught as being all that we might expect to be the case, when they are actually what we should expect if no other parameters vary. Here, we have a real world case where the parameters of the classical model do indeed vary from the model. The model is not complete.
Next, we move on to the Newsweek article. This has been critiqued by PZ Murtd, but I wish only to add that this is another case of people claiming that some modern result is “Lamarckian” when all it really is is a refinement of the ever-developing Darwinian tradition. The changes here are standard traits – the ability to respond to environmental changes at the individual level. That trait is inherited in a quite normal manner, and the trait, which is a disposition to grow in a particular way, just like most other developmental traits, is subjected to perfectly ordinary Darwinian selection and drift (note that drift was a post-Darwin theoretical development that has been assimilated into the Darwinian tradition quite solidly; we might say it is evidence that Darwin was wrong).
Now we should look at the Telegraph piece. It basically is following the New Scientist article, but it has a few items in it I would like to comment on. It includes comments that the existence of horizontal transfer undercuts the tree of life: “Evolution is far too complex to be explained by a few roots and branches”. And then there’s this gem: “In Darwin’s The Origin of Species, published in 1859, the British naturalist drew a diagram of an oak to depict how one species can evolve into many.” Ummm, no he didn’t. The sole diagram in the Origin is a stratigraphic schematic of how species might evolve, with lines connecting them. The oak was Haeckel’s innovation and it occurred in 1866 in German (according to Ebach and Williams 38f). Now ever since Gould ragged on Haeckel there has been no excuse for people not knowing this, but the experts quoted all do know this anyway.
There is a big difference between evolutionary histories of genes and the history of taxa. Swapping genes no more means the “tree of life” is a dead concept than swapping habitats would. There is a mismatch of things being considered. Genes can swap through many processes, both in single celled and multicellular organisms, ranging from simply taking in DNA floating in a medium, through to bacterial “sex”, to introgression of genes through hybridisation, through to the formation of entire species through hyridisation. And none of these, with the possible exception of speciation through hybridisation, affect the tree of life. If we have genes that are inserted into our genome from, say, worms, via a viral infection (as much as 40% of the mammalian genome is viral insertions from other species, including the viruses themselves), that doesn’t affect the fact that we evolved through ordinary speciation processes from a last common ancestor we share with chimps, and so on. And so we get to the New Scientist article. The cover heading is most likely written by a subeditor, or the editor, so we cannot make the journalist responsible for that, any more than the press release above is the fault of the scientists reported by it. But this is truly journalistic drama for the sake of it.
In many ways, we have known Darwin was wrong on various matters, especially heredity, from his own time. Almost nobody accepted his view of heredity, and the previaling view of speciation was due to Moritz Wagner and J. T. Gulick – which we now know as the theory of “allopatric speciation”, although Darwin’s own view, repackaged as “sympatric speciation” has had a revivial of a limited kind. But one thing he was not wrong about was the idea that animal and plant species had common ancestry with other related species. Yes, we know now that plants and occasionally animal species hybridise, but the only effect that has on the topology of the evolutionary tree at that scale, is that occasionally speciation happens to include three or more species rather than the two (ancestor and descendent). This is represented in phylogenetics as an “unresolved cladogram” in which three or more species diverge from the common ancestor of all of them. Now, open your copy of the Origin and look at the diagram Darwin shows there:
Notice that he allows for multiple speciation to occur in a single event? It’s not hybridisation, but the topology is roughly the same. So does this undercut the very idea of a tree of life? I think it does not. In particular the really insanely stupid comment by Eric Bapteste of Pierre and Marie Curie University in Paris that “We have no evidence at all that the tree of life is a reality” is so far from the mark that it makes no sense unless you suppose in his mind the evolution of genes and the evolution of species are supposed to be identical. But the distinction between gene trees and taxonomic trees is as old as genetics, although the terminology is recent. So, all in all, either you have really bad journalism here, of the kind I mistakenly ascribed to the Kao and Sherlock press release, or you have really bad rhetorical devices being used by a number of people who should know better, or both.
PS: In another “Film at 11″ press release, it is noted that there are mechanisms of inheritance that are not DNA based. Which we have known for lo! these many years now…