The current issue of Nature features this interesting essay by Nigel Goldenfeld and Carl Woese. The essay’s point is that recent discoveries about genomic interactions among microbes, particularly the phenomenon of horizontal gene transfer (HGT), is forcing us to reevaluate certain basic concepts in biology. They write:
One of the most fundamental patterns of scientific discovery is the revolution in thought that accompanies a new body of data. Satellite-based astronomy has, during the past decade, overthrown our most cherished ideas of cosmology, especially those relating to the size, dynamics and composition of the Universe.
Similarly, the convergence of fresh theoretical ideas in evolution and the coming avalanche of genomic data will profoundly alter our understanding of the biosphere — and is likely to lead to revision of concepts such as species, organism and evolution. Here we explain why we foresee such a dramatic transformation, and why we believe the molecular reductionism that dominated twentieth-century biology will be superseded by an interdisciplinary approach that embraces collective phenomena.
Provocative stuff, but I don’t think they have the goods to back it up.
In the wild, microbes form communities, invade biochemical niches and partake in biogeochemical cycles. The available studies strongly indicate that microbes absorb and discard genes as needed, in response to their environment. Rather than discrete genomes, we see a continuum of genomic possibilities, which casts doubt on the validity of the concept of a ‘species’ when extended into the microbial realm. The uselessness of the species concept is inherent in the recent forays into metagenomics — the study of genomes recovered from natural samples as opposed to clonal cultures. For example, studies of the spatial distribution of rhodopsin genes in marine microbes suggest such genes are ‘cosmopolitan’, wandering among bacteria (or archaea) as environmental pressures dictate.
If HGT really is as prevalent as Goldenfeld and Woese claims (my understanding is that this is controversial among biologists), then I would agree that it becomes difficult to talk about distinct species of microbes. But so what? That would just mean that a species concept that is very useful when talking about complex, multicellular organisms is not so useful when applied to simple, single-celled organisms. Hardly the stuff of revolutions.
Now, if they showed that HGT is prevalent among all organisms, that would be revolutionary! It also seems rather unlikely.
They get a little carried away a bit later:
Nowhere are the implications of collective phenomena, mediated by HGT, so pervasive and important as in evolution. A computer scientist might term the cell’s translational apparatus (used to convert genetic information to proteins) an ‘operating system’, by which all innovation is communicated and realized. The fundamental role of translation, represented in particular by the genetic code, is shown by the clearly documented optimization of the code. Its special role in any form of life leads to the striking prediction that early life evolved in a lamarckian way, with vertical descent marginalized by the more powerful early forms of HGT.
I’m not quite sure what they mean by saying that rampant HGT suggests that early life evolved in a lamarckian way. Typically lamarckism is thought to refer to the inheritance of acquired characters. I can only make sense of this paragraph if their intention is that the genes obtained via HGT are themsleves acquired characters. I also don’t see how that bit of definitional gymnastics constitutes a prediction.
The authors go on to make it clear that their observations are meant to apply only to the microbial world:
Refinement through the horizontal sharing of genetic innovations would have triggered an explosion of genetic novelty, until the level of complexity required a transition to the current era of vertical evolution. Thus, we regard as regrettable the conventional concatenation of Darwin’s name with evolution, because other modalities must also be considered.
I’m afraid that a revision to our understanding of the earliest stages of evolution does not strike me as a revolution.
Woese has been pounding this drum for a while, a fact that has made him a darling among creationists. He is deliciously quote-minable, since he says things like, “The Darwinian emperor has no clothes,” when he really meant to say “recent discoveries are forcing us to rethink certain aspects of the earliest stages of evolution. What I find ironic about the creationist embrace of Woese is that his work, shorn of its excessive rhetoric, does serious damage to the ID case. HGT is another natural mechanism by which genomic complexity can increase, in deifance of ID’s claims to the contrary. If Woese is correct in every particular evolutionary biology will find it easy to take it in stride. For ID his work is yet another nail in the coffin.