Biology’s Next Revolution?

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dramatic transformation, and why we believe the molecular reductionism that dominated twentieth-century biology will be superseded by an interdisciplinary approach that embraces collective phenomena.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.

They write:

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.

Comments

  1. #1 Morgan Price
    January 25, 2007

    There is an emerging consensus is that HGT in bacteria is indeed very common. The only papers that find that HGT is rare are the ones that consider only the most highly conserved genes. Since HGT is so common, gene content within a “species” varies dramatically, and although the concept of bacterial species is too useful to give up, it does seem rather problematic.

    Now, when I was in grad school 15 years ago, HGT was considered to be rare, spooky, and wierd. Yet it turns out that HGT is very common, and that HGT plays a major role in the evolution of new traits, such as antibiotic resistance or the ability to degrade novel man-made chemicals. I do think this qualifies as a revolution in our understanding of microbial evolution.

    Finally, this doesn’t just apply to bacteria. There is plenty of evidence for HGT in eukaryotes, although we don’t have nearly enough genome sequences to know how common it is yet.

  2. #2 richard handelsman
    January 25, 2007

    Re Woese’s “Thus, we regard as regrettable the conventional concatenation of Darwin’s name with evolution, because other modalities must also be considered.”: That “Darwin” = “evolution” has always been the “conventional” – public, media, “man in the street” – equation. But the scientific community has long considered “other modalities” – e.g., Gould’s Punctuated Equilibrium. So why’s he making such a big deal??

    Particle : quantum physics :: classical biology : genomic research? Both disciplines began with the large and are now studying the small, but beyond that I am ignorant. I would like to know if other parallels exist between these two relationships

  3. #3 Carl Zimmer
    January 25, 2007

    Woese went into more detail about “Lamarckian” early life in a paper last year that I wrote about here

  4. #4 Jason Rosenhouse
    January 26, 2007

    Morgan-

    I’ll accept that it’s revolutionary in our understanding of microbial evolution, but my impression is that Woese in particular is claiming it’s a revolution for our understanding of evolution generally. I think that’s indicated by some of his more dramatic statements about the Darwinian emperor having no clothes, or his objection in the present essay to tlaking about Darwinian evolution.

    Carl-

    Thanks for the link to your earlier post. But it seems to confirm what my impression of what he meant by “lamarckian.”

  5. #5 Matt
    January 26, 2007

    I will agree with the authors that HGT is revolutionary within bacteria- but that this will radically change ALL biology is a stretch.

    Given that HGT and recombination is so promiscuous in bacteria- species concepts are nightmarish- and probably not applicable. I write about this here and here.

  6. #6 sport
    January 29, 2007

    um….how can you evolutionists rationalize in your theory the notion that organisms can reconstruct their genome under environmental stress? I believe this is where Woese is going with is Lamarckism comment.

    Surely you guys know that Lamarckism (under the guize of epigenetics) is going to steamroll darwinism?????

  7. #7 tommyteo
    January 29, 2007

    That?s a fascinating personal opinion, Sport. But in addition to your content-free threat, would you mind posting explanations of: (1) How observed gene sharing in bacteria proves that rarely if ever observed gene sharing in multi-cellular organisms is actually very common? (2) How observed gene sharing in bacteria demonstrates that bacterial genomes must have been designed by Sky-God?

  8. #8 slpage
    January 29, 2007

    This will, of course, be wildly extrapolated by IDcreationists as indicating some big problem for evolution, and they will also use it to try to undercut the relevance of molecular phylogenetics.

    The big problem with that, of course, is that if HGT is such a problem for evolution and is so common in multicellular eukaryotes so as to render molecular phylogenetic analysis useless, they will need to explain to us all why such analyses produce results that are generally:
    1. congruent with other such analyses;
    2. congruent with evolution-based hypotheses of descent (for the most part);
    3. highly consistent regardless of which area of the genomes are being analysed

    I’m sure they will do this, rathet than just pull some quotes form the article and declare there to be some huge issue because Woese said so.

  9. #9 sport
    January 29, 2007

    tommy….I’m not geneticist…I’m not a scientist…I’m just a guy. I don’t know the answer to that question. I simply asked how in the world darwinists can rationalize a microorganism that can reconstruct its genome. I’m not sure exactly what all the implications of this are, but I’m pretty sure that it nullifies the concept that bacterial resistance happens by way of the evolutionary mechanism RM + NS…which has long been the story. (correct me if I’m wrong here.)

  10. #10 sport
    January 29, 2007

    this stuff is popping up all over. I think darwinism is in big trouble.

    http://www.i-sis.org.uk/fluidGenome.php

  11. #11 slpage
    January 30, 2007

    What do you mean by ‘darwinism’? Is that like Newtonism?

    By the way – Ho and Lipton and their ilk are gurus more intent on furthering an agenda with the help of a technically and scientifically illiterate following then they are about engaging in any sort of legitimate scientific discourse.

  12. #12 Tom
    January 30, 2007

    sport – You are wrong here. RM + NS almost certainly gave rise to the initial genes for antibiotic resistance in one bacterium. However, if these genes arose on a transmissible plasmid, or were transferred to a transmissible plasmid, they could be (and have been) transferred to other bacterial species very easily. This type of lateral gene transfer was well known before the term ‘lateral gene transfer’ was coined. It all fits quite well with evolutionary theory.

  13. #13 sport
    February 1, 2007

    Tom: “It all fits quite well with evolutionary theory.”

    Then why does the article express regret that darwin’s name is attached to evolution?

  14. #14 Prabhu Patil
    October 6, 2007

    Jason

    You are right that “HGT is another natural mechanism by which genomic complexity can increase”.

    I can also smell ID in this essay by Woese. There is no place for Lamark in an article on revolution in biogy:)
    Lamarks place is only in history and text books.

    Prabhu

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