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Thursday, October 18, 2007

Celebrating the Three Domain Hypothesis


This press release from the University of Illinois at Urbana-Champaign (USA) says it all.
Thirty years ago this month, researchers at the University of Illinois published a discovery that challenged basic assumptions about the broadest classifications of life. Their discovery – which was based on an analysis of ribosomal RNA, an ancient molecule essential to the replication of all cells – opened up a new field of study, and established a first draft of the evolutionary “tree of life.”

To mark the anniversary of this discovery, the university is holding a symposium Nov. 3-4 (Saturday-Sunday), with a public lecture at the Spurlock Museum on the evening of Nov. 2. “Hidden Before Our Eyes: 30 Years of Molecular Phylogeny, Archaea and Evolution” will detail the exacting work that led to the discovery of a “third domain” of life, the microbes now known as the archaea. The event will revisit the program of research that led to the discovery, explore its impact on the study of evolution, and describe the way in which genetic analysis continues to revolutionize biology, in particular microbial ecology.
There's nothing in the press release to suggest that the third domain is still controversial. Looking at the list of speakers, it's not clear whether this point will come out in the symposium although I note that Carl Woese is on the program and he's recently been lukewarm about his own hypothesis.

The best hope for the journalists in attendance is Jan Sapp, a biologist at York University here in Toronto (Canada) who has studied the history of this "discovery" over the past three decades. As I reported last year, Sapp has documented the rise and fall of the Three Domain Hypothesis and he has taken note of the fact that former supporters of the hypothesis have recently become more skeptical [The Three Domain Hypothesis (part 2)]. Hopefully, Sapp will say things like the following from his book Microbial Phylogeny and Evolution. On the other hand it may be difficult to rain on the parade so the symposium may end up ignoring the controversy and pretending that the domain of Archaea is established fact.

The Three Domain Hypothesis
Defection grew from within the ranks of molecular evolutionists during the late 1990s. Several leading microbial phylogeneticists saw in Mayr's critique much that they considered to be true, as central features of the Archaeal story of the 1980s were challenged. First, analysis of whole genomes (more than 70 had been sequenced by 2003) had shown that Archaebacteria and Eubacteria possessed numerous genes in common; they shared a rich biochemical complexity. These data did seem to contradict the hypothesis that the Archaea were so very different from Bacteria because the two groups diverged when life was quite new. Second, comparisons of genes for other functions seemed to contradict the the phylogenetic lineages deduced from rRNA sequences....

There was a third fundamental issue. Not only did the phylogenies from the new genomic studies disagree with the traditional rRNA-based phylogenies but the new genome data also conflicted among themselves. Comparisions of individual gene phylogenies (other than those concerned with the translation machinery) often indicated different organismic genealogies. Phylogeneticists suspected that the mix-up was caused by evolutionary mechanisms whose scope and significance they may have severely underestimated: gene transfer between groups.
I have argued elsewhere that the current consensus among those who are concerned with early evolution is that the early stages were characterized by rampant gene exchanges so that it is simply not possible to say what the phylogeny of bacteria lineages was before the main lines formed. It is not possible to say with any certainty that archaebacteria are one of the earliest branching lineages and in the absence of this certainty it is certainly not possible to say that archaebacteria form a disctinct domain of life.


  1. It's a little unclear what exactly you doubt in this post. Or rather what you're arguing for. You're saying that archaea and eubacteria are in the same domain because they forked later? How should the tree of life look instead in your opinion? And what should eubacteria and archaea be called instead of domains?
    Thanks for any insights.

  2. I'm saying that Archaea is probably not a separate domain of life. It may be just another bacterial lineage.

  3. If "defection grew from within the ranks of molecular evolutionists during the late 1990s", how exactly do you explain that Woese 1) won a US National Medal of Science in 2000, 2) won the Crafoord, (the Nobel equivalent for evolution and ecology) in 2003 and 3) was just recently (in 2006) inducted into the Royal Society of London as one of the rare foreign members? Don't such honors go to the discovers of accepted principles? (Of course this doesn't mean that they have to be right, just accepted).

    Sure, members of the "Canadian school" such as Gupta, Golding, Cavalier-Smith, and yourself object to the three domains, but then they *always* objected to them, and make a tiny fraction of the scientific community.

  4. I have no problem with Woese being honored. I think he deserves it. He started a whole new field of inquiry.

    As I documented in earlier blogs, even Woese has backed off from the major claims of the Three Domain Hypothesis. And he's not a Canadian!

    Jonathan, do you still believe that archaebacteria are the closest relatives of eukaryotes in spite of all the evidence to the contrary?

  5. Yes, nobody (including Woese) now believes exactly in what Woese wrote in 1977, or even in the revised picture of 1990, but they still believe in the three domains -- that's how science works, just like how scientists still believe in Darwinian evolution even though we don't believe in everything Darwin wrote in 1859.

    I certainly agree that for pioneering microbial molecular phylogeny, Woese would deserve honor even if the three domains fell out of favor; however that doesn't seem to be what's happened. Why was Woese awarded the Crafoord in 2003? According to the site it was “for his discovery of a third domain of life”.

    And yes, I *do* believe archaea are the closest relatives of eukaryotes -- and unless someone can find a bacterium with transcription and translation that are more eukaryotic-like than that of archaea, neither I nor the majority of the scientific community are likely to change our minds, even if many metabolic systems are shared between bacteria and either archaea or eukaryotes.