Darwin’s Tree of Life Uprooted; Ring of Life Planted in its Place

Perhaps no icon of evolution has been more pervasive than Darwin’s “tree of life” (see 06/13/2003 headline).  A drawing of a branching tree was the only illustration in Darwin’s Origin of Species.  145 years later, scientists are saying the metaphor of a tree is wrong; it should be a ring, at least in the family tree of eukaryotes.  This surprising turnaround was published in Nature¹ Sept. 9 by James A. Lake and Maria C. Rivera of UCLA’s Astrobiology Institute.  Lake said in a UCLA press release, “It’s not a tree; it’s actually a ring of life.  A ring explains the data far better.”  EurekAlert reported, “UCLA molecular biologists uproot the tree of life.”
    What’s this all about?  Are they denying evolution?  Certainly not: Lake said, “If we go back a hundred billion generations, our ancestor was not a human, and wasn’t even a primate.  But we are distantly related to archaeal eocyte- and proteobacterial-ancestors, just as we are related to our parents and grandparents.”  So far that sounds like typical tree-of-life Darwinism.  The ring metaphor comes from their proposal that eukaryotes (see 09/08/2004 headline) arose not by branching off of early prokaryotes or archaebacteria, but rather by the fusion of the genomes from those two groups: one that could do photosynthesis, and another that could survive extreme environments.  The press release expresses Lake’s confidence in his new proposal:

“At least 2 billion years ago, ancestors of these two diverse prokaryotic groups fused their genomes to form the first eukaryote, and in the processes two different branches of the tree of life were fused to form the ring of life,” Lake said.  “A major unsolved question in biology has been where eukaryotes came from, where we came from.  The answer is that we have two parents, and we now know who those parents were.”   (Emphasis added in all quotes.)

Their conclusion was based on an analysis of 30 genomes of prokaryotes and eukaryotes.  Martin and Embley, commenting on the paper in the same issue of Nature,² said “they call for a radical departure from conventional thinking.” 

Unknown to Darwin, microbes use two mechanisms of natural variation that disobey the rules of tree-like evolution: lateral gene transfer and endosymbiosis.  Lateral gene transfer involves the passage of genes among distantly related groups, causing branches in the tree of life to exchange bits of their fabric.  Endosymbiosis – one cell living within another – gave rise to the double-membrane-bounded organelles of eukaryotic cells: mitochondria (the powerhouses of the cell) and chloroplasts (of no further importance here).  At the endosymbiotic origin of mitochondria, a free-living proteobacterium came to reside within an archaebacterially related host….  This event involved the genetic union of two highly divergent cell lineages, causing two deep branches in the tree of life to merge outright.  To this day, biologists cannot agree on how often lateral gene transfer and endosymbiosis have occurred in life’s history; how significant either is for genome evolution; or how to deal with them mathematically in the process of reconstructing evolutionary trees.  The report by Rivera and Lake bears on all three issues.  And instead of a tree linking life’s three deepest branches (eubacteria, archaebacteria and eukaryotes), they uncover a ring.

Martin and Embley say the proposal is “at odds with the view of eukaryote origins by simple Darwinian divergence,” but consistent with the endosymbiont theory, the idea that organelles like mitochondria and chloroplasts were once free-living cells that became incorporated into another organism in a cooperative merger.  Since this event must have occurred over 1.4 billion years ago, “such time-spans push current tree-building methods to, and perhaps well beyond, their limits.”  Because of the problems inferring ancient episodes from present data, and the confusing mix of functions between the three groups, Rivera and Lake admit their ring metaphor, based on a merger of two groups into eukaryotes, is only a working hypothesis.  “The ring of life does not explain why this happened, but it does provide a broad phylogenetic framework for testing theories for the origin and evolution of the eukaryotic genome,” they conclude.
    So a ring may replace a tree as the metaphor of evolution.  Lake and Rivera must be Tolkien fans; they almost titled their paper, “One ring to rule them all,” but that might have associated their endeavors with those of the Dark Lord.

¹Maria C. Rivera and James A. Lake, “The ring of life provides evidence for a genome fusion origin of eukaryotes,” Nature 431, 152 – 155 (09 September 2004); doi:10.1038/nature02848.
²William Martin and Martin Embley, “Evolutionary biology: Early evolution comes full circle,” Nature 431, 134 – 137 (09 September 2004); doi:10.1038/431134a.

Well, this ought to be testable.  Put some photosynthetic prokaryotes together with archaebacteria in a hot spring, and see if they merge.  Are we supposed to believe that this happened only in the unobservable past but is impossible today?  It should be going on all the time, and should be common knowledge to microbiologists.  It should not be a mystic story imagined by Darwinists alone.
    Did Lake or Rivera observe anything like this happen?  No.  Did they explain how genome fusion could have overcome the barriers and defenses cells use today to protect their information?  No.  Did they do any real scientific, empirical, lab work?  No.  Did they just play with their favorite phylogenetic computer games?  Yes.  Did they find major problems with the standard evolutionary trees?  Yes.  Did they get tired of the old worn-out metaphor?  Maybe.  In the end, they do not have a scientific theory, only a metaphor, and metaphors bewitch you, Saruman.