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Steve LaBonne and Mitochondrial genetic codes

Sean Eddy eddy at wol.wustl.edu
Tue Aug 29 18:26:58 EST 1995

In article <41kpkj$b3k at newsbf02.news.aol.com> hpyockey at aol.com (HPYockey) writes:
  [much edited, for brevity]

  >...As usual Steve LaBonne presents himself as an expert without quoting any
  >of his publications....
  >You need to pay more respect to your betters!...

Boy, I sure hope we don't need to trot out our CV's in this forum and
start arguing from authority. LaBonne made a cogent point. I don't
care if he's a Nobel Prize winner or if he's a dishwasher at
Dartmouth. Can you refute his argument?

To summarize what I understand to be the question: were the
non-standard genetic codes of mitochondria and ciliated protozoa
derived late in evolution from the universal code? Or, as you argue,
did the origin of the variant codes predate the last common ancestor
of archaea, eubacteria, and eukaryotes?

LaBonne rightly points out that if one plots the positions of
non-standard genetic codes on the accepted phylogenetic tree, one sees
that these positions are scattered in the "leaves" of the tree. This
is the behavior expected of a derived character, not an ancestral one.

Your only parry seems to be the following:

  >In the first place 'phylogenetic evidence' is hardly written in letters of
  >gold on tablets of jade. Notice the African Eve controversy. Not being
  >able to follow phylogeny back a few million years puts great doubt about
  >following it back 3.8 billion years to the Isua formation. The authors who
  >contributed to that ran their prefered program tens of thousands of times
  >and took a vote. I suggest that is not very good science.

Presumably, this means you agree with LaBonne that the accepted
phylogenetic tree is inconsistent with your theory. The Woese rRNA
tree must be wrong for your idea to be correct.

The Woese rRNA tree and African Eve are apples and oranges on this
point. The placement of the mitochondria in the eubacterial lineage is
obvious to the eye. There doesn't exist a first year grad student, let
alone a phylogenetic tree building program, that will put
mitochondrial rRNA anywhere but firmly in the eubacterial lineage.

How do you propose to move the mitochondria from there?

- Sean Eddy
- Dept. of Genetics, Washington University School of Medicine
- eddy at genetics.wustl.edu

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