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Steve LaBonne and Mitochondrial genetic codes

aroger at ac.dal.ca aroger at ac.dal.ca
Wed Aug 30 15:03:04 EST 1995

In article <41kpkj$b3k at newsbf02.news.aol.com>, hpyockey at aol.com (HPYockey) writes:

> 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.

The validity of this kind of argument is suspect.  Consider the following
parallel argument:

Investigator employed approach X and incorrectly inferred result Y,
Therefore anyone who employs approach X will incorrectly infer a result.
The problem with the mitochondrial eve work is not that the methods
do not work, it is that those employing the methods:
1) incorrectly used the methods
2) overstated conclusions based on the methods

In addition,
Yockey is suggesting that because it is impossible to infer the branching
order of a tree generated in the last few million years  therefore
this difficulty will only become worse when branching events occurred
much earlier in the history of life are considered.  I suggest that
this is unlikely.  The problem of resolving branching orders in phylogenies
can be stated in a parsimony framework: if two organisms have diverged more
recently from each other than a third organism, then there will have
been changes (in DNA sequence or morphology) on the common branch they share
which the third organism will not exhibit.  In distance terms, more closely
related organisms will be more similar to each other than either is to
more distantly related organisms.  From this it is clear that, at least
for molecular phylogeny, as the time separating events of branching 
becomes less, then there will be less time to accumulate changes in sequence
(synapomorphous changes). Since methods depend upon these changes to
resolve branching orders, the shorter the time between cladogenetic
events the less likely a method of phylogenetic reconstruction will
correctly resolve the true relationships.
The upshoot of all of this is that there are "hard" phylogenetic
problems- those where time between successive branching events is
very small and there are "easy" problems- where lots of time has
accumulated between branching events.  The mitochondrial Eve problem
is one of the former.  It is not necessarily the case that "deeper"
phylogenetic problems are going to be harder in this sense...there
are some very easy ones- for instance the holophyly of eukaryotes
is supported by morphology, SSU ribosomal RNA, and numerous protein
-coding genes...yet the common node shared by all eukaryotes is at least
1.5-2.2 billion years old.

> Chapter 7 applies to a critter that appeared earlier than the urgenote,
> whatever that may mean. Chapter 7 concludes that were several of these and
> there may have been more than one origin of life event, as Darwin
> suggested in the last chapter of the Origin of Species. The standard story
> is that several of these early critters got eaten and became mitochodria.

This standard story is completely outdated.  I suggest you read some
of the literature on the endosymbiotic origin of mitochondria that has
appeared in the molecular evolution literature in the last two decades.
There is strong evidence that the endosymbiont which gave rise to
the mitochondrion was related to a group of extant eubacteria called
alpha purple (or proteo-) bacteria.  Mitochondrial small subunit
ribosomal RNA genes have a strong phylogenetic affinity to alpha purple
bacteria.  This same connection is found for mitochondrial cytochrome
oxidase subunit I and for mitochondrial chaperonin 60.  Thus there
are multiple congruent molecular phylogenies which support the same
affinity with multiple methods of phylogenetic inference.  Some references
Yang et. al., (1985) Proc. Natl. Acad. Sci. USA, 82, 4443-4447
Cedergren et. al. (1988) J. Mol. Evol. 28, 98-112
Gray, M.W. (1992) Int. Rev. Cytol. 141, 233-357
Viale et. al. (1994) FEBS letters 341, 146-151

> They took their own genetic code with them. The critters with the standard
> code appeared and after their meal of simpler critters they continued to
> evolve and became what you call the urgenote.  Perhaps their remains
> formed the kerogen of the Isua formation. Presumably they later became
> Eukaryota, Eubacteria, and Archea. Their ancestors continue to contain
> mitochondria with their separate genetic system today. 

I hope you mean that only the Eukaryota retain mitochondria.

Look, this whole argument is based on a dim knowledge of the diversity
of organisms and mitochondrial genetic systems.  Altered genetic codes
DO NOT APPEAR IN ALL MITOCHONDRIA.  Most of the generalizations made are
based on the animal mitochondrial genetic code. This represents 540-600
MYA only of the 1.8-2.0 billion years of eukaryotic (and possibly)
mitochondrial diversity.  For instance most of the changes in the
code in animal mitochondria are restricted to animal mitochondria-
only UGA encoding tryptophan is found elsewhere in mitochondria. 
But this UGA is not found in chlorophyte mitochondria. Moreover,
the two subgroups of the alpha purple bacteria which are outgroups
to mitochondria both use the canonical genetic code.  All other
eubacterial groups (with the exceptions of mycoplasmas) use the
universal code.  Archaebacteria all use the universal code as far
as anyone knows and MOST eukaryotes also do (the exceptions
being ciliates, acetabularia and candidas). In every case of genetic
code difference from the "universal" code, the change seems tightly
restricted to a clade with numerous outgroups lacking the change.It is 
thus most parsimonious to suggest that the "universal" code is
> Steve: If you go to the library you will find (with the help of the
> librarian) a book called Molecular Biology of the Gene by Watson, Hopkins,
> Roberts, Steitz and Weiner  Published by  Benjamin Cummings. Read Chapter
> 15 The Genetic Code. 
> You will find the answers to your questions in that chapter. 

The pot calls the kettle black!

This kind of polemicy I find really unnecessary.  If you would stop
reading out of date textbooks and start reading the primary literature
then you might be able to keep current with ideas in the field of
molecular evolution. 

> As Ludwig Wittgenstein was oft heard to say: "Wovon man nicht sprechen
> kann, darueber man muss schweigen. Steve: "Schweigen sie bitte bis sie das
> Buch gelesen und verstanden haben." If you were multicultural you could
> read that!

I always thought the use of other languages was to express meaning
that one couldn't otherwise.  This serves only to obfuscate. 
Just remember that your ability to express yourself in multiple
languages could also allow you to communicate your ignorance to
a larger audience.

Andrew J. Roger
aroger at ac.dal.ca

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