Australopithecus and orangutans

[B.J.Tindall]

Jason,
I took the trouble to download the reference and read it through. Okay in
theory, but rather uncoupled from the "facts". The authors use 18S rDNA as
their model system. In the case of the 16S rDNA (indirectly the 16S rRNA)
there have been some detailed studies on the struture and role of this
molecule in the small subunit ribosome. This work indicates a significant
interaction between structure and function of the 16S rRNA together with
interactions with the accompanying proteins. The consequences can be seen
if you actually do alignments of closely related 16S rDNA - if there is
about 7-8% sequence divergence the changes are usually located in certain
regions of the 16S rDNA - usually what one would call the hypervariable
regions. This is even more pronounced the more similar two sequences are.
In the paper you quote the authors assume that by introducing mistakes
randomly into the 16S rDNA that they have a suitable reflection of real
evolution. What we see in reality is the fact that changes are not randomly
distributed in the gene, but a located in hot-spots, which reflect the
structural and functional limitations/flexibility of the 16S rRNA. Given
the fact that there are regions where no changes are allowed, while there
are others where changhes are more frequent, the model the authors use does
not fit the real situation. There is also no evidence that hot-spots are
not saturated. In this case I would say the paper may be mathematically
sound, but biology is operating by different "rules". Again I have to
repeat that a) I don't belive everything which is published and that b) I
fully accept a role for gene and protein sequences, but one should at least
try to corelate models and reality.
As for your interest in "ancient bacteria" I will get back to that later.
Brian


At 11:36 15.5.2003 -0400, Jason de Koning wrote:
>>
>> Sanson et al., 2002.  Experimental phylogeny of neutrally evolving DNA
>> sequences generated by a bifurcate series of nested polymerase chain
>> reactions.
>> http://www.ncbi.nlm.nih.gov:80/entrez/
>> query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11801745&dopt=Abstract
>>
>> If one chooses to ignore molecular data out of principle, one must
>> confront their principles with evidence from in silico experiments
>> (simulation), in vitro experiments (PCR), in vivo experiments
>> (bacteriophage experiments), and from congruence between large
>> morphological and molecular datasets, which all suggest that the
>> cladistic analysis of molecular data (as defined conventionally) all
>> lead to known, correct, or congruent answers.
>>
>> - Jason
>>
>


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