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Re: T. rex DNA



>1) The assumption that the *T. rex* sequence is an artifact is silly.  Any
>bacteriologist knows that maintaining aseptic conditions in a test tube (or
>an eppendorf tube) is easy.  The chance of contamination and the actual
>frequency of its occurrence is nearly zero.

        This isn't really accurate. I've been involved with PCR diagnostics
and systematics for some years now and the presence of false positives, 
even with safeguards such as aerosol pippette tips, fumehoods, acid 
treatment, -ve controls, etc. is still a problem. Additionally, when you're 
attempting to amplify with highly conserved primers (as they almost certainly 
will have done) the chances increase. 


>2) If contamination should occur, it is easy to identify.  If contaminated,
>the sequence in question will not be new to your data base.  It will align
>with, and be identical to, a sequence that is already in your computer.

        I agree it could be relatively easy to identify. A search with
NCBI's Blast program should tell you if you have a likely contaminant. 
Unfortunately not every sequence you might amplify will be on the 
database. Of course the most likely one is your positive control and 
this sequence will certainly be know to you. 

>3) Regarding similarity of the *T. rex* sequence to a bird (or any other
>chosen outgroup):  There is very little information regarding the mean
>sequence divergence between species, as was asked in this forum.  That is
>because sequencing is labor intensive and expensive.  Therefore, very few
>species have been completely sequenced.  Molecular systematists simply
>choose the "appropriate" gene (or hunk of a gene) for the question they are
>asking.  This choice is based on trial and error and familiarity with the
>literature.  All genes accumulate mutations at different rates.  Genes that
>code for histone proteins are identical in bacteria and humans! 

        For this study I'm sure they've chosen some portion of the 
mitochondrial genome. It's undoubtably been sequenced in a bird such as 
chicken and in on the Genbank. The abundance of the mitochondral genome
and the wide variety of genes it contains make it the likely choice.
        For molecular systematics, the choice of the gene
you analyse is very important, but I think in this case the paramount 
consideration would be getting a product from the PCR reaction. They 
probably don't care if the sites are informative or not (ie. silent
changes have been swamped) if they can show it (amplification)
is possible.
        Sorry if I seem to be sceptical about this finding. I would be
thrilled if it turned out to be true. Unfortuantely my enthusiasm is
tempered with my experiences in this area. I'll be watching my Science.


Les Willis
Research Station 
Agriculture Canada