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Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)



Roberto Takata <rmtakata@gmail.com> wrote:

> Here the zebra finch DNA sequence:
> GGT CCT CCT GGT GAG AGT GGT GCT GTT GGC CCT GCT GGT CCC ATT GGA AGC CGT
>
> Remembering that the chicken DNA sequence is:
> GGT CTT CCT GGT GAA AGC GGT GCT GTT GGT CCT GCT GGT CCT ATT GGA AGC CGT
>
> If we had compared T-rex with zebra finch the conclusions would be
> essentially the same.
>
> What we could do now is compare the chicken and zebra finch, using the
> chicken DNA and peptide sequences and the zebra finch peptide sequence
> (or vice-versa). Using the same rationale used in the T-rex/chicken
> comparison, the C in the first position of the second codon would be
> correctly inferred. The first and second positions in the sixth codon
> of zebra finch DNA would be correctly inferred as being A,G.


Yeah.... except that the zebra finch and chicken are both birds.  I'd
guess it'd also be the same for the turkey, with it (_Meleagris
gallopavo_) being a kissing cousin of the chicken (_Gallus gallus_).
Doesn't mean a thing as far as _T. rex_ is concerned - even if the
peptide sequence is the same for this fragment.  Trying to
retro-translate a peptide sequence back to DNA sequence is a *very*
dangerous business - degenerate base positions (Y, R, W, S, N, etc)
exist for a very good reason.   (Assuming that the vaunted _T. rex_
collagen peptide actually came from _T rex_.)


So let's say with all your jiggery-pokery (comparative analysis,
maximum likelihood, substitution rates, codon bias - and whatever
other molecular biological thingies you brought up) you do come up
with "likely" _T. rex_ DNA sequence for this peptide.  What then?
What can you do with it?  You'll never know if you're right, because
we're never going to find _T. rex_ DNA.  Not only do I regard the
entire exercise as methodologically flawed, but I don't understand the
point of the exercise.





Cheers

Tim