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

Roberto Takata <rmtakata@gmail.com> wrote:

> Of 60 codons, 14 would be dubious for the first and second position
> analysing only the aa sequence and using the vertebrate mithocondrion
> genetic code table. Using G. gallus DNA sequence as a guide, those
> positions for 8 codons was right, 3 was wrong and 3 could not be
> determined. Surely it is an improvement.

I think Dora Smith had a point when she said: "Well, I think that the
assumption that the least possible change occurred over time most
parsimoniously implies that evolution itself does not occur."

Simply filling in the blanks in a _T. rex_ DNA sequence based on the
chicken DNA sequence goes way further than parsimony.

> It is not ignored. What is regarded is that, under parsimony, as few
> mutations as possible is allowed (or we could use other parameters as
> codon usage bias, transition/transversion rate and so on to build a
> more complex model).

Yes, the model could be very complex indeed.  And yet, this model
would still be utterly useless.

> The technique could be tested with extant organisms - and I did it
> with birds and croc. And yes it could potencially be tested for T-rex.
> Lets put aside the possibility of ancient DNA be obtained. We could
> get eventually more proteins.

More _T. rex_ proteins (even assuming we have any now) would still be
no help at all in reconstructing the exact DNA sequence.

> It must be taken into account, but it is not the only factor. As I've
> said: the secondary and tertiary strucuture of mRNA is very important.
> Even some post-translational modification depends on the some
> sequences.

In these cases, I thought that the untranslated regions (UTRs) of the
mRNA were paramount.  Much more so than the part that is translated
into protein.