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

Roberto Takata <rmtakata@gmail.com> wrote:

>>  Even if you manage get the homologous sequences from more birds or
>> crocodilians, it still won't tell you what the _T. rex_ DNA sequence
>> actually was.
> Oh, it will.

No, it won't.  You can obtain as many sequences as you like (bird,
crocodilian, whatever) but it won't bring you any closer to knowing
what the sequence of _T. rex_ was.  You may believe that it does, but
it really won't.

> Bird DNA sequences, crocodilian DNA sequences and
> dinosaurian peptide sequences. I've showed how bird DNA sequence help
> to complete croc DNA sequence with the info obtained with croc peptide
> sequence.

Did you really "show" this... or did you just speculate that it could be done?

> So it shows that unkown ancient (and lost) DNA sequences could, in
> principle, be recovered (in a probabilistic manner).

You're overlooking or ignoring a key point here.  A consensus sequence
includes degenerate codon positions, where the base position can be
two or more alternative bases.  So along with C,G,A,T you'll also have
degenerate bases such as R,S,W,M,N and so on.  There's no escaping
that.  For example, you may get the base right for the first codon
position for a leucine residue (such as C), and the second one will
always be T; but the third codon position for leucine will be a wild
card because it's essentially silent.  No amount of hand-waving about
"probabilities" and "parsimony" is going to tell you what base was at
that position for _T. rex_.

And this is all assuming that _T. rex_ conforms to the consensus
sequence.  Even if crocodilians and birds conform to CTN to encode a
certain leucine residue, who's to say _T. rex_ didn't encode TTA or
TTG for this leucine?  You've told me that it will be C in the first
base position of this leucine codon because that's what the chicken
has, and the zebra finch too for the aligned proline codon.  But your
arguments in support of this extrapolation are totally unconvincing.

> Practical use? Maybe the same practical use of to know the ancient
> dinosaur colour pattern or its mating behaviour.

No, I'm not talking about practical use.  I'm talking about what's the
point of proposing a hypothetical DNA sequence for a _T. rex_ peptide
when there's no way of testing your hypothesis.

Many hypotheses regarding dinosaur behavior can actually be tested.
Anatomical studies and biomechanical modelling can rule in or out
certain behaviors by extinct animals - such as powered flight in
_Archaeopteryx_, or head-butting in _Stegoceras_, or digging in
_Mononykus_.  In each case, an explicit hypothesis is proposed, and
then tested against the available evidence.  Even phylogenies can be
tested, when new fossils come to light, or old ones are re-described -
and new taxa and/or characters are added to the matrix.  Sure, we'll
never *know* what the answer is.  But the most parsimonious
explanation can be determined based on the available data.

On the other hand, the DNA consensus sequence you obtain from bird DNA
sequences (and crocodilian, should you get your hands on those) is a
dead-end as far as the _T. rex_ DNA sequence is concerned.  As I said
above, you can accumulate as many DNA sequences as you like from birds
and crocodilians, but it won't bring you any closer to determining
what the sequence of _T. rex_ actually was.

> A very distant (far-fetched) potential use would be in
> pharmacogenetics. Suppose that we find a ancient fungal lineage and
> recover from it a peptide with antibiotic activity. The secondary and
> tertiary mRNA structure have some importance in the control of the
> protein synthesis, and it depends on the RNA sequence. If we want to
> synthetize a gene that code such a peptide and make a transgenic
> organism that produce such peptide in industrial scale, it could helps
> if a genetic sequence similar to the original one is used.

I'd say not.  If you're expressing a peptide transgenically, and you
want to maximize expression of that peptide, you'll want the codon
usage to match that of the host organism that is expressing the
peptide, not the organism it came from.  In other words, you'll want
the transcription and/or translation mechanisms of the transgenic host
to 'see' the foreign RNA transcript or peptide as one of its 'own'.