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

[Erik Boehm <erikboehm07@yahoo.com>]

> > Now lets say we have an extinct sequence indicating
> Serine.
> > Now lets say in extant organisms we also find Serine.
> > What then?
> 
> Then we have the DNA sequence of extant organisms...

And when we find that extant organisms use more than 1 of the 4 possible codon 
sequences to encode Serine at that position?

> > Suppose we find its sometimes also Threonine or
> Alanine.
> 
> Align the protein sequences - including the paleoprotein;
> align the
> DNA sequences. Analyze phylogenetically: where in the three
> the fossil
> organism settle down?

Lets take an example of humans and chips as the extant organisms.
In more than one case (such as hemoglobin), Humans and chimps have the exact 
same amino acid sequence, but a slightly different DNA sequence to encode that 
protein.
Suppose we find a fossil ape that is just outside the Human-Chimp clade.
Which DNA sequence do we use? 
What if it is on the human branch, but very basal, do we assume in every case 
where there is ambiguity between humans and chimps that we use the human 
version. Sure you could compare to gorillas, but what of the cases where the 
protein sequence is different (as the amino acid identity with them is not 
100%). If we find consensus between the chimp and gorilla, sequence, we 
conclude the chimp sequence is basal, but this basal member of the human 
branch.... we still don't know when to go with the human encoding for a 
particular aa, or the chimp encoding.


You simply cannot reconstruct the DNA sequence that made the amino acid 
sequence with any certainty. You will be reduced to arbitrary guessing.

Every single codon assignment is going to involve some level of guessing 
(unless it is methionine in a vertebrate).
Even when consesnus sequences exist, you still find many variations from 
species to species (SNPs)....
Its a pointless endeavor. Your DNA sequence generated won't be any more useful 
than the amino acid sequence (which you can still use for phylogenetic 
analysis).

It is pointless to generate a DNA sequence from an amino acid sequence of an 
extinct organism. I can say with well over 95% confidence that whatever 
sequence you generate (assuming its of any reasonable length) will be wrong.