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Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)
On Fri, Sep 16, 2011 at 2:54 PM, Erik Boehm <firstname.lastname@example.org> wrote:
> And when we find that extant organisms use more than 1 of the 4 possible
> codon sequences to encode Serine at that position?
Align the sequences, put on a tree.
> 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?
The reconstructed common ancestral one. We do it with humans - SNPs
and other intrapopulational variations are taken into account.
> 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.>
We could use maximum likelihood, for example.
> You simply cannot reconstruct the DNA sequence that made the amino acid
> sequence with any certainty. You will be reduced to
> arbitrary guessing.
"cannot with *any* certainty" is an exaggeration. It is made all the
time when the ancestral state is inferred from extant sequences.
> Every single codon assignment is going to involve some level of guessing
> (unless it is methionine in a vertebrate).
It is true. Actually even when we find a methionine it will involve
some level of guessing. It is just that it will not be a random
> Even when consesnus sequences exist, you still find many variations from
> species to species (SNPs)....
Not only from species to species, but *within* species - between
individuals of the same species. Actually this SNPs are *informative*.
> 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
There is no need of being useful. Many people think that guessing the
origin of avian flight is useless.
> 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.>
If you regard 'wrong' as "we can't be 100% sure that the sequence
obtained have a 100% match with the actual - and unkown - sequence",
then yes. In this regard, it will be true to any sequencing - and I'm
talking about direct DNA sequencing here - even with fresh sample.
I think that it is better to say: "We can say, within 95% of
confidence, that the obtained sequence differ no more than +/-X% from
the actual sequence".