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

Pardon, by 'you' you mean me (Roberto Takata)?


Roberto Takata

On Fri, Sep 16, 2011 at 9:30 PM, Dora Smith <villandra@austin.rr.com> wrote:
> I think the question was, now that we've gotten you to believe that it is
> actually possible to have the DNA of the same protein coded two different
> ways, how would you reconstruct what was teh ancestral protein?
> "Maximum likelihood" hardly does it - this is circular reasoning!    The
> question is, how would you arrive at which one is most likely?
> Dora
> ----- Original Message ----- From: "Roberto Takata" <rmtakata@gmail.com>
> To: <dinosaur@usc.edu>
> Sent: Friday, September 16, 2011 1:33 PM
> Subject: Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)
>> On Fri, Sep 16, 2011 at 2:54 PM, Erik Boehm <erikboehm07@yahoo.com> 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
>> guessing.
>>> Even when consesnus sequences exist, you still find many variations from
>>> species to species (SNPs)....
>> Not only