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



Since you said 'this', not 'that' so I assume that it was a
self-criticism. I'm really really impressed by your humbleness.

[]s,

Roberto Takata

On Sat, Sep 17, 2011 at 12:37 PM, Dora Smith <villandra@austin.rr.com> wrote:
> Roberto, this post is exactly as clear as mud.
>
> Dora
>
> ----- Original Message ----- From: "Roberto Takata" <rmtakata@gmail.com>
> To: <dinosaur@usc.edu>
> Sent: Friday, September 16, 2011 11:23 PM
> Subject: Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)
>
>
>> Well, since you said: "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", I've got a bit confused.
>>
>> It assumes that there was a time in which the mentioned 'you' thought
>> that it was not possible to have two (or more) different DNA sequences
>> coding for the same peptide sequences... Since it is not my case, I
>> was wondering if you (Dora Smith) have had make a misadressing.
>>
>> The fact that you (Dora Smith) used the pronoun 'we' was of no help
>> here, since I was arguing with Erik Boehm; and I'm not recollecting
>> any message of your in this thread, except for the one addressed to
>> Mike Keesey.
>>
>> Well, clarified that you was addressing to me. As implied from what
>> was said above the sentence: "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" is completely misguided. In any other way I would
>> not talk about "margin of error" since my first message about the
>> possibility of infer the DNA sequence from the coded peptide aa
>> sequence. And there will be no need of comparative sequence alignment.
>>
>> So the answer to your first question: "how would you reconstruct what
>> was teh ancestral protein"? was given even before you asked it: by
>> comparison of the peptide sequences of the descendants. It is done not
>> only with protein sequences, but with morphological characters,
>> behaviour and a plethora of heritable characters.
>>
>> Maximum likelihood - combined by other techniques - help us to manage
>> the probablity of alternative paths. If in a lineage the transition
>> mutation is more common than by chance, then that probability is taken
>> into account. No circular reasoning here.
>>
>> []s,
>>
>> Roberto Takata
>>
>> On Sat, Sep 17, 2011 at 12:57 AM, Dora Smith <villandra@austin.rr.com>
>> wrote:
>>>
>>> The person I was replying to. The person who argued about maximum
>>> likelihood whatever would surely recognize himself.
>>>
>>> Dora
>>>
>>> ----- Original Message ----- From: "Roberto Takata" <rmtakata@gmail.com>
>>> To: <dinosaur@usc.edu>
>>> Sent: Friday, September 16, 2011 7:35 PM
>>> Subject: Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)
>>>
>>>
>>>> Pardon, by 'you' you mean me (Roberto Takata)?
>>>>
>>>> []s,
>>>>
>>>> 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
>>>>>
>>>>>
>>>
>>>
>
>