On 8/4/2012 1:39 PM, Ron O wrote:
> On Aug 4, 11:10 am, "Steven L." <
sdlit...@earthlink.net> wrote:
>> On 8/4/2012 11:17 AM, Ron O wrote:
>>
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>>> On Aug 4, 7:19 am, Nivalian <
rhed...@gmail.com> wrote:
>>>> On Friday, August 3, 2012 1:22:28 PM UTC-4, Rolf wrote:
>>>>> Says Nivalian. After coming here "hoping to learn a lot and have clean
>>
>>>>> interesting debates with some of you."
>>
>>>>> A cheater.
>>
>>>> A cheater? Here I gave you a database with mapped genomes with actual data and compare the orthologues and you call me a cheater.
>>
>>>> Also, some accused me of cherry-picking. Choose any gene and you will have a different phylogenetic tree.
>>
>>>> Lets compare the 9 primates, which are...
>>
>>>> Gibbon
>>>> (Nomascus leucogenys)
>>
>>>> Chimpanzee
>>>> (Pan troglodytes)
>>
>>>> Macaque
>>>> (Macaca mulatta)
>>
>>>> Orangutan
>>>> (Pongo abelii)
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>>>> Gorilla
>>>> (Gorilla gorilla)
>>
>>>> Marmoset
>>>> (Callithrix jacchus)
>>
>>>> Mouse Lemur
>>>> (Microcebus murinus)
>>
>>>> Bushbaby
>>>> (Otolemur Garnettii)
>>
>>>> Tarsier
>>>> (Tarsius syrichta)
>>
>>>> Here's a look at the CD163 gene:
http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?collapse=none;d...
>>
>>>> Scroll down and find human (in red font). Look at the tree.
>>>> Notice how the Mouse lemur, and Bushbaby are on a separate branch.
>>
>>>> Here's a look at the FOXP1 gene:
http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?collapse=131522...
>>
>>>> Notice that we are closely related to the Mouse Lemur. Compare this tree with the CD163. They look nothing alike.
>>
>>>> A look at the FOXP2 gene:
http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?collapse=131525...
>>
>>>> This depicts chimpanzees closer to humans than gorillas. Please note that there are only 6 primates on the branch. The Bushbaby is in with the cow, pig, and dolphin. The Tarsier more closely related to the squirrel (non-primate). The Mouse Lemure is more closely related to the kangaroo rat (also non-primate).
>>
>>>> In the search, type in any gene. Try the MAP3K3, DCAF7, SHOX...
>>
>>>> You will get a different tree. This simply falsifies the theory of evolution and common descent.
>>
>>>> You support the theory because of philosophical reasons; not scientific reasons.
>>
>>> What you need to do is not cherry pick if you want to deny cherry
>>> picking. You are literally putting up a handful of genes and claiming
>>> what? Does it negate all the other gene data? Can you determine that
>>> none of the known factors that mess up gene phylogenies is not
>>> operating with your examples? Have you ruled out things like gene
>>> conversion? Just using inappropriately highly conserved genes to
>>> analyze recent events is stupid. You were trying to make a big deal
>>> about a gene that hasn't changed much in 40 million years and tried to
>>> make a big deal about a 95% divergence between gorilla and human and
>>> my guess is that you didn't even try to determine if the gorilla gene
>>> was the same gene that they were comparing in the other analyses. Was
>>> gene conversion involved? Did one exon get swapped out? etc. Are
>>> all the same copies of multigene families in the right analysis?
>>
>>> If you don't want to be accused of cherry picking go in alphabetical
>>> order and look at the gene trees. Rule out the multigene families
>>> unless you can rule out gene conversion between family members and
>>> don't use highly conserved genes to analyze an event that happened
>>> only around 5 million years ago. About the best material to use for
>>> this type of recent divergence is the mitochondrial sequence. The
>>> third position changes have not been saturated and you have a bunch of
>>> genes and variable conservation of protein sequence. You have 13
>>> protein genes that have all been inherited as a block among mammals
>>> because paternal transmission of mitochondrial genomes is rare if it
>>> happens at all. You don't have to worry about recombination and gene
>>> conversion events, but you do have to worry about horizontal transfer
>>> (we observe it between closely related species.
>>
>> I admit I don't understand your explanation.
>>
>> Why should there be any genes that depict humans as to closer to
>> non-apes than to apes?
>>
>> How did that come about with the FOXP1 gene, which has humans as more
>> closely related to the Mouse Lemur?
>>
>> --
>> Steven L.
>
> I can't reproduce those results doing my own analysis. The FoxP1
> coding sequence is amazingly similar between the primates. I just
> took NM_032682. This is the human reference sequence for FoxP1
> transcript variant 1. The DNA sequence is 99% similar to the chimp,
> gibbon and orang sequence. Gorrila doesn't show up in my Blast
> search. This is an incredibly highly conserved gene. Horses and
> humans separated by around 80 million years are 96% similar in their
> DNA sequence of the coding region. If you look at the expanded
> phylogenetic tree that Nivalian put up the human transcript map
> associated with mouse lemur is missing a major exon and some other
> exons seem to be altered in size compared to primates. I can't find
> this transcript, the identification number given isn't on the list of
> human transcript variants for FoxP1. I don't know what human FoxP1
> sequence was used for Navalian's comparison, but the reference human
> FoxP1 sequence doesn't come up with the same similarity. The
> reference sequence is the sequence picked to represent the gene. This
> doesn't mean that it can't be a wrong selection or that there isn't
> another sequence that could be better, but it has passed some hurdles
> in its identification. As an example the reference chicken
> mitochondrial sequence has known sequencing errors and may be a
> chimeric molecule (composed of the sequence of two mitochondrial
> sequences) so it isn't the one that I would pick to do phylogenetic
> analysis, but a lot of people that don't know any better keep putting
> it in instead of picking one that would be more accurate.
So you're saying that this was just inadequate or poor sequencing. I
didn't know there were alternatives. Thanks.
--
Steven L.