Re: Why don't mitochondria have junk DNA?

rev.goetz wrote:

> John Harshman wrote:
>
>>rev.goetz wrote:
[snip]

>>>>>Yes, no natural selection is required. Neutral theory helps to explain
>>>>>this. On the other hand, the hierarchal transfer of ribosomal protein
>>>>>small unit (_rps_) genes from mitochondrial genomes to nuclear genomes
>>>>>most likely resulted from natural selection because the hierarchy
>>>>>relates to the importance on the functional importance of respective
>>>>>the _rps_ genes.
>>>>>
>>>>
>>>>Words missing or added here? It doesn't parse. Not sure what you mean by
>>>>"hierarchal transfer" either. At any rate, plase explain why rps
>>>>transfer to the nucleus is any less potentially the result of neutral
>>>>processes than, say, cytochrome c transfer.
>>>
>>>
>>>I do not know enough about cytochrome c to make the comparison, but I
>>>will try to explain the hierarchy and the relationship to natural
>>>selection. Buratovich (2005) notes an approximate hierarchy in the
>>>transfer of rps genes from the mitochondrial genome to the nuclear
>>>genome based on a comparison of 14 species. The approximate hierarchy
>>>follows: rps1, rps10, rps11, rps2, rps7, rps8, rps4, rps19, rps19,
>>>rps13, rps14, rps12, and rps3.
>>
>>Still not clear what "hierarchy" means here. Do you mean that there is
>>an ordering to the probability of transfer, with one end high and the
>>other end low? Or that transfer of one gene on the list is a
>>prerequisite for transfer of the next? Or what?
>
> The hierarchy includes both the historical sequence of the transfer and
> the probability of the transfer. The sequence, however, is not a
> prerequisite, but a typical order with occasional exceptions.

You have amazing powers of non-clarity.

>>>The genes that encode the proteins that are more vital for ribosomal
>>>function are more likely to be transferred and preserved according to
>>>the probabilities of natural selection. Likewise, the genes that encode
>>>proteins that are less important to ribosomal function are less likely
>>>to be transferred and preserved according to the probabilities of
>>>natural selection.
>>
>>Why?
>
> I conjecture that the genes that are more vital for ribosomal function
> have a higher relative fitness compared to the genes that are less
> vital for ribosomal function.

This makes no sense in standard biological terms. Loci are not competing
between each other and have no relative fitnesses in any usual sense.
Perhaps you mean it in some non-usual sense, but I don't know what you mean.

> And relative fitness corresponds to the
> percent of selective advantage. And the percent of selective advantage
> corresponds to the probability of fixation by postive natural
> selection. So if a mutation puts a mitochondrial gene into the nuclear
> genome, then the selective advantage of the given gene determines the
> probability of fixation for that gene. Likewise, the vitalness of the
> gene function corresponds to the probability of fixation for the
> respective gene. (I hope that I made myself clear, but I will try again
> if I am still unclear.)

This is relatively clear, but highly confused. What is the advantage to
the organism or to the mitochondrion if a given gene is in the nucleus
or mt genome? What is driving the nuclear copy to fixation and the mt
copy to extinction? Why should the vitalness of a gene change that
advantage, whatever it is?

> By the way, Buratovich orignally proposed that front-loaded ID caused
> the hierarchal rps gene transfer. But in a Letter to the Editor, I
> (December, 2005) proposed that the probabilities of natural selection
> can explain the hierarchy. And Buratovich personally conceded to me,
> "With respect to selection and mutations being solely responsible for
> the hierarchy, I must admit that this is wholly possible."

And I still don't understand what this hierarchy is. Step back a bit.
What are the raw data that are being interpreted here? Are you looking
at lists of species with particular genes either in mt or nuclear
genomes? Are you looking at phylogenetic trees with gene transfers
mapped onto them? Or something else?

>>Buratovich (June 2005) _Perspectives on Science and Christian Faith_.
>>Table 2, p.107.

Could you give a complete citation for this, just in case I can locate
it somewhere? Author's full name, article's title, page numbers, etc.

.

Relevant Pages

  • Re: Why dont mitochondria have junk DNA?
    ... > once transferred, remained under purifying selection. ... wherever its coding gene happens to be located. ... I conjecture that the duplication in the nuclear genome was ... > Hierarchy is a bad word to use here. ...
    (talk.origins)
  • Re: Why dont mitochondria have junk DNA?
    ... Buratovich notes an approximate hierarchy in the ... > an ordering to the probability of transfer, with one end high and the ... >> the probabilities of natural selection. ... So if a mutation puts a mitochondrial gene into the nuclear ...
    (talk.origins)
  • Re: Why dont mitochondria have junk DNA?
    ... >> the probability of the transfer. ... >> selection. ... So if a mutation puts a mitochondrial gene into the nuclear ... >> genome, then the selective advantage of the given gene determines the ...
    (talk.origins)
  • Edser: semantic insanity.
    ... > another probability) that the replicate gene (note: ... > independent gene level of selection. ... > FACT that not one single independent gene fitness has ever ...
    (sci.bio.evolution)
  • Re: The Irony of Hamiltons Success
    ... by the probability of genes identical ... selection within just the ONE body: ... organism level and the Hamiltonian genomic gene ... No rationale has ever been provide as to how Hamilton's ...
    (sci.bio.evolution)