Re: Why don't mitochondria have junk DNA?


John Harshman wrote:
> rev.goetz wrote:
>
> > John Harshman wrote:
> >
> >>rev.goetz wrote:
> >>
> >>
> >>>John Harshman wrote:
> >>>
> >>>
> >>>>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.
> >>>
> >>>Most of the rps genes transferred from the mitochondial genome to the
> >>>nuclear genome in several lineages.
> >>
> >>In a particular order?
> >
> > There was a typical order with occasional exceptions. I already gave
> > you the order: "The approximate hierarchy follows: rps1, rps10, rps11,
> > rps2, rps7, rps8, rps4, rps19, rps19, rps13, rps14, rps12, and rps3."
>
> Don't confuse order with hierarchy. And don't confuse me by confusing
> them. OK, so that's the order. Now, how did the author figure out the
> order? It would be necessary for some species to exist with all possible
> intermediate states, i.e. all except rps3 transferred to the nucleus,
> all except rps12 and rps3 transferred, etc., and all the taxa with those
> conditions arranged as subsets with the proper nesting. Is that the case?

I think that you are accurately describing the data. Buratovich has a
rich bibliography with dozens of references. While I disagree with his
conclusions about ID, I recommend the review sections of his article.
Here is one of his primary references: Lang BF, Gray MW, Burger G.,
"Mitochondrial genome evolution and the origin of eukaryotes"
_Annu_ _Rev_ _Genet_ (1999) 33:351-97.

>
> >>>And the genes were conserved after
> >>>the transfer, and they currently perform vital ribosomal functions.
> >>
> >>Well, duh.
> >>
> >>
> >>>Since the genes were conserved after the transfer and they currently
> >>>perfom vital functions, I conjecture that the transfer was caused by
> >>>natural selection as opposed to random drift. On the other hand, I do
> >>>not have the slightest idea why the transfer had a selective
> >>>andvantage.
> >>
> >>Sorry, this makes no sense. We're talking about the transfer. Of course
> >>the genes are conserved by selection. All functional genes are conserved
> >>by selection. If there are two copies, it's likely that only one of them
> >>will be conserved, which accounts for loss of the mitochondrial copy.
> >>(Note that even if we flip a coin to see which copy is conserved after
> >>any duplication event, the mitochondrion will progressively lose genes,
> >>since there is no force copying nuclear-encoded mt genes back into the
> >>mt genome. If, by chance, the mt copy is lost, that's it. If the nuclear
> >>copy is lost, we never hear about it. We will sometimes see nuclear
> >>mt-pseudogenes, and we do.)
> >>
> >>Don't confuse the forces maintaining the existence of at least one
> >>functional copy with the forces that cause transfer of genes to the
> >>nucleus (which includes two steps: 1) copying; 2) loss of the mt copy).
> >
> > Okay, I conjecture that the duplication in the nuclear genome was
> > preserved by natural selection since the original mutation event. And
> > the loss of the mt copy could have been drift or selection. However, if
> > the mt copy was lost by drift, the lack of selection on the mt copy
> > occurred only because of the selection preserving the nuclear copy. So
> > even if drift was involved, natural selection was still a factor.
>
> Yes, yes. Natural selection preserves one copy. Drift disposes of the
> other. This is not in dispute. The point is that natural selection does
> *not* explain the transfer of function to the nucleus. Nor does it
> explain in any way why there should be an order to the transfer of rps
> genes. Or at least you have not proposed any explanation so far.

Buratovich (June, 2005: p. 109) notes that the typical order of the
gene transfers correspond to the importance of each respective nuclear
gene function in regards to the ribosome. And I (December, 2005)
conjecture that the various levels of importance for each nuclear gene
correspond to various levels of selective advantage for each nuclear
gene. And this helps to explain how natural selection caused the
typical order of the gene transfers.

On the other hand, I have no clue as to why in various lineages say the
nuclear rps1 had a significant positive selective advantage while the
mt rps1 was not preserved by natural selection. Perhaps an extensive
literature review would answer that question for me, but for now I do
not have the time to do such a literature review.

>
> >>>If you want more details about the history of the rps gene transfers,
> >>>you will have to look up the Buratovich (2005) article and its
> >>>respective references.
> >>>
> >>>Buratovich, Michael. "The Serial Endosymbiosis Theory: Cellular
> >>>Origins and Intelligent Design Theory," _Perspective on Science and
> >>>Christian Faith_, 57:2, p. 98-1??, June 2005.
> >>>
> >>>Below is a link to a list of libraries that carry _Perspective on
> >>>Science and Christian Faith_:
> >>>http://www.asa3.org/ASA/asalib.html
> >>
> >>I don't suppose this is online anywhere that you know of? I see there is
> >>a library near me, and I may try it. Interesting that Buratovich is (or
> >>at least once was) on the NCSE advisory board. Based on press releases
> >>from his sectarian college, his argument seems like a seriously naive
> >>misunderstanding of Darwinian theory, i.e. his claim that natural
> >>selection explains only competition, never cooperation.
> >
> > I know that the journal publishes all articles online after roughly 2
> > years. But I do not know of an online source in the meantime.
> >
> > I agree with you that his argument is weak. In personal communication,
> > I refuted Buratovich on 2 points. First, I refuted his claim that the
> > rps hierarchy resulted from ID instead on natural selection. Second,
> > his article does not credit Darwin for Darwin's discussions of
> > co-evolution, which I think has some similarity to endosymbiosis, at
> > least conceptually. But my Letter to the Editor (December, 2005)
> > included only the first point.
>
> Endosymbiosis is one form of co-evolution.
>
> > On the other hand, the article gave me an excellent review of
> > endosymbiosis theory.
> >

.

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