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:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>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.
>
> Thanks for that reference.
>
> >>>>>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.
>
> No it doesn't. Unless there is an advantage to the transfer itself,
> natural selection doesn't explain it. The importance of the gene has
> nothing to do with this. The importance (or lack thereof) of the
> *location* of the gene is what you need to explain. If there is indeed
> an ordering of transfers by importance, you have so far not managed to
> connect that phenomenon with any explanation. You supposed explanation
> is empty.
>
> > 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.
>
> Actually, I can think of a reason why there might actually be a bias
> toward preservation of the nuclear copy. However, this bias has no
> relationship to the importances of the genes. If, during the period
> when two functional copies exist, one of the genes experiences a loss of
> function mutation, the other one will take over and the other will no
> longer be subject to selection. mtDNA has a much higher mutation rate
> than nDNA (in most metazoans, at least -- not true throughout life) and
> therefore the mt copy is more likely to experience that first loss of
> function mutation. Interestingly, green plants have a much slower rate
> of mtDNA than nDNA evolution, and I seem to recall that their mt genomes
> are unusually large. Coincidence? Don't know.
>
> [snip]

Do you think that the importance of the gene could correspond to the
probability of fixation for the duplication in the nuclear genome?

.

Relevant Pages

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  • Re: Why dont mitochondria have junk DNA?
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