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:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>>John Harshman wrote:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>>rev.goetz wrote:
> >>>>>>>>
> >>>>>>>>[snip]
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>>>>Do you think that the importance of the gene could correspond to the
> >>>>>>>>>>>probability of fixation for the duplication in the nuclear genome?
> >>>>>>>>>>
> >>>>>>>>>>I see no reason why it should. Do you?
> >>>>>>>>>
> >>>>>>>>>Well, I think that the importance of a gene corresponds to the relative
> >>>>>>>>>fitness of the gene after gene duplication.
> >>>>>>>>
> >>>>>>>>Genes don't have fitnesses. Alleles do. Now we could talk about
> >>>>>>>>differences in fitness between a duplicated gene (mt and nuclear copies)
> >>>>>>>>and an unduplicated gene (mt copy only), if that's what you mean. I
> >>>>>>>>don't see why we would expect such a difference, though.
> >>>>>>>
> >>>>>>>
> >>>>>>>Okay, I am referring the initial mutational event of the mt gene
> >>>>>>>inserting into the nuclear genome of an individual specimen. That
> >>>>>>>initial mutational event resulted in essentially a new allele in the
> >>>>>>>nuclear genome. Instead of using the term "fitness, we will say that
> >>>>>>>the new allele had an advantage that was positive or neutral or
> >>>>>>>negative. And the new allele either became fixed or became extinct. And
> >>>>>>>in most cases the new allele became extinct. But in some cases, the new
> >>>>>>>allele fixed in the nuclear genome. And if the new allele had a
> >>>>>>>positive advantage, the new allele fixed by natural selection.
> >>>>>>>
> >>>>>>>So I will say that the importance of the allele corrosponds to the
> >>>>>>>advantage of allele.
> >>>>>>
> >>>>>>The question to ask is why there should be such an advantage.
> >>>>>
> >>>>>
> >>>>>Your question sounds deeply philosophical and beyond the realm of
> >>>>>science. Science cannot answer questions about why should there be
> >>>>>anything.
> >>>>>
> >>>>>Or did you mean say that the question to ask is why there was such an
> >>>>>advantage?
> >>>>
> >>>>"Why" has several meanings, and the teleological meaning is irrelevant
> >>>>here. Note that you yourself use "why" in your question. This is a red
> >>>>herring.
> >>>>
> >>>>In order to ask why there was such an advantage, we have to establish
> >>>>that there indeed was such an advantage, which you have not done. I was
> >>>>asking for a theoretical reason why there would have been such an
> >>>>advantage. If we can come up with a plausible reason, we have made progress.
> >>>
> >>>
> >>>I was not suggesting anything teleological about the use of the word
> >>>"why." But your phrase "why should" was confusing, enough with that.
> >>>
> >>>Apart from any knowledge of gene function, we know that there was a
> >>>molecular convergence of homologues in several lineages where
> >>>functional rps genes duplicated and were conserved for hundreds of
> >>>millions of years. It would be hard for me to imagine if this resulted
> >>>from drift. This looks like selection to me, at least in the cases of
> >>>the duplicated functioning genes that were conserved for hundreds of
> >>>millions of years.
> >>
> >>You remain seriously confused, and this is reflected in your ambiguous
> >>language. By "molecular convergence of homologues" you appear to mean
> >>that the same genes were transferred from mitochondrial to nuclear
> >>genome several times. "And were conserved" seems to mean that the genes,
> >>once transferred, remained under purifying selection. But that has
> >>nothing to do with transfer, only with conservation of a functional
> >>product, wherever its coding gene happens to be located. Again, nobody
> >>is arguing that functional genes were not preserved by selection. The
> >>question is whether there is any reason to believe that the transfer of
> >>those functional genes from mitochondrion to nucleus had anything to do
> >>with selection. You have presented no reasons why we ought to think so,
> >>nor have you suggested any possible mechanism of such selection.
> >
> >
> > You are distorting the context of my statements while you are ignoring
> > my previous posts on this topic from Jan 5 2006 7:19 pm and Jan 6 2006
> > 5:51 pm. There would be no confusion about my statements if you stop
> > ignoring previous statements.
>
> I don't think so.
>
> > For example, Jan 5 2006 7:19 pm I wrote:
> > "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."
>
> If that's all we're arguing about, I agree. Functional genes are
> preserved by selection. If instead we are having some discussion about
> why genes are transferred from the mitochondrion to the nucleus, this is
> irrelevant.
>
> > And Jan 6 2006 5:51 pm I wrote:
> > "Okay, I am referring the initial mutational event of the mt gene
> > inserting into the nuclear genome of an individual specimen. That
> > initial mutational event resulted in essentially a new allele in the
> > nuclear genome. Instead of using the term 'fitness', we will say
> > that the new allele had an advantage that was positive or neutral or
> > negative. And the new allele either became fixed or became extinct. And
> > in most cases the new allele became extinct. But in some cases, the new
> > allele fixed in the nuclear genome. And if the new allele had a
> > positive advantage, the new allele fixed by natural selection."
>
> So now I ask again: what might cause the new allele to become fixed by
> natural selection? What advantage might it have? And again, we need to
> be clear about what we mean by "allele". We are talking about one
> "allele" in which there are two copies of the gene, one mitochondrial
> and one nuclear, and the other allele had only a mitochondrial copy. I
> think this is the step you are talking about here?
>
> The second step might also involve selection, and here we are talking
> about two different "alleles": one with both mt and nuclear copies, and
> the other with a nuclear copy only.
>
> Feel free to present reasons why any of these "alleles" might be
> advantageous vs. the alternate allele.
>
> > If you would follow the context of my discussion, you would see that I
> > divide the gene transfer into two major steps: 1) the mutation and
> > fixation of the functioning gene duplication in the nuclear genome, 2)
> > the loss of the mt copy. And I conceded that the loss on the mt copy
> > may have resulted from drift. And if that was the case, then the loss
> > of the mt copy by drift depended upon natural selection preserving the
> > nuclear copy. This suggests that we have to only confirm evidence that
> > natural selection fixed and preserved the gene duplication in the
> > nuclear genome to show that natural selection was responsible for the
> > gene transfer.
> >
> > And on my last post of this topic on Jan 8, I purposefully focused on
> > the evidence of natural selection in rps gene duplications that have
> > been preserved in the nuclear genome of several species for hundreds of
> > millions of years. The context for all of this should not confuse you.
>
> But it does. You are presenting evidence for conservation of a
> functional gene copy after all other copies have been lost, as if this
> is at all relevant to the fixation of that gene in the presence of
> another functional copy. But it isn't. And that's because you are
> yourself confused about the event you are trying to explain. Once more,
> you want to explain why, of the two genotypes below, the one on the left
> might have an advantage:
>
> Genotype A Genotype B
> n-genome gene X -
> mt-genome gene X gene X
>
> Notice that it is no explanation to say that gene X is important; both
> genotypes contain gene X. In fact, given that there are many
> mitochondria in the average cell but only one nucleus, the difference in
> copy number between genotypes must be negligible.

Before I go further with this, I want to make sure that I understand
you on various points of the first major step of the gene transfer,
which is the fixation of the duplication in the nuclear genome. And
that you understand my definition of "allele." And I think that
your definition of "allele" is really should be used only for the
term "genotype."

I use a different definition of "allele" than you in the case of
gene transfer. I keep the concept of allele to apply to a single locus
while in the case of gene transfer there are two loci in two respective
genomes are involved. In the first step of the transfer, the new allele
is the duplication in nuclear genome. And in the case of rps1, the
first set of the transfer, the fixed duplication into the nuclear
genome occurred at least 33 times.

And you are saying that the preservation by natural selection for the
nuclear genome copy may have only occurred after the transfer was
completed. Is that correct? If I understand you correctly, you are
saying that rps1 may have fixed in the nuclear genome by drift in 33
separate occasions. Is that correct? (At this point, let us refrain
from talking about the complete gene transfer that by definition
includes the loss in the mt genome. We will get back to that later.)

>
> >>>the importance of each gene in regards to the function of the ribosome.
> >>
> >>Hierarchy is a bad word to use here. What you mean is an ordering.
> >>
> >>
> >>>For example, rps1 is high in importance to the ribosome, where the
> >>>ribosomal protein S1 has RNA unwinding activity, helps the binding of
> >>>mRNA to the ribosome, and influences the affinity of ribosomes for
> >>>different mRNA initiation sequences.
> >>>
> >>>If indeed there is a rps gene hierarchy related to the importance of
> >>>each gene in regards to the function of the ribosome, then that
> >>>hierarchy may correspond to a hierarchy of selective advantage.
> >>
> >>Selective advantage how? One gene doesn't have a selective advantage
> >>over another. They aren't in competition. Increase in frequency of one
> >>doesn't change the frequency of the other. This makes no sense unless
> >>you have your own personal definition of selective advantage, different
> >>from the standard one.
> >>
> >>
> >>>And so
> >>>far you have not shown me any reason why a hierarchy of gene function
> >>>importance would not correspond to a hierarchy of selective advantage.
> >>
> >>I have no idea what you would mean by that. More importantly, I have no
> >>idea how this would relate to the matter at hand, transfer of genes from
> >>mitochondrion to nucleus.
> >>
> >>
> >>>>>>>>>Could genes with ribosomal function have more importance to the nuclear
> >>>>>>>>>genome as compared to the mitochondrial genome?
> >>>>>>>>
> >>>>>>>>No, since the genes in question are specific to mitochondrial ribosomes.
> >>>>>>>>Eukaryotic ribosomes need a whole different set of ribosomal proteins,
> >>>>>>>>coded for by different nuclear genes.
> >>>>>>>
> >>>>>>>
> >

.

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