Re: Spin - John Part 3.

hersheyh wrote:
On Sep 24, 3:58 pm, John Harshman <jharshman.diespam...@xxxxxxxxxxx>
wrote:
hersheyh wrote:
On Sep 24, 11:25 am, John Harshman <jharshman.diespam...@xxxxxxxxxxx>
wrote:
hersheyh wrote:
On Sep 24, 5:16 am, spintronic <spintro...@xxxxxxxxxxx> wrote:
On Sep 23, 9:06 pm, John Harshman <jharshman.diespam...@xxxxxxxxxxx>
wrote:
spintronic wrote:
On Sep 23, 6:58 pm, Prof Weird <pol...@xxxxxxxxxxxxxxxxxxxxx> wrote:
On Sep 23, 12:45 pm, spintronic <spintro...@xxxxxxxxxxx> wrote:
Before I submit my final reply.
I have a few queries.
1) You never explained why a sea urchin (seems te be) expressing fly
genes.
You say (contamination) yet, you have not explained how.
Gee - the FACT that it is a FLY gene in a SEA URCHIN EST pool isn't
enough ?
No.
A second, third scan would be conclusive. Do you have that data?
Scan of what? You should understand that complete genomes are assembled
from multiple overlapping clones. To be considered finished, the typical
standard is 8-10x coverage. That is, each sequence must have been
covered by between 8 and 10 individual BACs, at a minimum. And if any of
those BACs didn't fit into the genome assembly, that would have been
noticed. Contamination is not really an issue in a genome project.
The sequences are commonly discarded because of human bias. Not
because
the sequence dont belong there.
It took this guy months and a lot of eye rubbing to finally accept
what
he was seeing was true.
http://www.nsf.gov/news/news_summ.jsp?cntn_id=109957
And who here has denied that there can be horizontal transfer of
genetic information from an internal parasite to host? As was pointed
out in the article, mitochondria and chloroplasts are earlier examples
of this. In fact, we know, from those organelles that such horizontal
exchange is possible *and* can even be selected for when the
internalized organism is beneficial. What better way to ensure its
retention than by taking over some of its functions to prevent it from
successfully leaving.
Bad evolutionary biology there.
I (largely) agree, particularly wrt the role of neutrality vrs
selection for the individual switch of a gene between parasite and
organism. But, see below, it may incidently have selective
consequences. I also certainly was not intending to imply or imput
any teleological "plan" on the part of the eukaryote.
Didn't mean to say so, only that the events the teleological language
alluded to were not credible.



It's imputing some kind of plan on the
part of the eukaryote. And if we remove the metaphorical teleology, it
implies selection where there can be none. In order to tie the
mitochondrion to the eukaryote, not only does the nucleus have to start
making essential mt proteins, the mitochondrion has to stop making them.
So a scenario involving conflict of interest won't work. Drift seems
more reasonable. If there's a nuclear gene making the necessary protein,
a deletion in the mitochondrion isn't selected against. It may actually
be advantageous if replication efficiency matters.
[snip]
I agree that the initial and individual steps of gene transfer are
likely to be neutral. However, selection might still be involved in
favoring the 'parasite' to 'mutalistic' to 'irreversably and
intrinsically integrated' 'symbiotic' transitions. Especially if
infection with 'moderated or domesticated parasite' prevents
superinfection by more virulent forms (having such a 'pet' would be
beneficial to the eucaryote) and also obviates the risks of an
attenuated parasite having to compete in an external environment where
it might 'live free and (frequently) die' (apologies to NH
residents). In such a case, the individual events of transfer (either
simultaneous transfer and loss
No mechanism for that, as far as I can see.

Plasmid (or any reproducing or non-reproducing circular subchromosome)
formation producing a deletion in the bacterial genome (popping out
via IS elements), with the gene to be transferred now on a plasmid or
small circular fragment and transfer of that to the eucaryotic
genome. Eucaryotic genomes tend to integrate DNA somewhat
indiscriminately without the need for much sequence specificity
(unlike bacteria). Subsequent loss of an excessively large (hence
slowly reproducing) plasmid is a high frequency event. Just a
thought.

You have perhaps forgotten that the typical cell has not just one mitochondrion but a large population thereof. Deletion of a gene from one mitochondrion would not delete it from the rest of the population. And unless that transfer happened mighty fast, the mitochondrion in question would not survive without its necessary protein.

or sequential transfer and subsequent
loss)
That's a known mechanism.

that are themselves, and perhaps individually, neutral or near
neutral events can cummulatively have selective consequences by
favoring a switch to increasingly moderating virulence and increasing
integration of the initial parasitic state.
Not sure how this would work. At what level does the selection operate?
Are you saying that individuals whose symbiotes were more integrated
might have greater reproductive success?

Relative to individual eucaryotes without the moderated (but
immunizing) parasite or the moderated parasite in competition with a
more lethal but more infective form. The first step could drive
further integration.

If so, it would be a long time
between selection events, because we would have to wait for a gene to be
transferred to the nucleus and lost from the symbiote population (by
drift) before any selection would kick in.

If the gene to be transferred were on a plasmid (or a circular mini-
chromosome like those that form in aged eucaryotic nuclei) with a
deletion of the gene at the original site, the second step would
merely involve loss of plasmid, a relatively high frequency event
(Poisson distribution is often involved).

Well, first the transfer to plasmid would have to become fixed in the symbiote population. Do mitochondria even have plasmids?

It would help if there was a
selective advantage to having a small genome within the symbiote
population. Then two separate selection pressures in different organisms
would push the same direction.

That would work.

In much the same way
individual translocations or inversions can be selectively near
neutral but cummulatively lead to speciation into selectively
different populations.
Are you saying that speciation is adaptive?

In cases where there is hybrid dysgenesis at some locus, perhaps one
linked to the translocation. The dysgenesis would favor speciation.

Seems to me it would more likely favor extinction of the rare haplotype.

The rearrangements (or any other mutation that led to reproductive
isolation) would help minimize the flow of dysgenic alleles between
populations.

But there is only one population here, unless you also want to postulate some pre-existing isolation.

.

Relevant Pages

  • Re: Spin - John Part 3.
    ... Contamination is not really an issue in a genome project. ... genetic information from an internal parasite to host? ... implies selection where there can be none. ... If there's a nuclear gene making the necessary protein, ...
    (talk.origins)
  • Re: Spin - John Part 3.
    ... genetic information from an internal parasite to host? ... particularly wrt the role of neutrality vrs ... implies selection where there can be none. ... If there's a nuclear gene making the necessary protein, ...
    (talk.origins)
  • Re: Spin - John Part 3.
    ... genetic information from an internal parasite to host? ... implies selection where there can be none. ... If there's a nuclear gene making the necessary protein, ... If so, it would be a long time between selection events, because we would have to wait for a gene to be transferred to the nucleus and lost from the symbiote population before any selection would kick in. ...
    (talk.origins)
  • Re: Evolutionary compassion
    ... The mess that gene centric Neo Darwinism has gotten itself into over the ... mathematical model of Darwinian theory. ... cell which in turn can only be derived from one fertile organism. ... No natural selection or sexual selection. ...
    (sci.bio.evolution)
  • Re: Ernst Mayr: Where Are We (1976)
    ... >> to determine when organism fitness altruism could evolve in nature, ... >> gene fitness been developed allowing a minimally VALID simplified ... selection exist is required to produce a valid theory of same. ... Understanding how gene fitness epistasis can be coded and inherited ...
    (sci.bio.evolution)