Re: More shotgunning of ocean microbial ecology.

But I am just an amateur OOL enthusiast observing all of this activity
from the sidelines and cheering the participants on.
But OOL and evolution are two very different topics, with only a slight
bit of overlap. This shotgun sequencing is going to help with
evolution, not with OOL, so why are you following this thread?
Because until we trace evolution back to the point where it started,
we will have no idea what kind of organism we need to generate from
our hypothetical OOL processes.

IMO you have chosen a futile course. We may be able to estimate the
LUCA(s) with reasonable accuracy, but earlier is mostly speciulation.
Without a target to work back toward, there's no way to refine that
speculation to be more reasonable. Extrapolation (off the end from all
known data) is always less accurate than interpolation (between two
known points of data). I respectfully propose that you work from the
other end for a while, doing lab experiments to see what kind of
abiogenesis might happen under different circumstances, and seeing how
far forward you can get along various paths. Then compare the paths
forward from abiogenesis with the estimates backward from LUCA(s), and
see if any pairs are a good match, where you can fill in the middle
plausibly. If you can get *any* reasonble polymeric linear digital
genome from abiogenesis, then perhaps you can devise a series of
takeovers to fill the gap between there and the LUCA(s).

I mentionned a week or so ago that I now have what I consider good
reason to believe the "RNA world" was the last genomic system prior to
our current DNA world, and I even proposed a sequence of reasonable
events that constituted the RNA-to-DNA takeover. Did you see that?
<http://groups.google.com/group/sci.bio.evolution/msg/384023d6ee400f24>
= Message-ID: <dt86sa$2u0h$1@xxxxxxxxxxxxxxxxxxx>

You can learn more about this viewpoint of mine by finding a thread
in this group about a year ago entitled something like "OOL I -
Manifesto and Metatheory".

I see you present some additinal reasons why "RNA world" likely came
before our current DNA world, such as co-enzymes. But that whole thread
seems to be only the very first part of your thesis. I looked for
the other parts, but all I could find were:
OOL X - The origin of the RNA world.
OOL XIII - The "Zymes"
OOL XI - Elements of a Lipid-World Model.
Are there any parts II or III or IV or V or VI or VII or VIII or IX?
Hmm, in my search for OOL only the four above came up (three shown, and
part I Manifesto). But if I search manually for each set of roman
numerals individually, I get for example:
OOL II - Building Blocks
OOL III - Connecting the Blocks
It'll take me some time to find all the pieces and study them to see
whether you ever came up with my idea of why RNA genome came before DNA
genome based on current transcription to RNA and then genetic code
applied to RNA rather than DNA. (Or you could cut to the chase and tell
me whether you did or did not include any such argument in your
multi-thread thesis, and maybe even which of the threads has that
particular tidbit. Also, did you specify a sequence of steps involved
in the RNA-to-DNA takeover, as I did? Even if the sequence turns out to
be wrong, I like *some* proposed sequence to consider, rather than just
vagueness. There *is* a difference between a thought-out plausable
sequence, compared to a "just so" story whose only appeal is to
children and Kipling fans willing to ignore all consideration of
plausability. I rather like my idea that synchronization between RNA
replication and cell division was keeping DNA operations as only a
backup systme, until synchronization was changed to DNA-cell at which
point suddenly the roles between backup and mainsystem reversed. Maybe
there was an intermediate state of *no* tight synchronization, somewhat
like a pre-prokaryote version of multi-nucleated Fungi cells, or maybe
an intermediate state of double synchronization competing with each
other, and finally DNA-cell synch beat out RNA-cell synch.)

Hmm, now that my mind is on this subject, here's a brand new thinking
of the most likely sequence:
- Longstanding "RNA world" includes: synch between RNA replication and
cell division, plus RNA-to-amino-acid genetic code and RNA enzymes.
Then the following new mechanisms during the "takeover":
- Basic machinery to make DNA units by modifying the already-existing
RNA units. Somehow one of the four didn't go the same way as the other
three, hence the Uracil being lost and replaced by whatever. But since
DNA is more stable than RNA, this allowed longterm storage of surplus
RNA units just as fat provides longterm storage of fatty acids and food
calories.
- Enzyme to polymerise those loose DNA units to make strands for
mechanical support. Sequence and length were both random, requiring
careful tuning to avoid runaway length consuming all available
resources, and strength was very unreliable.
- RNA-to-DNA transcription, so that length of RNA genome directly
controlled both length and sequence of DNA. At this point, "junk" RNA
in ur-karyotes was good because then the sequence used to make nice
strong DNA strands of the appropriate lengths didn't need to match the
sequence used to code amino-acid strands for proteins. Since there was
just one strand of RNA in the genome, copies had to pass from the
genome part of the cell to the other part where they were chopped at
weak points to make the various-lengths of aa-exons and DNA-exons.
(Multiple RNA strands would have made synch between RNA replication and
cell fission impossible, so that's why I dismiss that possibility.)
- DNA-to-RNA transcription, so that now DNA serves both a structural
function (nice strong strands) and a RNA-backup function. Now *all*
RNA, not just the strand-RNA, can get transcribed to DNA, for different
purposes. Only the exons get transcribed back to RNA, when restoring
from backup.
- DNA replication, not synchronized yet, just "backup of backup" for
additional redundancy, tricky regulation to avoid runaway consumption
of resources.
- Some synch between cell division and DNA replication, thereby
providing just the right number of copies of backup, for best tradeoff
between redundancy and consumption of resources.
- Mutations in DNA backup cause conflicts between the RNA true genome
and the DNA backup genome. If the DNA mutation was bad, that clade goes
extinct, and the mutation is erased. If the DNA mutation was *good*,
the conflict remains until by chance the only copy of the RNA conflict
is deleted and restoration from the DNA backup eliminates the conflict.
Because DNA is more stable than RNA, hence fewer mutations in DNA, and
because most non-neutral mutations are harmful, there's selection
pressure to disable RNA replication entirely.
- One day that mutation indeed happens, and that clade enjoys selective
advantage over all clades that still have the conflicting DNA+RNA
replicating system, so now the system with only DNA replicase takes
over, with horizontal gene flow converting some other clades and not
others, the not-converted clades all going extinct. Hello DNA World!!

So did you have any sequence like that for the RNA-to-DNA takeover?
..

.

Relevant Pages

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