Re: Cope's rule and bacterial evolution

bacteria ... are optimizing by discarding rarely needed functionality
and thereby gaining a competitive edge in a narrowly specialized niche.
But, in doing so, they risk eventual extinction.
And of course, counter to this micro-evolutionary trend, there
is the macro-trend. It is the generalist bacteria with the
relatively large genomes which branch and produce new bacterial
species.
Extrapolating backward we can imagine that the LUCA (Last Universal
Common Ancestor) was the most versatile and generalist micro-organism
of them all, and had the biggest genome.

Or maybe there was no single LUCA. Did you ever consider that possibility?
You talk like it's been mathematically proven there must have been a
single LUCA, and all we need to do is figure out how it was.

What if there were a whole bunch of separate common ancestors, each in
a tiny eco-niche where it originated. It was totally sloppy in just
about everything regarding security, because it didn't come into
contact with the others elsewhere. For example, it'd leak out DNA and
protein products indiscriminately and then take them back in later,
from its neighbors rather from itself most usually, but it didn't
matter because neighbors were brothers. Cellular structure helped
concentrate biochemical pathways to make them more efficient, but
cellular structure weren't used to defend the genome against neighbors.
(Earlier there might have been adhesion on particles of clay, or
adhesion on metallic surfaces, instead of enclosure in a membrane, to
hold enzymes close together to make pathways more efficient. But later
enclosure in membranes gave good-enough close-holding combined with
much better freedom of motion during reactions, so was an improved
tradeoff, hence the takeover from adhesion to enclosing.)

These early forms of life were not very good at filling eco-niches
worldwide. Most of the ocean was devoid of life. Only in those very fea
places *most* hospitable for life was there any yet. There were huge
gaps between adjacent eco-niches that had life in them.

As the surface of the Earth cooled and tektonic plates moved around and
fissures opened and closed and modulated intensity, ecological niches
expanded and contracted and moved around. From time to time two
eco-niches of *different* kinds of life would get close enough together
that some DNA leaking from one would get into the other, the first
instances of horizontal gene flow (HGF). Depending on the environment,
selection pressure might merge genomes, or have one drive the other to
extinction, or favor cells which happened to be able to defend against
invasion of alien DNA. Most likely most parts of each genome would be
kept while a few parts would be eliminated as redundant and not as good
as their counterparts.

As eco-niches split apart, a single genome would remain in *both*
parts, separate from each other, allowing divergence of genomes to
occur. Meanwhile more meetings of formerly-separate genomes would
happen. The combination of natural selection and merging of disparate
genomes resulted in overall better fitness of the surviving genomes, so
they now occupied a larger portion of the ocean, and encounters between
adjacent genomes became more and more common, until eventually nearly
all of the eco-niches had merged to form a single eco-niche that
spanned the globe. So instead of separate genomes in separate
eco-niches, there was a graduation of genome from one kind of
environment to another kind of environment, with constant leakage of
DNA in both directions. At this point there would be advantage to
defending against invasion of alien DNA, to avoid this
cross-environment pollution that kept diluting any local natural
selection that had occured. So there was now selection pressure to
develop cell walls that blocked nearly all intake of alien DNA, and
also to block nearly all leakage of DNA since once it leaks out it can
no longer ever come back in. Those genomes which survived this time,
i.e. those which indeed chanced into reasonably good (but not perfect,
just good enough) protection against HGF, thereby became the very first
true quasispecies/strains/clades of cellular life, the LUCAs of all
present-day life. Prior to that "clade" was meaningless. Now (ignoring
a low level of HGF which continued occurring) we had true clades at the
cellular level.

Now tack on the scenerio I discussed a few weeks ago, where these first
true clades (ignoring low-level HGF) were not prokaryotes, only
pre-prokaryotes, (ur-karyotes as some call them) but eventually merged
their genomes in various combinations to yield three true prokaryote
clades, which were so immensely successful that they drove all
remaining ur-karyotes to extinction, and how one of the three clades
developed much more advanced cytostructure than the other two (not
discussed specifically in my earlier posting), evolving to form the
very first pre-eukaryotes, which later used their cytostructure to
invent mitosis, whereupon we'd consider them true eukaryotes despite
them not yet having mitochondria endosymbionts.

As to when the RNA-or-whatever to DNA takeover happened amidst that
complicated sequence: My best guess is very shortly before the merging
of the ur-karyotes to the three clades of prokaryotes. DNA replicase,
and the genetic code, is what made those three clades so much more
successful than the remaining ur-karyotes, driving ur-karyotes extinct.
Transcription and reverse transcription already existed in the
ur-karyotes, which is how DNA was created (as archival storage because
RNA was too fragile), and how DNA was retrieved to restore RNA later
from the backup (when regulatory machinery detected that RNA had gotten
degraded, or constantly in parallel so no detection of RNA damage would
be needed, but then the RNA genome would have a mix of restored
ancestral sequences and the very latest evolved sequences which would
slow the effective rate of evolution). After the DNA takeover,
retro-transcription was no longer needed, so most genomes eventually
lost that capability, but some viruses found it a wonderful tool so
they kept it. Since the genetic code actually works on RNA not DNA,
perhaps I should re-phrase the above. The genetic code and
transcription both directions between RNA and DNA was already in place,
and DNA replicase was invented as a way of making backups of backups,
which immediately made RNA-to-DNA transcription almost unnecessary, but
because cell fission was still synchronized with RNA replicase, RNA
replicase was still necessary for cell fission. That moment when cell
fission became synchronized with activity of DNA replicase (instead of
with RNA replicase as before) is the defining moment of the DNA
takeover, when both RNA replicase and RNA-to-DNA transcription became
no longer useful.

I think I've just convinced myself that RNA-world was the immediate
predecessor of our current DNA-world. So where I said whatever-or-RNA,
you can now replace that with a firm *RNA*. (I hope you don't mind
these train-of-thoughts articles I write, where you can observe my
actual train of thoughts as I conceive new ideas. If I ever become
famous for any of these hairbrained ideas of mine, and somebody wonders
where I got the ideas from, just look here, if Google preserves their
archive of newsgroups all that time, which is not guaranteed!)
..

.

Relevant Pages

  • Re: DNA, RNA and Protein questions
    ... Reptiles once dominated, mamals & birds came and reptiles survived ... genomes in free-living non-parasites did disappear. ... The only RNA ... That is *why* chemistry favors DNA for large genomes. ...
    (talk.origins)
  • Re: DNA, RNA and Protein questions
    ... as currently living organisms do indeed have *some* ... genomes in free-living non-parasites did disappear. ... do you think large genome RNA organisms would be favored. ... nearly all the part's they do require are not based on DNA ...
    (talk.origins)
  • Biochemistry of Genetic Mechanisms
    ... RNA, the same 20 amino acids & ATP) and many identical or nearly ... guanine & cytosine) in DNA. ... protein, acts as a template for the synthesis of RNA in transcription. ...
    (sci.bio.evolution)
  • Re: RNA World
    ... Proteins are phenotype. ... clues from present life back into the RNA world and even earlier. ... reason why you think that polypeptides appeared before DNA. ... Polypeptides offer a much wider variety of activity and much finer ...
    (talk.origins)
  • Re: More shotgunning of ocean microbial ecology.
    ... But OOL and evolution are two very different topics, ... I see you present some additinal reasons why "RNA world" likely came ... before our current DNA world, ... did you specify a sequence of steps involved ...
    (sci.bio.evolution)