Re: Evolution Strawbuster

Let's say we start our analysis of common descent via evolution from a
set of five or ten different species of proto-prokaryotes, which then
exchange massive amounts of DNA via lateral gene flow, yielding the
LCAs of the three clades of prokaryotes we see today. (One of the three
we see only in eukaryotes, the other two we see still living
independently even today.)
That's not true. If you're talking about mitochondria, they are not one
of the "three major clades of prokaryotes".
Actually, I think he is speaking of the theoretical ur-karyotes - the
now-extinct prokaryotic lineage ancestral to the first Eukaryotes.

Ancestral to the *nucleus* portion of the first Eukaryotes, yes.
I invented the specific idea myself, based on some similar reading, so
I wasn't aware that my hypothetical prokaryote pre-Eukaryote was
already given a name by others who thought of the same idea before me.
Thanks for citing the name! I did a Google search on that term, and
indeed that's what I was thinking of. I found some fascinating Web
pages from that search:

<http://www.bio.nagoya-u.ac.jp:8001/~hori/archaea04.html>
(Inaccessible, cached by Google:)
<http://72.14.207.104/search?q=cache:ttrSreJ4DcAJ:www.bio.nagoya-u.ac.jp:8001/~hori/archaea04.html+ur-karyotes&hl=en&gl=us&ct=clnk&cd=1&ie=UTF-8>
Nice debate about proposal by Woese et al (1977), based on 16S (18S)
rRNA, to divide cellular life into three domains, whether it's a
primitive tripartate division, or a two-level bipartate division whose
cladogram we haven't yet resolved. IMO it's either my pre-prokaryote
gene-sharing model with only three survivors, or it's two-level
bipartate but where we will *never* be sure which of the three domains
split off first, so it's best to leave it permanently unresolved in
either case.

Hori noted that a pair of gene-duplication events, namely elongation
factors Tu and G, and the alpha and beta subunits of ATPase by Iwabe et
al. (1989), may allow us to assign polarity along one of the branches,
thereby restricting where the true root might be. (My paraphrase of
what I understood that he meant. Harshman and Wilkins please check the
original wording and tell me if you understand it the same.)

<http://www.friesian.com/life-1.htm>
By comparison, this treatment I don't like, because it does *not*
organize the seven proposed kingdoms in a strict cladistic way. It
follows Margulis and Schwartz too closely in putting the three
multi-celled kingdoms (Plantae, Anamilia, and Fungi) as sister groups
with Protista, when fact all three multi-celled kingdoms are actually
*within* the Protista clade. Furthermore it violates cladistics again
in treating all five Superkingdoms as sisters, when clearly Urkaryotes
are ancestral to (nucleus of) Eukaryotes. Otherwise that Web page has
some interesting discussion, off-topic for this thread.

<http://genomebiology.com/2003/4/8/115>
Nice explanation why Woese&Fox deserve such credit for their work
revealing the extreme differences between the archaea and the
eubacteria, getting the right result despite the crude methods they had
available at the time (1977). Also:
hypothesis that replication of double-stranded DNA as the principal
form of replication of the genetic material was 'invented' twice,
independently: once in [eu]bacteria and once in the ancestor of archaea
and eukaryotes [22,23].
on the other hand:
metabolic pathways of archaea more closely resemble their bacterial
rather than eukaryotic counterparts [24-26].
Hmm, this conflict reminds me of the recent article citing evidence for
two different types of genes, one type that work in complexes which
break badly if parts from one complex are replaced by parts from
another homologous complex, and another type that are relatively
independent, where horizontal gene flow (HGF) doesn't cause any fatal
problems so lots of HGF appear represented in modern species. Perhaps
the DNA-replication machinery is of one type, and the metabolic
pathways are of the other type, so one of these commonalities
represents true ancestry of the bulk of the DNA via co-evolution along
cell-descent lines, while the other commonality represents the result
of massive HGF after eukaryotes had already developed defenses against
HGF so they didn't participate in this flow and thus maintained the
ancestral genes where archaea instead took eubacterial genes and lost
the ancestra genes. If we can get good cladograms for individual genes
of both types, we may be able to diagnose which genes follow strict
whole-cell co-evolution and which violate that hence must result from
HGF. But why did the massive HGF not occur until after eukaryotes had
defenses against it? Perhaps one of the mass extinctions caused by
ecological change put severe stress on the archaea, forcing them to
take on eubacterial metabolism in order to avoid extinction. Perhaps
all archaea outside the thermal vents or other very limited habitat
went extinct, then later over much time thermal-vent archaea eventually
took up eubacterial metabolism thereby allowing them to re-colonize the
other environments? Maybe that population bottleneck due to the mass
extinction event is why archaea are mostly extremophiles nowadays?

By the way, if DNA replication machinery was invented twice, maybe the
split between eubacteria and archaea+urkaryote happened before the DNA
takeover, during whatever was the prior system (RNA world, protein
world, or something we haven't even thought of yet), so there were two
separate paths from that prior system to the current DNA system.
Alternately, a crude form might have been invented once, allowing the
takeover to occur, but a better form replaced it, and that better form
was invented in two ways, two such very different ways that experts
today can't see any relation between the two except their function of
replicating DNA?

Ah, a nice way of explaining what I was talking about a few days ago:
When duplication(s) succeeds speciation, a family of paralogs
in one species should be considered orthologous to the corresponding
family in the other species [34].

Also much discussion of massive horizontal gene flow/transfer among
archaea in that same article, including conflicting cladograms of
different genes due to horizontal gene flow in different directions for
different genes.

Hey, here's a fun set of multiple-choice questions about evolution:
<http://www.csupomona.edu/~shbryant/110k1992.htm>

By the way, Stanley, I have always hated your signature. I find it
offensive and annoying. Originally I interpreted it as the traditional
Christian view, as modified by the ungrammatical use of the generic
class of being with capital letter as if some such being's actual name.
Now I interpret it as Gunderscored i.e.:
Omphalos
Great __________ Deceiver
(underscore)
where I don't find the term itself offensive, I merely find it
offensive that you would wish such a liar on all readers of your
articles in this newsgroup. I might retaliate by adopting my own
signature which expresses the hope that there is no such being.

- May you be forever free of the dastardly deceit of the mythical _Omphalos_.
(Note how I reverse the roles of underscored part and as-is part!)
..

.

Relevant Pages

  • Re: Cell DNA versus body DNA quantity?
    ... What percentage of animal DNA is devoted to cell-level issues versus ... flexible before multicellular life was competitive. ... order of 1000 genes. ... on the one hand Cavalier-Smith dates eukaryotes at 800m years, ...
    (talk.origins)
  • News: Where Is Human Evolution Heading?
    ... Where Is Human Evolution Heading? ... The race's DNA is changing faster than ever; ... our genes are playing catch-up against modern scourges?like ... it doesn't take a Nobel Prize in genetics to imagine that babies could ...
    (talk.origins)
  • DNA and Alleles
    ... One article on population genetics states, ... natural selection, genetic drift, mutation, migration and nonrandom ... What is the relationship between genes and a ... subset of a cell's DNA. ...
    (sci.bio.evolution)
  • Article: Genetic Network Guards Against Lethal DNA Damage
    ... 'Genetic Network' Guards Against Lethal DNA Damage ... The discovery in yeast cells of a genetic network that guards against lethal ... combinations of mutated human genes, according to researchers at The Johns ... The yeast cell is an excellent model for this kind of study because 25 ...
    (sci.bio.evolution)
  • Re: Developing a focused set of questions for IDists - Comments encouraged
    ... It could be given evidence by finding hidden messages or images inside ... of DNA. ... Nobody has claimed it not possible. ... duck could get cow genes. ...
    (talk.origins)
Loading