Re: Evolution Strawbuster

The 30S subunit is the small subunit.

Yes, that's correct. So now you will stop calling me a liar when I mention it?

There is no 30S ribosomal RNA, nor any single gene that codes for the
30S subunit.

I seem to recall that I said something like "the DNA which codes for
it", i.e. whatever set of DNA, regardless of whether it's one gene or
ten genes or half a gene or whatever, I don't care. So the 3-way split
evidenced by the morphology of that sub-unit (the penguin-like shape
with/without beak or feet) which is alleged to correspond to the three
proposed domains (nucleus-only of eukaryotes, all of eubacteria, and
all of archaebacteria), simply shows a correspondence between *that*
one set of genes and the three domains, not a whole-cell true cladogram
matching the three domains. I'd be curious to know whether other genes
match the same cladogram. Of course with only three taxa, one of each
branch, there's only one unrooted tree possible in the first place, so
of course they all match. But when you consider branch lengths for
rooting the tree, and when you consider more than one taxon within each
domain, as far apart as possible (deepest sub-division in each domain),
then you have more than one option, and it's an actual question whether
all of the genes show exactly the same root-level cladogram.

By the way, what is currently believed to be the deepest sub-division
within each of the three domains? TOLWEB isn't useful at all. In
Eubacteria it shows an unresolved 24-way node which is absurd, for
Eukaryotes it shows an unresolved 7-way node:
* Animals
* Fungi
* Stramenopiles
* Alveolates
* Rhodophyta
* Green plants
* The other protists
which is clearly grossly wrong, only Archaea shows a nearly-correct
2-way split:
* Crenarchaeota
* Euryarchaeota
Let me see if palaeos does any better:

Bacteria Cladogram
LIFE
|--Eubacteria
| |--Cyanobacteria
| `--+--Spirochaetes
| `--+--Acidobacteria
| `--+--Eobacteria
| `--Planctobacteria
`--Neomura
|--Archaea
| |--Eurythermea
| `--Neobacteria
`--Eukarya
|--Chlorobionta
`--+--Fungi
`--Metazoa

Master Cladogram
LIFE
|--Eubacteria
| |--Actinobacteria
| `--+--+--Thermotogae
| | `--Firmicutes
| `--Didermata
`--Neomura
|--Eukaryota
`--Archaea

What the ***?? Either of those looks better than what TOLWEB had, but
they disagree with each other, both in deepest sub-division within
Eubacteria (Cyanobacteria/allelse or Actinobacteria/allelse), and in
the name of Eukaryota or Eukarya!! So palaeos can't decide which of the
two cladograms to support?? Yet despite being contradictory as to
toplevel sub-division within Eubacteria, they both agree that
Eubacteria branched off before the Eukaryota(nucleusPresumably)/Archaea
split, which I personally feel is not yet decided.

<http://www.palaeos.com/Bacteria/default.htm>
Undoubtedly the most influential work in modern higher-level
prokaryote systematics was conducted by Carl Woese and associates in
the 1970s and 1980s. This led to the much-popularised SSU rRNA tree
in which life was divided into three "domains" separated from each
other by long branches the Eukaryota, the Archaebacteria, and the
Eubacteria (later named by Woese as Eucarya, Archaea and Bacteria
Pace, 1997).

So that's why the name confusion, just a name change Eukaryota ->
Eucarya? Was that done because we're talking only about the nuclear DNA
here, whereas the term "Eukaryota" refers t the entire modern symbiosis
icluding mitochondria, so "Eucarya" referring only to the nucleus is
the primitive "domain" we're talking about here as sister to Archaea?
Or not???

Ah, this discussion I like (regarding news headlines about Archaea):
Looked at from a more phylogenetic rather than a purely phenetic
viewpoint, it becomes difficult to see what all the hyperbole is
about. While Archaea have DNA-processing genes that resemble those of
Eukarya, their metabolic genes are more like those of Eubacteria.
Aha!! So the discussion really does agree with me, the topmost division
is unresolved as to which split came first, or even if a purely
cladistic view is correct in the first place! DNA-processing looks to
be split one way, while metabolism looks to be split a different way,
and whether this difference is due to horizontal gene flow (my
speculation) especially my scenerio for the pre-DNA-world shuffling of
domains, or different rate of evolution (the explanation expressed
above), clearly it's premature to attempt to resolve the toplevel node
as palaeos seemed to have done in the ASCII-cladograms above. As far as
I'm concerned, the correct concensus toplevel node of 2005-6 would show
a 3-way unresolved split, not successive 2-way fully-resolved splits.

This only appears as a conflict if one assumes
that all parts of the genome in all organisms are evolving at the same
rate. This assumption is often made in molecular biology due to the
influence of Kimura & Ohtas (1974) Neutral Mutation Hypothesis, which
suggests that the majority of genetic mutations are more or less
selectively neutral in effect, so should happen randomly with respect
to time. However, this theory only applies to mutations in non-coding
parts of the genome, or other mutations that do not affect the
[snipped some typo-cruft] resulting phenotype. When it comes to
alterations in phenotype, different selective pressures on different
parts of the genome and/or organism mean that evolution is not uniform
for all characters of the organism the principle known as mosaic
evolution.
Yes, very nicely stated (except the inserted typo cruft), and nice that
they included the jargon for this effect ("mosaic evolution", hopefully
not named after the scriptures of Moses).

Under this principle, the supposedly inexplicable combination of
characters possessed by Archaea is entirely explicable. Some of the
features shared with one domain will represent plesiomorphies that
have been lost in the remaining domain, while features shared with one
or the other domain may be apomorphies of a larger clade.
Actually that's a different effect. Different rates of evolution of
different characters in different niches, vs. actual reversion of a
character to an ancestral state, are **different** reasons for what may
in some cases be similar evidence. The typos earlier, and this sudden
accidental change of subject, show this Web site lacks a careful
WebMaster/proofreader, sigh. It has such good snippets of explanation
here and there, it's like a beautiful woman with acne or in a
wheelchair. (BANG, BANG, you shot me dead for that horrible metaphor!)

The rRNA tree is, like all
phylogenetic trees when they are first calculated, un-rooted.
(Yes, the point I repeatedly have been making in recent months!)
Normally the position of the root of a tree is established by
inclusion of an outgroup, a taxon that is definitely known to be
outside the group of interest.
(That's one way, but begs the question as I see it and keep arguing.)
Unfortunately, **somewhat** by definition,
no suitable outgroup exists for the totality of life.
(A Brit must have written that, typical gross understatement on that
one word "somewhat", **emphasis* added by me. I suspect a Brit who has
watched too much of Monty Python.)

The approach used was to select genes that had
duplicated before the Last Universal Common Ancestor of modern life
(referred to by the catchy acronym LUCA). The trees of these genes
should be able to be used to root each other and indicate the point
where Luca was to be found.
(Yes!!)
The first two gene pairs used by
independent researchers in 1989 were elongation factors (EF-Tu vs.
EF-G) and catalytic vs. regulatory subunits of eubacterial F-ATPases
with V- or V-like-ATPases of Eukarya and Archaea. Both these studies
found the root to be on the branch separating Eubacteria from the
other two domains. Philippe & Forterre (1999).
(Aha! The detailed answer to the question I asked here about a month
ago but never got an answer, apparently Harshman, my debate opponent,
didn't know this info. In particular, clear evidence that these two
gene families co-evolved within whole-cell or block-horizontal-flow
clades.)

(Then some discussion why we can't fully trust that data because
they're so very very ancient that mutations are saturated despite being
coding regions, etc.)

The suggestion has been made that the common ancestor of all three
domains was not yet a properly developed, integrated cell, but a
progenote. Woese (2002). Cell design was held to be shaped largely
by rampant lateral gene transfer, with genetic components functioning
as interchangeable modular units. Eventually, a Darwinian Threshold
was passed where genetic components of individual cells became
integrated enough that lateral gene transfer was no longer able to
occur enough to blur genealogical lines, and standard vertical descent
became predominant.

Aha! This is very close to the speculation I posted a few weeks ago,
which nobody seemed to like. I like Woese. He's my friend, like Google. :-)

This threshold was passed separately in each of
the three domains. The supposed sister status of Eukarya and Archaea
is actually an artefact of analysis resulting from Eubacteria crossing
the threshold earlier than the other two domains.

Now that part is a good idea/speculation why my (and Woese's) idea
might produce the artifact we have observed. Do you-all recall the
diagram I drew a few weeks ago?
http://groups.google.com/group/talk.origins/msg/9bcef46de3645b5a
= Message-ID: <10a1e$43e644db$c690c02a$24711@xxxxxxxxx>
! Date: Sun, 5 Feb 2006 10:28:25 -0800
! Consider the following descent diagram, where # denotes massive sharing
! of DNA across all/most kinds of life, among PreProkaryotes (pp):
! pp#pp->Eubac----------->(big clade)
! pp#pp->(extinct)
! pp#pp->Arch---------->(two big clades)
! pp#pp->(extinct)
! pp#pp->Urk->Eukaryotes----->(big clade)

Now with only a slight change we have basically Woese's idea, namely
the # region stops for some of the pre-prokaryote whole-cell-clades
sooner than for others, and in particular it stops for Eubacteria (and
possibly some of the extinct groups) sooner than it did for Eukarya and
Archaea, so that Eukarya and Archaea continued to share DNA back and
forth long enough to homogenize them more recently than either was last
homogenized with Eubacteria. As Woese astutely realized, the
massive-HGF-stopped-different-times idea produces the same evidence as
an actual hierarchial cladistic view. So here's one possible variation
on my above diagram (also changed name for nucleus-only of Eukaryota):

! pp#pp->Eubacteria----------->(big clade)
! pp###pp->(extinct)
! pp######pp->Archaea---------->(two big clades)
! pp########pp->(extinct)
! pp##########pp->Urk->Eukarya----->(big clade, nucleus of Eukaryota)
whereby Archaea and Eukarya share not a more recent whole-cell-LCA than
either with Eubacteria, but rather more recent pseudo-LCA due to
HGA-homogenization with each other than with Eubacteria. The last
whole-cell LCA of any two of those five whole-cell clades was way back
during the RNA world before the first of the DNA-based pre-prokaryotes,
before the very left of the above diagram. Or there may *never* have
been any LCA among the five whole-cell clades shown above. See for
example where I posted my speculation that abiogenesis occurred
independent in several local environments, very isolated by
inhospitable oceans between them, and then expanded to fill the ocean
and thereby start encountering each other, resulting in endosymbiosis
or fight-to-death each time, with rampant HGF all throughout that that
era and to the RNA takeover and maybe even to the DNA takeover, and
through the left-side of the above diagram where barriers against
rampant HGF finally occurred first in one whole-cell clade then another
then another etc. (My original idea had an arms-race forcing all
whole-cell clades to establish barriers against HGF virtually
simultaneously, but Woese's argument shows perhaps the arms race wasn't
so effective as I had guessed. Appearance of a gene providing a barrier
against *incoming* HGF to preclude molestation, or a gene providing a
barrier against *outgoing* HGF to preclude theft of intellectual
property, would have this difference, but it's nearly 6 AM and I
haven't slept hardly all night and I can't reason out which is which,
so somebody who is awake please finish this line of thought for me.)

Multiple gene trees for
Eubacteria show concordance at more recent nodes, but lower resolution
at older nodes, potentially compatible with a Darwinian Threshold.

Ah, very good. More evidence toward the Woese/anon1 theory! Anyway,
instead of LUCA, we have LUMHGF (Last Universal Massive Horizontal Gene
Flow), and more recent LMHGF (not LCA) between two modern domains than
between either of those and the third domain.

The existence of a Darwinian
Threshold seems similarly tenuous if lateral gene transfer was common
in the past, there seems to be little reason why it should not still
be so.

I strongly disagree. It's a major advantage over competitors to stop
them from stealing all your good ideas and to stop them from polluting
all your databases with noisy crap, hence barriers against both spying
and trojans.

"The" stem-ancestor of eukaryotes is a bit ambiguous. Do you mean the
very *first* species within the stem-based definition that includes the
Eukaryotic nucleus and cytoplasm but not Eubacteria nor Archaebacteria?
No. I mean the first species that is closer to Eukaryota than to
Eubacteria or Archaea.

That "closer to" jargon as defined by cladistics is meaningless unless
the quantity of horizontal gene flow was small enough that such
cladistic analysis is close to the truth and meaningful and decideable
based on modern DNA comparisons. I like the Woese/anon1 theory that
contradicts that assumption, making your usage meaningless.

However if we use last common massive HGF instead of last common
ancestor, then perhaps an appropriate stem-based definition does make
sense after all, and might be diagnosed from modern DNA sequences.

There are living eukaryotes without mitochondria, but it's possible
that none of them is primitively so.

Yeah. There's so little already known in DNA-based cladistics, and so
much we'll learn in the next twenty years. It's a bit like astronomy of
galaxies one year after Hubble realized they weren't all part of the
Milky Way galaxy and people had just barely started to study them as
individual separate galaxies.

and
something which has lots of the usual eukaryote's intracellular
structure but doesn't do mitosis as pre-eukaryote. Since somebody else
proposed "ur-karyote" I'm not willing to speak for where that term fits
in this sequence.
How do you know for sure that eukaryote characters were acquired in that
order?

I don't. That's my first guess as to the most plausable sequence, and I
welcome you to think about it carefully for a few days and then post
your best alternate guess as to the whole scenerio from the start of
the RNA world through the DNA takeover and the stepwise cecessation of
massive horizontal gene flow (or not if you don't like the Woese/anon1
theory) and the various endosymbiosis events and the "invention" of
mitosis (and presumably meiosis later as a modification of mitosis, but
feel free to disagree with that too), finally yielding the major
branches of protists and algae. So-far we have only two speculative
sequences that include the RNA to DNA takeover, the very vague one
posted several months ago by somebody else, and mine more recently that
put in a bit more speculative specifics about the sequence of events
during the gradual takeover thereby avoiding any IC barrier.

Even with all that information, what makes you think there would be any
one place more reasonable than another?

Only the Einstein/Occam principle, that the theory that makes the most
sense with the fewest problems is probably the correct one. That's why
he believed so strongly in special relativity. It was so beautifully
simple and logical and problem-free. That's why we believe in parsimony
(minimum evolution) trees. (And the Creator must like that principle too,
because Hamiltonian dynamics always gives the correct answer!! :-)

HT occurred between the first column and second column. Before the
first column, we have no idea what kidn of evolution there was. It
probably wasn't at all like the evolution we know about today, where
DNA is the carrier of the genome, etc.
Why? What makes you think so?

Because it's virtually impossible for DNA to spontaneously appear in
abiogenesis as a self-replicator. Much more likely DNA genome is the
result of a takeover. So before that takeover, evolution wasn't as it
is today with DNA mutations etc. Most likely RNA preceded DNA for the
genome carrier, but even RNA is unlikely to have been the original
abiogenesis self-replicator. So there must have been a something-to-RNA
takeover before the RNA-to-DNA takeover. At least with something
totally haphazard, some auto-catalytic set with no structure
whatsoever, we have a plausable idea how abiogenesis could have really
happened naturally. But there's no way a random auto-catalytic set
would have linear-digital genome like RNA did and DNA does now. So for
sure evolution would have been fundamentally different at first from
how it is now. So depending on where you draw the threshold between
totally unlike what we know today to essentially identical to what we
know today, that's the left edge of my diagram. The diagram simply says
that after we got linear digital genome (RNA or DNA) with the usual
ideas of mutation and natural selection, we still had rampant
horizontal-gene-flow for a while after then, until this linear digital
genome achieved barriers against HGF.

There is no reason to think that there is any more than one
abiogenesis event (I would call it a process rather than an event)
that has left surviving descendants.

I presented a rather strong argument why you are mistaken on this
point. The very first abiogenesis was probably in a very very
restricted local environment where conditions were "goldilocks" just
right for that particular version of abiogenesis. Without linear
digital genome, evolution was very very slow, so that first kind of
replicator remained very local for a very long time. Meanwhile, the
Pasteur/Darwin principle, that any new abiogenesis is impossible
because it would be eaten by the more-developed already-existing life,
wouldn't apply elsewhere, so there'd be plenty of time for separate
abiogenesis events to occur elsewhere, and likewise remain each very
local. Then when they start meeting each other, either fight-to-death
or food-web (exo-symbiosis) or endosymbiosis are the three options, and
I doubt that fight-to-death happened 100% of the time as you seem to
claim.

So the total of variation consists of:
(1) differences between the original separate abiogenesis events which
were not due to evolution at all;
Why would you say this?

Simply the differences between the clades that came down from each of
the indepedent abiogenesis events or various different endosymbioses
thereof.

(2) new variation that occurs during that early non-linear-genome
"evolution" totally unlike what we understand today;
And why would you say this?

Like I said above, there's just no way that DNA or even RNA could have
been the very first replicator from Miller-Urey or similar conditions.
Simple auto-catalytic sets, or clay micro-crystal dislocation patterns,
or whatever came first, wouldn't undergo linear digital triplet-code
evolution like we see today.

You have a strange way of saying things.
So does nearly everyone else. Have you ever really listened to:
- Dr. Phil
- Dr. Laura
- Alan Greenspan
- Dr. Ruth Westheimer
I try to avoid it. But are you holding them up as typical examples of
"everyone else"?

No, I'm holding them up as examples of people who express ideas nearly
as strangely as I do. Have you ever really listened to those four
people and noticed how strangely they express their ideas??

Maybe I should be compared instead to people who expressed their ideas
in strange written form instead of strange spoken form. For example,
compare me to Erich Fromm or somebody else like that I forget, gotta go
to bed very very soon, now almost 7 AM and I still haven't slept hardly
at all tonight.
..

.