Evolution Strawbuster
Iain
Feel free to add to the list :
Evolutionary theory does not claim:
That the development of life on earth until now relied on more
conspicuous mutation than that which provides common variation.
That individuals decidedly of ancestral species A can beget individuals
decidedly of descendant species B.
That life as it is is implicit in earlier forms of life.
That randomness is at the heart of the process.
Anything on the origins of life.
Anything on gods, God, theism, religion or morality.
~Iain
APOCALYPSE
That Intelligent Design is a badly-worded attempt at circumventing the
process of scientific methodology, is part of a campaign against any
and all science perceived to deny the hand of God in the workings of
the material world and is a trojan horse for the unfounded religious
theory of Creationism to be inserted into scientific curricula: in
short, religious-minded folks encroaching on science's territory. One
does not have to believe in evolution to know pseudoscience from
science.
Ken Shackleton
Add: That the earth is old....in fact...it has no opinion on the age of
the earth....that's left to the geologists.
>
> ~Iain
APOCALYPSE
the fossils found in lower geologic strata. Not to mention the tree of
life which starts in the Precambrian era, around 4 billion years ago.
Dave
apes should be giving birth to humans (unless you count humans as apes, of
course)
That individuals evolve.
That there is no purpose to life.
Iain
One can accept that present and future evolution is implicit in the
modern condition of life without necessarily concluding that it was the
past condition -- silly I know, but technically possible.
~Iain
Noone Inparticular
Iain wrote:
> Feel free to add to the list :
>
>
> Evolutionary theory does not claim:
>
> That the development of life on earth until now relied on more
> conspicuous mutation than that which provides common variation.
I don't know what this means.
>
> That individuals decidedly of ancestral species A can beget individuals
> decidedly of descendant species B.
>
> That life as it is is implicit in earlier forms of life.
>
> That randomness is at the heart of the process.
Well, "randomness" *is* in several very important ways at the heart of
the process.
There is the fact that mutations occur without regard for their
utility.
There is genetic drift.
There is environmental contingency.
Ernest Major
<iain_i...@hotmail.com> writes
>
>Feel free to add to the list :
>
>
>Evolutionary theory does not claim:
>
>That the development of life on earth until now relied on more
>conspicuous mutation than that which provides common variation.
>
>That individuals decidedly of ancestral species A can beget individuals
>decidedly of descendant species B.
One of the paths to polyploid speciation is the union of unreduced
gametes. This might actually result in a plant of diploid species A
producing a seed of tetraploid species C. I know that hybrids between
diploid species have produced seeds of tetraploid species (e.g. in Verne
Grant's work on Gilia), but there is a definitional question as to
whether the hybrids belong any species. There's a similar case to Gilia
in Galeopsis.
>
>That life as it is is implicit in earlier forms of life.
>
>That randomness is at the heart of the process.
>
>Anything on the origins of life.
>
>Anything on gods, God, theism, religion or morality.
>
>~Iain
>
--
alias Ernest Major
--
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Iain
> Iain wrote:
> > Feel free to add to the list :
> >
> >
> > Evolutionary theory does not claim:
> >
> > That the development of life on earth until now relied on more
> > conspicuous mutation than that which provides common variation.
>
> I don't know what this means.
They say that we say that development is driven by rare fortunate
macromutations, rather than the effect of selection upon manifold
variation.
~Iain
an...@sci.sci
> the earth....that's left to the geologists.
On the other hand, the primary purpose of evolutionary theory was to
explain the variations in fossils over geologic time, so if you omit
old-Earth then what's the point in having the theory in the first
place? IMO, explanation of old-Earth fossils is an essential part of
the overall framework of evolutionary theory, and old-Earth fossils
should be listed as one of the premises of the theory.
A secondary purpose of evolutionary theory is to explain the variety of
life we see today. (Darwin's book emphasized this purpose.) Without a
very very old Earth, the mechanisms proposed by evolutionary theory are
incapable of producing the current variety of life. So again old-Earth
is essential to this purpose of the theory. With a theory that explains
neither fossils nor variety of life, the theory is nearly worthless, IMO.
Evolutionary theory basically says that descent with modification acted
over billions of years, and that's why all those fossils were laid out
the way they were, and that's why we have such wide variety of life in
nested hierarchies today. Having it merely say that descent with
modification has happened for the past four thousand years, resulting
in new breeds of dogs and new viruses and not much else new, would
basically castrate the theory.
If you want, you could distinguish between the premises of the theory,
and the value added by the theory itself. So old-Earth fossils and
genetics and embryology and metabolism and hierarchial clustering of
types of current life etc. would be premises, and then descent with
modification etc. would be the value added by the theory per se.
Also IMO the purpose of this thread is to list strawman claims that are
blatantly contrary to evolutionary theory, which Creationists et al
tend to conflate with evolutionary theory, not to list premises that
are essential to the purpose of evolutionary theory despite them not
being formally part of the theory per se.
.
John Harshman
>>>Evolutionary theory does not claim:
>>
>>That the earth is old....in fact...it has no opinion on the age of
>>the earth....that's left to the geologists.
>
>
> On the other hand, the primary purpose of evolutionary theory was to
> explain the variations in fossils over geologic time,
Who ever said that? Or if you're the only one who says it, why?
> so if you omit
> old-Earth then what's the point in having the theory in the first
> place?
So your claim is that if the earth were, say, only 6000 years old, there
would be no evolution?
> IMO, explanation of old-Earth fossils is an essential part of
> the overall framework of evolutionary theory, and old-Earth fossils
> should be listed as one of the premises of the theory.
>
> A secondary purpose of evolutionary theory is to explain the variety of
> life we see today. (Darwin's book emphasized this purpose.)
Then why is it a secondary purpose?
> Without a
> very very old Earth, the mechanisms proposed by evolutionary theory are
> incapable of producing the current variety of life.
...assuming that you start with a single one-celled species.
> So again old-Earth
> is essential to this purpose of the theory. With a theory that explains
> neither fossils nor variety of life, the theory is nearly worthless, IMO.
Your opinion is certainly an opinion.
> Evolutionary theory basically says that descent with modification acted
> over billions of years, and that's why all those fossils were laid out
> the way they were, and that's why we have such wide variety of life in
> nested hierarchies today. Having it merely say that descent with
> modification has happened for the past four thousand years, resulting
> in new breeds of dogs and new viruses and not much else new, would
> basically castrate the theory.
Why? It wouldn't explain the diversity of life, but it would certainly
explain many interesting phenomena. It would no longer be the central
organizing principle of biology, though.
> If you want, you could distinguish between the premises of the theory,
> and the value added by the theory itself. So old-Earth fossils and
> genetics and embryology and metabolism and hierarchial clustering of
> types of current life etc. would be premises, and then descent with
> modification etc. would be the value added by the theory per se.
>
> Also IMO the purpose of this thread is to list strawman claims that are
> blatantly contrary to evolutionary theory, which Creationists et al
> tend to conflate with evolutionary theory, not to list premises that
> are essential to the purpose of evolutionary theory despite them not
> being formally part of the theory per se.
If one can make any sense of that last sentence, it would seem to render
your entire post off-topic.
an...@sci.sci
> > That the development of life on earth until now relied on more
> > conspicuous mutation than that which provides common variation.
> I don't know what this means.
Here's my understanding. Perhaps the OP can say if I understood correctly:
Creationists claim that what we observe today is "micro-evolution",
whereas what is needed to produce the variety of species is something
much grander, which they call "macro-evolution". But evolutionary
theory explains the origin of the species just fine by tiny changes
that accumulate over geologic time, no need for faster or bigger-jump
evolution in the past compared to what we observe today.
> > That randomness is at the heart of the process.
> Well, "randomness" *is* in several very important ways at the heart of
> the process.
> There is the fact that mutations occur without regard for their
> utility.
> There is genetic drift.
Agreed.
> There is environmental contingency.
Maybe. It could be viewed as a chaotic type of randomness, or it could
be viewed as game-theoretic, i.e. deterministic based on competing game
strategies. I'd welcome debate on how best to categorize this factor as
random or not.
.
Lt. Kizhe Catson
Iain wrote:
> Feel free to add to the list :
>
>
> Evolutionary theory does not claim:
>
> That the development of life on earth until now relied on more
> conspicuous mutation than that which provides common variation.
>
> That individuals decidedly of ancestral species A can beget individuals
> decidedly of descendant species B.
>
> That life as it is is implicit in earlier forms of life.
>
> That randomness is at the heart of the process.
Ambiguous. Mutation is random; fitness is not absolute, but a
statistical measure (faster legs don't *guarantee* you'll escape being
eaten by wolves, they just improve your chances). So there's certainly
randomness in there, but not in the simplistic sense of a pure
drunkard's walk.
> Anything on the origins of life.
Paging Deaddog...paging Deaddog...
See recent post at Pharyngula:
http://scienceblogs.com/pharyngula/2006/01/life_is_chemistry.php
It's a matter of deciding where you want to bound your definition. (Of
course, for some of our opponents, "evolution" includes Big Bang
cosmology, too).
> Anything on gods, God, theism, religion or morality.
-- Kizhe
Robert J. Kolker
>
>
> Ambiguous. Mutation is random; fitness is not absolute, but a
> statistical measure (faster legs don't *guarantee* you'll escape being
> eaten by wolves, they just improve your chances). So there's certainly
> randomness in there, but not in the simplistic sense of a pure
> drunkard's walk.
God throws dice. Most likely God is an addictive gambler and badly in
need of help.
Bob Kolker
Robert J. Kolker
It is possible but the odds are against it. So far natural selection is
the best available explanation.
Bob Kolker
Iain
an...@sci.sci wrote:
> > > Evolutionary theory does not claim:
> > > That the development of life on earth until now relied on more
> > > conspicuous mutation than that which provides common variation.
> > I don't know what this means.
>
> Here's my understanding. Perhaps the OP can say if I understood correctly:
> Creationists claim that what we observe today is "micro-evolution",
Right, but the thing is, even then their idea of "micro-evolution" is
still conspicuous, occasional mutation.
They still think "micro-evolution" involves the occasional fortunate
deformity, etc.
~Iain
Iain
I think "mutation" in their mind conjours images of ninja turtles --
"Variation" is the word to save confusion. It suggests randomness
itself.
~Iain
Stile4aly
I hear her would join a chapter of Gama-God but there aren't any other
members.
mel turner
news:add64$43de74d4$c690c02a$33...@TSOFT.COM...
> > > Evolutionary theory does not claim:
> > That the earth is old....in fact...it has no opinion on the age of
> > the earth....that's left to the geologists.
>
> On the other hand, the primary purpose of evolutionary theory was to
> explain the variations in fossils over geologic time,
Not really true. Fossils actually played relatively little role in the
early development of evolutionary theory. It's more about explaining
the relationships among groups of organisms, both living and fossil,
and about the changes that have occurred as they descended from common
ancestors. Natural selection theory is about explaining the origin of
the adaptive features of organisms.
> so if you omit
> old-Earth then what's the point in having the theory in the first
> place?
Sure, if YECs were right there'd be far too little time for much
evolution to take place. Still, evolution as we know it would have
been occurring for however long life had existed, so some "theory
of evolution" would be as valid as ever.
> IMO, explanation of old-Earth fossils is an essential part of
> the overall framework of evolutionary theory, and old-Earth fossils
> should be listed as one of the premises of the theory.
No. The evidence for evolution would still be overwhelming even if
for some hypothetical geological reason no fossils were ever formed.
The fossil record is important as evidence for life's past
diversity, but it's not needed as a premise of the theory.
> A secondary purpose of evolutionary theory is to explain the variety of
> life we see today. (Darwin's book emphasized this purpose.)
Therefore, it's primary, not secondary. Darwin spent relatively
little time discussing fossils.
> Without a
> very very old Earth, the mechanisms proposed by evolutionary theory are
> incapable of producing the current variety of life.
Sure, the common descent of all life or even of major groups of life,
needs a very old earth. However, life would be evolving very much as
we currently understand it to, even if the "kinds" were very young
and so had to have had independent origins.
>So again old-Earth
> is essential to this purpose of the theory. With a theory that explains
> neither fossils nor variety of life, the theory is nearly worthless, IMO.
Without the common descent explanation for life's diversity,
evolutionary theory would cover far less than it now does, but it
would still explain a lot about things we observe in biology. People
dealing with new strains of antibiotic resistant bacteria would still
be pretty interested, for example.
> Evolutionary theory basically says that descent with modification acted
> over billions of years,
No, evolutionary theory basically says that descent with modification
happens, and explains how and why it happens. It's the evidence for
the common descent of all life and yes, the evidence from the fossil
record that tells us that this process has been occurring for billions
of years.
[snip rest]
cheers
Frank J
All that would work if the earth were significantly older than 4.5
billion years old too. But that evolution at least does not contradict
the ages determined from other fields is a significant argument in its
favor. Nevertheless it's telling that YECs primarily challenge claims
that originate from those other fields, yet find it necessary to single
out evolution to direct their bogus arguments. And it's also telling
how OECs and especially IDers, who know that the YE arguments are
bogus, rarely devote "equal time" to challenging them.
Time to dust off the American Physical Society's quote from 2000: "So
much for the pretense that the debate is over the science."
Frank J
Nothing else off the top of my head, yet.
But it's amazing how even a one-page anti-evolution screed usually
promotes most or all of those misconceptions, even when the author has
been repeatedly told that evolution does make those claims.
Frank J
The difference is that when a pro-science type like PZ Myers address
abiogenesis as they are usually careful to define the terms, e.g. as in
Myers' "chemical evolution". When anti-evolutionists address
abiogenesis (invariably about the "impossibility" thereof) it's always
a bait-and-switch with biological evolution.
Noone Inparticular
Yeah, "random" can be a nuanced term. In this regard, it is meant that
environmental influences are impacted by unpredictable inorganic (if
you will) events, such as vulcanism, asteroid impacts, storms, etc and
that these have a direct impact on the history and diversity of life. I
can see where the argument will come from; we know that volcanos will
erupt, storms will blow and asteroids will smack into the earth. But
the point is that these events have unpredictable consequences for the
history of life.
Thurisaz the Einherjer
> Evolutionary theory does not claim:
...that the _strongest_ survive. If it would be like that, the dinosaurs
would still be here. There's a _tiny_ little difference between strongest
and fittest.
This especially refers to the tired old "hitler was an evilutionist!!111!!!"
babble. Go figure.
--
Romans 2:24 revised:
"For the name of God is blasphemed among the Gentiles through you
cretinists, as it is written on aig."
Why I am not a christian:
http://www.carcosa.de/nojebus/nojebus
Timberwoof
"Ken Shackleton" <ken.sha...@shaw.ca> wrote:
Well, no direct claim, but it is fair to say that if evolution depends on there
being a long time in which changes happen, then it's fair to say it claims the
Earth is at least "a long time" old.
--
Timberwoof <me at timberwoof dot com> http://www.timberwoof.com
Tim Christensen
> So your claim is that if the earth were, say, only 6000 years old, there
> would be no evolution?
>
No, but the ToE would not be able to explain the diversity of life on
earth. Common descent would also be impossible on 6000 year old earth.
John Harshman
But there would be evolution, and evolutionary theory would explain
quite a lot of interesting phenomena.
Stanley Friesen
Though Darwin himself did conclude that an old age for the Earth was
more conducive to his theory than a young.
--
The peace of God be with you.
Stanley Friesen
Bob Pease
"Dave" <da...@gebler.co.uk> wrote in message
news:drlqrk$aci$1...@newsg4.svr.pol.co.uk...
> That humans descended from a currently living species of ape or that
today's
> apes should be giving birth to humans (unless you count humans as apes, of
> course)
Listening to and reading hot air like AIG and 700 Club DOES give some of
us paws
RJ P
Bob Pease
"Iain" <iain_i...@hotmail.com> wrote in message
news:1138651062.3...@f14g2000cwb.googlegroups.com...
Maybe so...
But the disregard of some version of Uniformatarianism actually promotes
PHLUDD (Tm) Geology to equal status in credibility.
RJ P
an...@sci.sci
> > explain the variations in fossils over geologic time,
> Who ever said that? Or if you're the only one who says it, why?
If I amend my statement from:
- Primary purpose, explain fossils, secondary purpose, explain current diversity.
to this:
- Two equal primary purposes: explain fossils and explain current diversity.
would you then be in agreement?
> So your claim is that if the earth were, say, only 6000 years old,
> there would be no evolution?
No. I claim the total amount of evolution within such a short time span
could at best explain breeds of dogs, couldn't at all explain species
of finches on Galapagos islands as intended by Darwin. Accordingly the
theory would be worthless for any of its original purposes, and
wouldn't have been invented by Darwin, because there wouldn't have been
such varieties of finches for him to observe in the first place (except
if Omphalos specially created them to look like they had evolved of
course). Barring Omphalos, with only 6000 years of evolution, there'd
be no nested hierarchy and no ancient fossils, hence nothing would need
explaining, hence evolution wouldn't have been invented as a theory 150
years ago, and if some crackpot had proposed evolution nobody would
have thought it to have any value, and it would in fact even today have
no value in unifying the study of biodiversity.
> > Without a
> > very very old Earth, the mechanisms proposed by evolutionary theory are
> > incapable of producing the current variety of life.
> ...assuming that you start with a single one-celled species.
If you start with a million different species, and then do micro-evolution
to produce a tiny bit more variety beyond what you started with, like
breeds of dogs and not any larger differences, then the theory explains
only a tiny bit of the diversity. Consider this metaphor: You start
with thousands of cities all over the world, and within each city you
have several different neighborhoods, the larger city the more
neighborhoods, and within each neighborhood people can walk from place
to place, and you wish to explain that variety of places people can
live by walking. You explain that all the people in each neighborhood
start from a single point (Adam and Eve of that neighborhood if you
wish), and then as families grow from just those two ancestors each,
people can walk to other places in the neighborhood and thereby create
variety in places people live. Well that theory explains why from seed
neighborhoods we have people living all around the neighborhood instead
of just in a single apartment building at the center (origin) of the
neighborhood with nobody living even a hundred feet away. But it
doesn't explain why there are so many cities all around the world, all
populated with people that seem to be of the same species. To explain
the variety of locations of cities, you need to include other modes of
transportation (or a very very long time for people to walk to all
those places around the world).
6000 years of evolution is like walking in a neighborhood, not enough
time to spread worldwide, not enough time to produce the wide variety
of species, at best able to explain varieties of each single species.
To explain how the species themselves came to be, you need evolution
over hundreds of millions of years. Most of the variance between
individuals is between different species, not between individuals of
each single species, and that variance-between-species is not explained
by 6000 years of evolution. Only the tiniest bit of variance, that
within single species, is explained by 6000 years of evolution.
> > Having it merely say that descent with
> > modification has happened for the past four thousand years, resulting
> > in new breeds of dogs and new viruses and not much else new, would
> > basically castrate the theory.
> Why? It wouldn't explain the diversity of life, but it would certainly
> explain many interesting phenomena. It would no longer be the central
> organizing principle of biology, though.
It would explain a teensy bit of trivia of interest only to
professional biologists of the 20th & 21st century. It wouldn't unify
study of biodiversity or unify the various fields of biology, it
wouldn't explain most of what happens in biology such as why fish and
human embryos both have pharyangeal arches. It would be a tiny theory
of very little use, castrated compared to what it really is today.
.
an...@sci.sci
One bit extra I want to add after posting my main reply:
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.) In that case, evolution doesn't explain the
variety of genes within a single proto-prokaryote, nor the different
species of proto-prokaryotes, but it does explain the variety of the
three prokaryotes that resulted, and the production of the first
eukaryotes, and the subsequent variety within the three resultant
clades. Depending on how you measure total variance composed of various
components, both variance of genes within a single cell and variance of
different kinds of cells, I'd estimate that evolution would explain a
majority of the total variance we see today. That unexplained variance
at the very start of our analysis is very small compared with the
variance that is added later due to evolution.
So you don't have to start with a single one-celled species to have
evolution (over billions of years) explain a majority of the variance
we see in life today, a vast majority of variance between different
species and individuals, and maybe even a majority of variance within a
single cell (because of gene duplication, whereby even a single cell
nowadays has more variance of DNA sequence than all the
proto-prokaryotes together had).
.
Tracy P. Hamilton
an...@sci.sci wrote:
> > > On the other hand, the primary purpose of evolutionary theory was to
> > > explain the variations in fossils over geologic time,
> > Who ever said that? Or if you're the only one who says it, why?
>
> If I amend my statement from:
> - Primary purpose, explain fossils, secondary purpose, explain current diversity.
> to this:
> - Two equal primary purposes: explain fossils and explain current diversity.
> would you then be in agreement?
>
> > So your claim is that if the earth were, say, only 6000 years old,
> > there would be no evolution?
> > No. I claim the total amount of evolution within such a short time span
> could at best explain breeds of dogs, couldn't at all explain species
> of finches on Galapagos islands as intended by Darwin. Accordingly the
> theory would be worthless for any of its original purposes, and
> wouldn't have been invented by Darwin, because there wouldn't have been
> such varieties of finches for him to observe in the first place (except
> if Omphalos specially created them to look like they had evolved of
> course). Barring Omphalos, with only 6000 years of evolution, there'd
> be no nested hierarchy and no ancient fossils, hence nothing would need
> explaining, hence evolution wouldn't have been invented as a theory 150
> years ago, and if some crackpot had proposed evolution nobody would
> have thought it to have any value, and it would in fact even today have
> no value in unifying the study of biodiversity.
Makes you wonder - why are young-earth creationists so dead-certain
evolution can't occur, if it makes no practical difference?
Well here is the thinking:
If evolution is not true, then there is no way that the ideas about the
long history of life on earth can be true. So they make theoretical
arguments about evolution that they think trump the age of the earth
and the universe, when all they show is deficiencies in their
theoretical
model or their understanding (most commonly both).
Now, a nested hierarchy is possible even if all creatures were
made at once, IF the Designer felt like ordering them that way.
Of course this is falsified by the time aspect - they were not made
in that pattern, but one of common DESCENT.
[snip of agreement, mostly]
Tracy P. Hamilton
John Harshman
>>>On the other hand, the primary purpose of evolutionary theory was to
>>>explain the variations in fossils over geologic time,
>>
>>Who ever said that? Or if you're the only one who says it, why?
>
>
> If I amend my statement from:
> - Primary purpose, explain fossils, secondary purpose, explain current diversity.
> to this:
> - Two equal primary purposes: explain fossils and explain current diversity.
> would you then be in agreement?
No. But it makes a nice lead-in to a Spanish Inquisition bit (...among
our primary purposes...). I would say that the primary purpose of
evolutionary theory (if indeed we want to single out just one for some
reason) is to explain the adaptive features of organisms. And in
addition to that (and the two you mention) it explains patterns in the
distributions of traits, adaptive or not; biogeographical patterns; and
all manner of other phenomena like sex ratios in wasps, variations in
the genetic code, and why big fierce animals are rare.
>>So your claim is that if the earth were, say, only 6000 years old,
>>there would be no evolution?
>
> No. I claim the total amount of evolution within such a short time span
> could at best explain breeds of dogs, couldn't at all explain species
> of finches on Galapagos islands as intended by Darwin.
Actually, I think it could be stretched to explain finch species. That's
the sort of speciation and adaptation that can happen in a short time.
It just happens that some of the speciation in Darwin's finches is older
than that.
But what I'm saying is that you overstate your case considerably.
> Accordingly the
> theory would be worthless for any of its original purposes, and
> wouldn't have been invented by Darwin, because there wouldn't have been
> such varieties of finches for him to observe in the first place (except
> if Omphalos specially created them to look like they had evolved of
> course).
I agree that evolution wouldn't be as important a scientific principle
as it is in this world, and wouldn't explain nearly as much. But
"useless" is hyperbole. And in a 6000-year-old world, who knows what
Darwin would have done? Everything would be too different for us to
imagine, and science would take a quite different form.
> Barring Omphalos, with only 6000 years of evolution, there'd
> be no nested hierarchy and no ancient fossils, hence nothing would need
> explaining,
Only if you agree that those are the only, or even the major, things to
be explained.
> hence evolution wouldn't have been invented as a theory 150
> years ago, and if some crackpot had proposed evolution nobody would
> have thought it to have any value, and it would in fact even today have
> no value in unifying the study of biodiversity.
Parts of that are true.
[snip]
>>>Having it merely say that descent with
>>>modification has happened for the past four thousand years, resulting
>>>in new breeds of dogs and new viruses and not much else new, would
>>>basically castrate the theory.
>>
>>Why? It wouldn't explain the diversity of life, but it would certainly
>>explain many interesting phenomena. It would no longer be the central
>>organizing principle of biology, though.
>
> It would explain a teensy bit of trivia of interest only to
> professional biologists of the 20th & 21st century.
So you say. I think it's only because you don't know that much about
biology. Our disagreement, though, is a matter of degree. You think
evolution would, in such a world, explain nothing. I think it would
explain a great number of interesting things and would be an important
scientific theory. Just not the dominating principle it is in the real
world.
[snip]
John Harshman
>>...assuming that you start with a single one-celled species.
>
> One bit extra I want to add after posting my main reply:
> 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". They are a little branch in
one group of prokaryotes, among many equally large branches. There are
two major groups of prokaryotes: Archaea and Eubacteria. Further
subdivision gives you many more than three groups.
> In that case, evolution doesn't explain the
> variety of genes within a single proto-prokaryote, nor the different
> species of proto-prokaryotes, but it does explain the variety of the
> three prokaryotes that resulted, and the production of the first
> eukaryotes, and the subsequent variety within the three resultant
> clades. Depending on how you measure total variance composed of various
> components, both variance of genes within a single cell and variance of
> different kinds of cells, I'd estimate that evolution would explain a
> majority of the total variance we see today. That unexplained variance
> at the very start of our analysis is very small compared with the
> variance that is added later due to evolution.
I have no idea whether you're talking about the real world here or the
creationist world, or what the start of our analysis is supposed to be,
or what this paragraph is supposed to tell me in general.
> So you don't have to start with a single one-celled species to have
> evolution (over billions of years) explain a majority of the variance
> we see in life today, a vast majority of variance between different
> species and individuals, and maybe even a majority of variance within a
> single cell (because of gene duplication, whereby even a single cell
> nowadays has more variance of DNA sequence than all the
> proto-prokaryotes together had).
Apparently you are going to all this trouble in order to say that
evolution doesn't have to begin with a single ancestor in order to be a
big deal. OK, I agree. Why did you bring this up?
Nick Roberts
an...@sci.sci wrote:
"That the process is entirely random"?
--
Nick Roberts tigger @ orpheusinternet.co.uk
Stanley Friesen
>an...@sci.sci wrote:
>
>>>...assuming that you start with a single one-celled species.
>>
>> One bit extra I want to add after posting my main reply:
>> 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.
John Harshman
Possible, though I keyed on the phrase "living independently" to suppose
he was talking about some kind of endosymbiote.
Matt Silberstein
<sar...@friesen.net> in <uvj1u1t2vlpd68l7q...@4ax.com>
wrote:
As opposed to the nauseating urk-aryotes, the frequently regurgitated
lineage that tend to descend from yeast by-products.
--
Matt Silberstein
Do something today about the Darfur Genocide
http://www.beawitness.org
http://www.darfurgenocide.org
http://www.savedarfur.org
"Darfur: A Genocide We can Stop"
John Wilkins
> On Wed, 01 Feb 2006 07:15:06 -0800, in talk.origins , Stanley Friesen
> <sar...@friesen.net> in <uvj1u1t2vlpd68l7q...@4ax.com>
> wrote:
>
>> John Harshman <jharshman....@pacbell.net> wrote:
>>> an...@sci.sci wrote:
>>>
>>>>> ...assuming that you start with a single one-celled species.
>>>> One bit extra I want to add after posting my main reply:
>>>> 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.
>
> As opposed to the nauseating urk-aryotes, the frequently regurgitated
> lineage that tend to descend from yeast by-products.
>
>
--
John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
University of Queensland - Blog: evolvethought.blogspot.com
Servum tui ero, ipse vespera
Matt Silberstein
<jo...@wilkins.id.au> in <drrcl7$1tdb$3...@bunyip2.cc.uq.edu.au> wrote:
>Matt Silberstein wrote:
>> On Wed, 01 Feb 2006 07:15:06 -0800, in talk.origins , Stanley Friesen
>> <sar...@friesen.net> in <uvj1u1t2vlpd68l7q...@4ax.com>
>> wrote:
>>
>>> John Harshman <jharshman....@pacbell.net> wrote:
>>>> an...@sci.sci wrote:
>>>>
>>>>>> ...assuming that you start with a single one-celled species.
>>>>> One bit extra I want to add after posting my main reply:
>>>>> 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.
>>
>> As opposed to the nauseating urk-aryotes, the frequently regurgitated
>> lineage that tend to descend from yeast by-products.
>>
>>
>And the eury-arkotes, those who still think there was an Ark.
Then there are the ureka-ryotes, who either find things or take lots
of baths, I forget which.
Walter Bushell
"Iain" <iain_i...@hotmail.com> wrote:
> Feel free to add to the list :
>
>
> Evolutionary theory does not claim:
>
> That the development of life on earth until now relied on more
> conspicuous mutation than that which provides common variation.
>
> That individuals decidedly of ancestral species A can beget individuals
> decidedly of descendant species B.
>
> That life as it is is implicit in earlier forms of life.
>
> That randomness is at the heart of the process.
>
> Anything on the origins of life.
>
> Anything on gods, God, theism, religion or morality.
>
> ~Iain
Actually sexual selection is under control by Aph rodite.
--
"The power of the Executive to cast a man into prison without formulating any
charge known to the law, and particularly to deny him the judgement of his
peers, is in the highest degree odious and is the foundation of all totali-
tarian government whether Nazi or Communist." -- W. Churchill, Nov 21, 1943
Walter Bushell
Stanley Friesen <sar...@friesen.net> wrote:
Ur-kayotes weren't the original restaurants without seating in the city
of Ur?
an...@sci.sci
> > be no nested hierarchy and no ancient fossils, hence nothing would need
> > explaining, hence evolution wouldn't have been invented as a theory 150
> > years ago, and if some crackpot had proposed evolution nobody would
> > have thought it to have any value, and it would in fact even today have
> > no value in unifying the study of biodiversity.
> Makes you wonder - why are young-earth creationists so dead-certain
> evolution can't occur, if it makes no practical difference?
Well the obvious answer is that they know the Earth is a lot older than
6009 years, but they need to lie to maintain their stupid religion.
Or they have not the slightest idea how slowly evolution happens, and
hence they don't realize that evolution within species, which is almost
all you get in only 6009 years, is perfectly consistent with YEC. (They
read that evolutionary theory claims humans evolved from common
ancestor with chimps, contrary to their Bible, and they're too stupid
to separate that allegation which requires millions of years from
evolution itself which could have operated just fine over 6009 years
without contracting any of their Bible.)
Or somebody else in their church said that evolution is contrary to
their religion, and they just believed that without understanding it.
Perhaps we should confront them like this:
We: How old is the Earth?
They: 6009 years.
We: If evolution happened during all of those 6009 years, how much
evolution would accumulate? Enough to convert a monkey into a man?
Then depending on how they respond, enlighten them. Once they
understand that micro-evolution has actually been observed in the lab,
that evolution of breeds of dogs has occurred in historical times,
etc., emphasize how evolution isn't a contradiction to their religion.
In that way, get them to accept the fact of evolution, so that when a
poll is conducted, they respond that they agree with evolution as fact.
> Well here is the thinking: If evolution is not true, then there is no
> way that the ideas about the long history of life on earth can be true.
No, I don't agree at all. It's perfectly consistent that (1) the Earth
is 4.6 billion years old, with life on it for 3.5 billion years, and
(2) there's never been any natural evolution, only recent stuff where
humans deliberately breed dogs or manipulate E coli in the lab, and
ancient stuff done by some unknown supernatural means. Of course that
supernatural agent would have to be Omphalos, somehow contriving to
make the succession of forms look very much like natural evolution,
both in anatomical or botanical detail, and in DNA sequence change and
corresponding biochemistry for the 5% of DNA that affects biochemistry.
But that's not a logical contradiction. It's just a reason for not
trusting any such supernatural being to ever tell the truth.
> So they make theoretical arguments about evolution that they think
> trump the age of the earth and the universe, when all they show is
> deficiencies in their theoretical model or their understanding (most
> commonly both).
So you say they mistakenly believe that evolution implies long Earth,
despite the fact there's no such implication (see previous paragraph of
mine), and because of that false belief they furthermore conclude
falsely that evolution is the main reason anybody would believe in such
an old Earth, and so they figure if they knock out evolution they will
knock out all support for an old Earth? I can't believe they're quite
that stupid, maybe 70% that stupid, but not 100% that stupid. Can you
find any YEC to admit such a line of argument?
> Now, a nested hierarchy is possible even if all creatures were
> made at once, IF the Designer felt like ordering them that way.
The word "ordering" is ambiguous here. At first I read it as "arranging
in sequence", but maybe it means "commanding" or "requesting" as a
customer in a restaurant? Please clarify your usage of "ordering".
Note that the nested hierarchy of types of life (per Linnaeus for
example), basically like a multi-level department-store catalog,
implies nothing chronological whatsoever.
For example, just because Sears Roebuck has categories of:
Appliances / Baby / Clothing / Computers & Electronics / For the Home /
Gifts / Jewelry & Watches / Lawn & Garden / Movies, Music & Games /
Sporting Goods / Tools / Toys
and Sporting Goods for example is sub-divided into:
Apparel / Baseball, Softball & T-Ball / Basketball / Bicycling /
Camping, Fishing & Hunting / Electronics / Fan & Memorabilia / Fitness
/ Football / Game Room / Golf / Packs, Bags & Accessories / Scooters /
Sports / Sports Medicine / Water Recreation / Winter Recreation
doesn't imply that all items in each such sub-department is a clade
that arose from a single sub-department-common ancestor, and all the
sub-department ancestors within each department arose from a single
department-common ancestor, and all department ancestors arose from one
all-Sears common ancestor.
The point I'm making is that even if the Designer created *current*
life to be a nested hierarchy like a Sears catalog, that doesn't mean
the Designer created life to look like the result of evolution. The
Designer might have merely created life to look like a department store
catalog (with omniscient-future knowledge that department stores would
someday arise as human artifacts), perhaps as a boasting joke (hey
looky, I did it before you did it, that makes me smarter than you),
perhaps a guide to mankind (maybe Sears got the idea from Linnaeus who
got the idea from observing the Designer's works, which was the whole
idea), or perhaps simply re-inventing the Wheel (hierarchial
organization is a good idea, re-invented by Linnaeus and Sears and many
other folks, heck even the Bible has a 3-level hierarchy within each of
the two 'Testaments', namely book and chapter and verse).
So what you suggested, that I quoted, that the Designer made life look
like a nested hierarchy, simply means that he organized life into
categories and sub-categories etc., not that he made anything to look
like evolution. It's only when you look at timestamped fossils, or DNA
sequences, or protein families, or vestigal organs, that you see any
clear evidence of clades instead of merely Sears Catalog organization.
> Of course this is falsified by the time aspect - they were not made
> in that pattern, but one of common DESCENT.
That's poorly worded. With "this" referring to your previous two lines
within the same paragraph, you literally are saying life was not made
to look like a nested hierarchy (false, life *was* so), but rather like
a result of common descent instead (false, life was made to look like
*both* a nested hierarchy organization like a Sears catalog *and* like
the result of common descent), when the time aspect of the evidence is
included. Could you please re-phrase what you wrote there to clearly
indicate that you meant to say life was created to look not like *just*
a nested hierarchy without any cladistic implication but instead like a
nested hierarchy *with* a cladistic implication? Or whatever you really
meant to say there? Please look at both your last four quoted lines
(two doublets I quoted separately) and try to make them fit together
better, to answer my critique, to make sure we're on the same wavelength.
Now here's my view of the evidence: Assuming some Designer made each
species of life separately, the evidence shows that the Designer made
current life to look like a Sears Catalog, a nested hierarchy, as
Linnaeus astutely figured out (even though he made a few mistakes in
the details), which does *not* imply any time structure. But the
Designer laid out fossils to look clearly like the result of descent
with modification. As a result, the nested hierarchy of current life
would have to be re-interpreted as the result of that descent with
modification (since obviously the current life fits in nicely with the
past pattern of fossils) instead of as a Sears-style ad hoc static
organizational pattern. Then when we compare DNA sequences, and and
study protein families, and compare embryo development, we see this too
matches the kind of pattern we'd expect from descent with modification,
and indeed we get almost exactly the same cladistic analysis for each
of these different lines of evidence, which is consistent with **one**
pattern of descent with modification plus our occasional mistakes in
analysis of the pattern which break from the true pattern.
Note I'm phrasing this in the most E-Prime or abstract-algebra way
here. I'm not saying fossil life *was* following descent with
modifaction, and that current life *is* the result of that descent with
modification. All I'm saying is that the overall set of data is
consistent with a *pattern* of descent with modification.
Here's a mathematics metaphor: Consider the rational numbers, and
Dedekind cuts of rationals to construct the real numbers, and the a 1-1
isomorphism between the rationals and a subset of the reals, the
"rational reals" (the Dedekind cuts which have a rational cut-point).
Are the "rational reals" the same set of objects as the rationals? No.
Not at all. But the arithmetic and ordering *structure* of the rational
reals is isomorphic to the arithmetic and ordering structure of the
rationals that we started with. The two systems are isomorphic.
Another math metaphor: Consider a finite set of objects S, and a set of
permutations on those objects G such that G is closed under
permutation-composition. Theorem: G ,with permutation-composition as a
single binary operation, has the structure of a (mathematical) *group*.
(Closed, identity, inverses, associative.) Now we ask *is* G a group?
No, it's just a set of permutations. So what *is* a group? Nobody
really cares. All any mathematician cares about is what mathematical
structures satisfy the defintion of group, i.e. what set with binary
operation has the *structure* of a (mathematical) group.
Now apply those metaphors to life and evolution: Science doesn't
actually say that life *did* evolve, or that life today *is* the result
of such evolution. Science merely says that the structure or pattern we
see in the natural history of life is entirely consistent with a
structure of pattern of descent with modification, and that based on
that isomorphism between reality and our model we can make predictions
in the model which can then be tested against reality, and indeed we
find again and again the predictions of the model match subsequent
observations of reality.
So we don't have to convince the YEC that descent with modification
really happened. Per a discussion we had a few days ago re Kurt Wise:
<http://groups.google.com/group/talk.origins/msg/5e1000dfca4c7a75>
= Message-ID: <aa561$43e06a05$c690c02a$30...@TSOFT.COM>
all we need to show is that however life happened, it presented
evidence entirely as if descent with modification had happened, that
the descent-with-modification modem nicely agrees with evidence.
We can let the YEC continue to "believe" that everything is only 6009
years old, but the Great Omphalos Deceiver made it look as if the
Universe is appx. 13.7 billion years old, and as if the Earth was over
4.5 billion years old, and as if life was over 3.5 billion years old
and experienced descent with modification over most or all of that time
span. Since the YEC chooses to spend most of his time and energy
studying the works of Gunderscored, why not tap that energy by having
the YEC believe that what science really studies is the Word of
Gunderscored as revealed by the illusion of ancient Earth?
So then there are three Testaments, the Old and New, and Science/Nature.
Note also that by saying only that evidence shows a *pattern* like
descent with modification, we are in no way contradicting the Bible or
anybody else's sacred writings, and in fact we're even admitting all of
the evidence could be a (very consistent) illusion/forgery, so there's
no valid claim that we're trying to preach an anti-Christian belief
system in public schools.
.
an...@sci.sci
> indeed we want to single out just one for some reason) is to explain
> the adaptive features of organisms.
But why would anybody think of such a theory, if it were not for
natural history which shows ancient fossils? It seems to me that *now*,
after somebody already looked at fossils and got an idea for descent
with modification, that we can post hoc adapt evolution to explain
adaptive features, and maybe even claim that *now* that is the primary
value of it. But the *purpose* of it, the reason it was invented in the
first place, was IMO to explain fossils.
What is the *purpose* of invading Iraq? To find WMD. As it turns out,
no such were found, so that value has fizzled, and now other reasons
are given why it was a good idea anyway. But the primary purpose when
we actually invaded Iraq was supposed to be to stop the production of
WMD, right?
So I say the primary purpose of any theory of evolution in the first
place when it was conceived, was to explain fossils, although at the
time it was a linear sequence rather than a tree, a la Lamarck. But
then Darwin realized that a tree structure was a better model for the
variety of life on the Galapagos islands, and so he modified the old
theory to be treelike, and then with Malthus's idea he realized that
survival of the fittest was a good mechanism behind both linear
adaption and tree-splitting, whereupon his published theory served to
explain both fossils and current bio-diversity, all as a combination of
adaptive features.
So here's my new wording: The basic idea of descent with modification
(without survival of fittest per Malthus yet, and without much tree
structure) was for the purpose of explaining the already-discovered
fossils spread over time and varying with each epoch. That theory had a
false explanation of current bio-diversity, via Lamarck's ladder with
different species having started their per-kind trek at various times
and therefore having reached different rungs of the ladder by the
current Epoch (Holocene at the time of Darwin, but now a major
Extinction Event in Progress, new Epoch started sometime during the
20th century, I forget the new name that has been assigned. Edit: Hmm,
after researching the stuff below, I'm thinking the new epoch is called
something like "Anthro[po]cene"?? See later below.).
Side remark:
<http://www.enchantedlearning.com/subjects/Geologictime.html>
The first geologic time scale was proposed in 1913 by the British
geologist Arthur Holmes (1890 - 1965). This was soon after the
discovery of radioactivity, and using it, Holmes estimated that the
Earth was about 4 billion years old - this was much greater than
previously believed.
Wow, that's an amazingly good first-estimate from a new methodology,
especially considering very few rocks anywhere in the world are older
than 3.5 billion years. He erred in the correct direction to anticipate
Apollo lunar rock dating which finally established the true age of the
Moon (4.56 billion years) and therefore approximately the true age of
the Earth.
Another side remark: Here's a refreshing new look at paleontology,
starting from the foundation of plate tectonics rather surface
appearance of biodiversity!
<http://www.paleoportal.org/time_space/period.php?period_id=8>
World Paleogeography: During the Tertiary, the last phase of the
breakup of Pangea was accompanied by several continental collisions.
Another side remark: Here's a fine overview of mass extinctions:
<http://hoopermuseum.earthsci.carleton.ca/extinction/extincmenu.html>
Note IMO: There's a basic difference between the end-ice-age
extinction, probably caused mostly by hunting of food animals (all
large non-human animals in North America for example) with only local
disruption of habitat around cities and farming centers, and the
current mass extinction, caused mostly by massive destruction of rain
forests and other habitats as well as gross encrochment of humans into
previously multi-species areas. I don't think the end-ice-age
extinction and the current extinctions by habitat destruction and
encroachment should be considered merely a single long extinction
process, even if human activity is the primary cause of both. The type
of human activity is different in the two cases.
OK, here's what I finally found about new Epoch name:
<http://64.233.179.104/search?q=cache:4FRPNAn4p4gJ:www.populationaction.org/resources/publications/naturesplace/NaturesPlace.pdf+anthrocene+holocene&hl=en&gl=us&ct=clnk&cd=3&ie=UTF-8>
Indeed, a case could be made that Earth has entered a new epoch. Call
it the Anthrocene, a period initiated and defined by Homo sapiens'
unprece-
dented population and its capacity to influence the planet's global
cycles.
If scientists poke into the planet's crust thousands or millions of
years
from now, they may be able to identify the opening of the Anthrocene
by a
layer of lead, mercury and other relatively rare metals released from
buried
plastics and the settling smoke particles of fossil fuels.
<http://www.mpch-mainz.mpg.de/~air/anthropocene/Text.html>
To assign a more specific date to the onset of the 'anthropocene"
seems somewhat arbitrary, but we propose the latter part of the
18th century, although we are aware that alternative proposals can
be made (some may even want to include the entire holocene).
However, we choose this date because, during the past two
centuries, the global effects of human activities have become
clearly noticeable. This is the period when data retrieved from
glacial ice cores show the beginning of a growth in the atmospheric
concentrations of several 'greenhouse gases", in particular C0[2]
and CH[4 ](7). Such a starting date also coincides with James
Watt's invention of the steam engine in 1784.
<http://geology.about.com/library/weekly/aa080402a.htm>
... Paul Crutzen, a Nobel Prize winner for his work on the
ozone layer, has set out to give the future a new name.
... he says, humans have become a geologic agent
comparable to erosion and eruptions, and accordingly "it seems to us
more than appropriate to emphasize the central role of mankind in
geology and ecology by proposing to use the term 'anthropocene' for
the current geological epoch." ...
Crutzen's would-be Anthropocene Epoch isn't based on fossils. He would
start it in the late 1700s, at the start of the Industrial Revolution. ...
To me, the best way to respond to Crutzen's proposal is to add the
Anthropocene Age under the Holocene Epoch. ...
<http://en.wikipedia.org/wiki/Anthropocene>
(More on Crutzen's proposal.)
<http://web.pdx.edu/~chulbe/>
... I'm thinking of forming a new fake society, one to rename
the Holocene the Anthropocene.
<http://web.pdx.edu/~chulbe/cv.html>
(Hey, she's in Portland. Maybe I should go meet her sometime.)
<http://web.pdx.edu/~chulbe/amazing/amaze33.html>
(Good news: Buffalo is no longer extinct.)
I'll let you guess where I saw this advice:
PREPARE IMMEDIATELY FOR WHATEVER IS GOING TO HAPPEN NEXT.
.
John Harshman
This new trend of yours to eliminate all attributions is a bad thing.
Please stop.
>>I would say that the primary purpose of evolutionary theory (if
>>indeed we want to single out just one for some reason) is to explain
>>the adaptive features of organisms.
>
> But why would anybody think of such a theory, if it were not for
> natural history which shows ancient fossils?
For all the other reasons Darwin sets out in the Origin. Really, do you
think that fossils were his primary impetus? If so, you just didn't read
the book.
> It seems to me that *now*,
> after somebody already looked at fossils and got an idea for descent
> with modification, that we can post hoc adapt evolution to explain
> adaptive features, and maybe even claim that *now* that is the primary
> value of it. But the *purpose* of it, the reason it was invented in the
> first place, was IMO to explain fossils.
Is this opinion based on anything? Have you in fact ever read the
Origin? Have you read Wallace's paper? They both came to their theories
mostly by examining the similarities among living species.
> What is the *purpose* of invading Iraq? To find WMD. As it turns out,
> no such were found, so that value has fizzled, and now other reasons
> are given why it was a good idea anyway. But the primary purpose when
> we actually invaded Iraq was supposed to be to stop the production of
> WMD, right?
Actually, I think that was an excuse and that the real purpose was
otherwise. But I fail to see the relevance anyway.
> So I say the primary purpose of any theory of evolution in the first
> place when it was conceived, was to explain fossils, although at the
> time it was a linear sequence rather than a tree, a la Lamarck.
Have you read Lamarck? (I haven't.) Can you support, from his writings,
the idea that his primary purpose was to explain fossils?
> But
> then Darwin realized that a tree structure was a better model for the
> variety of life on the Galapagos islands, and so he modified the old
> theory to be treelike, and then with Malthus's idea he realized that
> survival of the fittest was a good mechanism behind both linear
> adaption and tree-splitting, whereupon his published theory served to
> explain both fossils and current bio-diversity, all as a combination of
> adaptive features.
>
> So here's my new wording: The basic idea of descent with modification
> (without survival of fittest per Malthus yet, and without much tree
> structure) was for the purpose of explaining the already-discovered
> fossils spread over time and varying with each epoch.
Interesting notion. Can you back it up?
[snip digressions]
Robert J. Kolker
>
> For all the other reasons Darwin sets out in the Origin. Really, do you
> think that fossils were his primary impetus? If so, you just didn't read
> the book.
I got the impression that he was very very impressed by animal and plant
breeders. That and Malthusian pessimism is what drove him.
Just as the equivalence princple drove the General Theory of Relativity
(not the anomalous precession of the perihellion of Mercury), the
Struggle for Existence is what drove Darwin's thinking, or so I conclude.
Bob Kolker
an...@sci.sci
> > independently even today.)
No, that's not what I'm talking about. I'm talking about whatever DNA
codes for 30S subunit of ribosome in eukaryotes. That DNA most have
some from a different source than either the LCA of modern Eubacteria
(which are missing the "bill" and "lobes") and the LCA of modern
Archaebacteria (which are missing only the "lobes"). Eukaryotes have
both bill and lobes in their 30S subunit. Whatever formed the first
nucleus of eukaryotes must have descended from some prokaryote-like
cell very different from both current clades of prokaryotes, a third
primary division of prokaryote life before eukaryotes evolved from them
and drove their non-eukaryote brothers to extinction.
Caveat: I'm working from Haeckel-style diagrams of the 30S subunit,
allegedly from a 1983 article in Cell, not actual electron-microscope
images, so I don't know for sure I'm working from trustworthy
information. A lot of work has been done since then, which might show
exceptions, and a relatively recent common ancestry of Eukaryote
nuclear DNA and one of the other two domains of prokaryotes. Somebody
in a followup to your article guessed correctly, and referred to them
as something like ur-karyotes, which started a fur-coyote pun radiation.
> > In that case, evolution doesn't explain the
> > variety of genes within a single proto-prokaryote, nor the different
> > species of proto-prokaryotes, but it does explain the variety of the
> > three prokaryotes that resulted, and the production of the first
> > eukaryotes, and the subsequent variety within the three resultant
> > clades. Depending on how you measure total variance composed of various
> > components, both variance of genes within a single cell and variance of
> > different kinds of cells, I'd estimate that evolution would explain a
> > majority of the total variance we see today. That unexplained variance
> > at the very start of our analysis is very small compared with the
> > variance that is added later due to evolution.
> I have no idea whether you're talking about the real world here or the
> creationist world, or what the start of our analysis is supposed to be,
> or what this paragraph is supposed to tell me in general.
I'm talking about a hypothetical way the tangled-root of the tree of
life might have formed, from massive horizontal gene flow between
pre-prokaryotes that finally stablized with extinction of all but three
transitions to true prokaryotes, two of which survive today in
prokaryotes, and one of which survives today as the nucleus in
eukaryotes.
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 there's some variation already in the first column of pp, both
between various genes within a single pp, and differences from one pp
to another. During the # period, some of the pp acquire genes from
other pp, making their individual genomes more complete so they're less
dependent on the other pp for basic biochemical functions, more able to
live independently for extended periods of time, relying on other pp
only for relatively stable compounds such as sugars and methane etc.
Due to new mutations, a small amount of new variation accumulates
between the first and second row of pp. Then three of the pp are
sufficiently self-supporting that they no longer depend on close
exo-symbiosis with other pp, so they can directly compete, driving all
of the other (all but three) pp to extinction. Now it's no longer
useful to allow massive quantities of horizontal gene flow from
unrelated species, so the three domains evolve to block incoming gene
flow (except from closely related species), and to specialize their
biochemistry in ways that weren't possible with all that incoming gene
flow. So now life mostly follows cladistics, for example:
+-----Eubac1
Eubac--+ +--Eubac2
+--+ +Eubac3
+-+Eubac4
New variation occurs along branch to Eubac1, along common branch to
Eubac234, along branch from there to Eubac2, along common branch to
Eubac34, along branch to Eubac3, and along branch to Eubac4. The total
amount of variation is larger than the single amount of variation along
a single path from Eubac to Eubac<n>. Now consider the really large
evolutionary trees that yield millions of species. Initially there are
only a few parallel lines of evolution, so the total rate of new
variation is only a few times what'd you get from a single line of
descent. But by the Cambrian there must have been millions of different
species (of which only a few left fossils, and only a few survived to
have modern clades, not the same few in those two cases), after which
the total rate of new variation would be millions of times the rate for
a single line of descent.
Evolution as we know it doesn't explain the *original* variation among
and within the first column of pp, but it does explain the little bit
of new variation between first column and second column of pp, and the
little bit of new variation during the very early stages of each of the
three surviving clades, and the much larger amount of variation
accumulated in millions of parallel branches of evolution during the
later stages of evolution in the three clades.
If you count only today's variation, some of which was original between
and within the first column of pp, but most of which was accumulated
later along the various surviving branches, not counting all the
parallel evolution that went extinct before the Holocene, the average
factor of parallel evolution was probably less than a million. Still
that's probably an average factor of hundreds of thousands over a time
span of 3 billion years which is much more total variation than what
must have already existed in the first column of pre-prokaryotes.
Therefore evolution as we know it, from that first column of pp to the
present, accounts for a vast majority of current variation
(bio-diversity).
Does that explanation help your understanding?
By comparison, if life started 6009 years ago, by special creation, and
then evoution added some new variation since then, the amount of added
variation would be trivial compared to the variation that was specially
created back then, so evolution wouldn't be a good explanation for the
bulk of bio-diversity we see today.
> Apparently you are going to all this trouble in order to say that
> evolution doesn't have to begin with a single ancestor in order to be a
> big deal. OK, I agree. Why did you bring this up?
Well, it's a handwave if you just say that without any math to back it up.
I think the tens or hundreds of pre-prokaryotes exchanging DNA,
followed by three surviving clades that radiate quickly to millions of
parallel branches of evolution, suffering extinctions along some
branches but filling the gaps with further radiation within the
remaining clades, with massive numbers of parallel branches at any time
for 3 billion years, shows that whatever variation there was at the
start, even if there were tens or hundreds of different pre-prokaryotes
(in the first column above), would be a drop in the bucket compared to
the massive variation added later by evolution as we know it, so that
evolution does indeed explain nearly all the variation we see today,
all but that initial drop-in-bucket.
.
an...@sci.sci
> >> 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!)
.
John Harshman
>>>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, ...
>
>
> No, that's not what I'm talking about. I'm talking about whatever DNA
> codes for 30S subunit of ribosome in eukaryotes.
There is no 30S subunit. Do you mean 28S? Or are we talking about the
combined 5S + 28S? But OK, you're talking about the stem-ancestor of
eukaryotes. It's unclear whether you want to count that as a prokaryote
or not. It all depends on your definition of eukaryote. And if that
definition is based on several characters, it depends on what you count
organisms that have some but not all of those characters as being.
But never mind, I misunderstood you. You were talking about the 3 domains.
> That DNA most have
> some from a different source than either the LCA of modern Eubacteria
> (which are missing the "bill" and "lobes") and the LCA of modern
> Archaebacteria (which are missing only the "lobes"). Eukaryotes have
> both bill and lobes in their 30S subunit. Whatever formed the first
> nucleus of eukaryotes must have descended from some prokaryote-like
> cell very different from both current clades of prokaryotes, a third
> primary division of prokaryote life before eukaryotes evolved from them
> and drove their non-eukaryote brothers to extinction.
>
> Caveat: I'm working from Haeckel-style diagrams of the 30S subunit,
> allegedly from a 1983 article in Cell, not actual electron-microscope
> images, so I don't know for sure I'm working from trustworthy
> information.
EM images won't show anything.
> A lot of work has been done since then, which might show
> exceptions, and a relatively recent common ancestry of Eukaryote
> nuclear DNA and one of the other two domains of prokaryotes. Somebody
> in a followup to your article guessed correctly, and referred to them
> as something like ur-karyotes, which started a fur-coyote pun radiation.
OK. Now I get what you're saying.
Sure it does. Why not? The only thing is that the amount of horizontal
transfer was, hypothetically, greater then than it is now.
> but it does explain the little bit
> of new variation between first column and second column of pp, and the
> little bit of new variation during the very early stages of each of the
> three surviving clades, and the much larger amount of variation
> accumulated in millions of parallel branches of evolution during the
> later stages of evolution in the three clades.
>
> If you count only today's variation, some of which was original between
> and within the first column of pp, but most of which was accumulated
> later along the various surviving branches, not counting all the
> parallel evolution that went extinct before the Holocene, the average
> factor of parallel evolution was probably less than a million. Still
> that's probably an average factor of hundreds of thousands over a time
> span of 3 billion years which is much more total variation than what
> must have already existed in the first column of pre-prokaryotes.
> Therefore evolution as we know it, from that first column of pp to the
> present, accounts for a vast majority of current variation
> (bio-diversity).
>
> Does that explanation help your understanding?
More or less. You have a strange way of saying things.
> By comparison, if life started 6009 years ago, by special creation, and
> then evoution added some new variation since then, the amount of added
> variation would be trivial compared to the variation that was specially
> created back then, so evolution wouldn't be a good explanation for the
> bulk of bio-diversity we see today.
Agreed.
>>Apparently you are going to all this trouble in order to say that
>>evolution doesn't have to begin with a single ancestor in order to be a
>>big deal. OK, I agree. Why did you bring this up?
>
> Well, it's a handwave if you just say that without any math to back it up.
What math?
> I think the tens or hundreds of pre-prokaryotes exchanging DNA,
> followed by three surviving clades that radiate quickly to millions of
> parallel branches of evolution, suffering extinctions along some
> branches but filling the gaps with further radiation within the
> remaining clades, with massive numbers of parallel branches at any time
> for 3 billion years, shows that whatever variation there was at the
> start, even if there were tens or hundreds of different pre-prokaryotes
> (in the first column above), would be a drop in the bucket compared to
> the massive variation added later by evolution as we know it, so that
> evolution does indeed explain nearly all the variation we see today,
> all but that initial drop-in-bucket.
This was never at issue.
an...@sci.sci
But I thought Alpha males didn't need rogain to perform?
Or is there something they're not telling,
that rogain is *why* they are so Alpha?
Poor me, I'm the ____ carotene type, you know the missing word.
Maybe if I paid more attention to that spam, I'd become _____ ?
Sigh, what is this newsgroup coming to anyway.
(Ooops, for Brits, replace "coming to" by "arriving at".)
(And for classic SNL fans, never mind.)
>"The power of the Executive to cast a man into prison without formulating any
> charge known to the law, and particularly to deny him the judgement of his
> peers, is in the highest degree odious and is the foundation of all totali-
> tarian government whether Nazi or Communist." -- W. Churchill, Nov 21, 1943
I wish G.W.Bush wouldn't try to emulate Hitler so much. I wish he'd pay
attention to Churchill's warning, and abandon the mis-named "Patriot Act".
But G.W.Bush has never been famous for his forward-looking vision,
such as understanding the longerm consequences of his misguided actions.
.
an...@sci.sci
> > No, that's not what I'm talking about. I'm talking about whatever DNA
> > codes for 30S subunit of ribosome in eukaryotes.
> There is no 30S subunit. Do you mean 28S? Or are we talking about the
> combined 5S + 28S?
I don't know. I got the "30S" designation out of a book, which cited
Cell 33:318-319 (1983), but I have no access to Cell so I can't check
whether the designation was copied wrong or was in the original.
Google shows 156 thousand matches for 30S subunit, so could you
possibly be mistaken in saying there's no such thing? For example:
<http://alf1.mrc-lmb.cam.ac.uk/~ribo/30S/>
Work in our laboratory has focused on the structure of the ribosome,
especially the 30S ribosomal subunit. We have determined the complete
atomic structure of the 30S subunit and its complexes with several
antibiotics.
<http://www.bio.cmu.edu/Courses/BiochemMols/ribosome/70S30.htm>
The 30S subunit structure is described in Yusupov, M. M., Yusupova, G.
Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. D., Noller,
H. F. (2001) "Crystal structure of the ribosome at 5.5 E resolution"
Science 292:883.
I'm beginning to suspect you posted your "no such" remark as a prank.
> But OK, you're talking about the stem-ancestor of eukaryotes. It's
> unclear whether you want to count that as a prokaryote or not. It all
> depends on your definition of eukaryote.
"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?
I agree that where you draw the boundaries along the path from
prokaryotes through ur-kryotes to pre-eukaryotes to fullfledged
eukaryotes is a matter of personal opinion. I would consider a
eukaryote with mitochondria as fullfledged, one without mitochondria
but which does mitosis as not fullfledged but true eukaryote, 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.
Someday we may understand the function of genes and proteins well
enough that we can decide which changes in the genome from the top of
the stem all the way down to true eukaryotes happened in which
sequence, such that there's a meaningful scaffold at each stage, such
that each significant mutation provides an advantage. At that point we
might legitimately claim to have the full sequence along that
evolutionary path despite lack of any surviving side branches or useful
fossils. Then it may be possible to establish criterion for drawing the
boundaries at totally reasonable places.
> But never mind, I misunderstood you. You were talking about the 3 domains.
Almost. In two cases, there's a direct unitary line of descent from
the LCA of all three domains down to the crown LCA of each surviving
clade. So it was a single domain all the way between those two points.
But in the case of modern eukaryota, there were several symbioses along
the way, merging several old domains into a single new domain, so it's
not really the same domain from one to the other end of the primary
line of 30S-coding descent and whatever other genes co-evolved with
that one gene. So "the" 3 domains is ambiguous depending on whether
we're talking about the ur-karyote domain way back then or the
eukaryote domain more recently.
> > Evolution as we know it doesn't explain the *original* variation among
> > and within the first column of pp,
> Sure it does. Why not? The only thing is that the amount of horizontal
> transfer was, hypothetically, greater then than it is now.
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. Whatever variation there was
between the different very-first-replicators, each of which arose via
an independent abiogenesis event, was not generated by evolution as we
know it, but instead was merely an artifact of the gazillions of
different possible abiogenesis events, combined with the fact that each
such actual event was in a different environment hence selected from a
different subset of all possible abiogenesis events.
We already know that complicated biochemistry starts very easily in
reducing conditions such as Miller-Urey apparatus. What we don't know
is whether over hundreds of millions of years in a natural ocean the
biochemistry is likely to form a replicator. If so, then it's probably
easy to form in not just one place but many places, and not in just one
way but gazillions of different ways. So multiple independent
abiogenesis events in different local environents seems likely to me.
With each of them starting as a single auto-catalytic set, there's zero
evolution-caused variation (initially) within a single such replicator,
so 100% of the variation is between the different such events, none of
which is caused by evolution. Then each such abiogenesis-generated
replicator somehow evolves to some kind of linear digital genome, and
all of that evolution is *not* anything like the kind of evolution we
understand today. It's only after linear digital genome has appeared
that evolution is even remotely like what we understand today.
So the total of variation consists of:
(1) differences between the original separate abiogenesis events which
were not due to evolution at all;
(2) new variation that occurs during that early non-linear-genome
"evolution" totally unlike what we understand today;
(3) new variation that occurs during pre-DNA linear-genome, which is
only slightly similar to today's kind of evolution;
(4) finally new variation that occurs during the DNA era.
Only part 4 and maybe 3 are explained by "evolution" as we currently
understand it. That's a majority of the variation we see today, but not
100%.
> 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
.
John Harshman
>>>>That's not true. If you're talking about mitochondria, ...
>>>
>>>No, that's not what I'm talking about. I'm talking about whatever DNA
>>>codes for 30S subunit of ribosome in eukaryotes.
>>
>>There is no 30S subunit. Do you mean 28S? Or are we talking about the
>>combined 5S + 28S?
>
>
> I don't know. I got the "30S" designation out of a book, which cited
> Cell 33:318-319 (1983), but I have no access to Cell so I can't check
> whether the designation was copied wrong or was in the original.
> Google shows 156 thousand matches for 30S subunit, so could you
> possibly be mistaken in saying there's no such thing? For example:
> <http://alf1.mrc-lmb.cam.ac.uk/~ribo/30S/>
> Work in our laboratory has focused on the structure of the ribosome,
> especially the 30S ribosomal subunit. We have determined the complete
> atomic structure of the 30S subunit and its complexes with several
> antibiotics.
> <http://www.bio.cmu.edu/Courses/BiochemMols/ribosome/70S30.htm>
> The 30S subunit structure is described in Yusupov, M. M., Yusupova, G.
> Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. D., Noller,
> H. F. (2001) "Crystal structure of the ribosome at 5.5 E resolution"
> Science 292:883.
> I'm beginning to suspect you posted your "no such" remark as a prank.
I hadn't been thinking about it much. The 30S subunit is the small
subunit. That counts all the proteins and RNAs that make up the subunit.
There is no 30S ribosomal RNA, nor any single gene that codes for the
30S subunit. We are talking about rRNA and several (20-something)
proteins here. I thought you were trying to refer to a rRNA; that's
certainly what I was thinking about.
>>But OK, you're talking about the stem-ancestor of eukaryotes. It's
>>unclear whether you want to count that as a prokaryote or not. It all
>>depends on your definition of eukaryote.
>
>
> "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. Whether it had a nucleus is another question.
Whether it arose from a fusion of two genomes is another question.
> I agree that where you draw the boundaries along the path from
> prokaryotes through ur-kryotes to pre-eukaryotes to fullfledged
> eukaryotes is a matter of personal opinion. I would consider a
> eukaryote with mitochondria as fullfledged, one without mitochondria
> but which does mitosis as not fullfledged but true eukaryote,
There are living eukaryotes without mitochondria, but it's possible that
none of them is primitively so.
> 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?
> Someday we may understand the function of genes and proteins well
> enough that we can decide which changes in the genome from the top of
> the stem all the way down to true eukaryotes happened in which
> sequence, such that there's a meaningful scaffold at each stage, such
> that each significant mutation provides an advantage. At that point we
> might legitimately claim to have the full sequence along that
> evolutionary path despite lack of any surviving side branches or useful
> fossils. Then it may be possible to establish criterion for drawing the
> boundaries at totally reasonable places.
Even with all that information, what makes you think there would be any
one place more reasonable than another?
>>But never mind, I misunderstood you. You were talking about the 3 domains.
>
>
> Almost. In two cases, there's a direct unitary line of descent from
> the LCA of all three domains down to the crown LCA of each surviving
> clade. So it was a single domain all the way between those two points.
> But in the case of modern eukaryota, there were several symbioses along
> the way, merging several old domains into a single new domain, so it's
> not really the same domain from one to the other end of the primary
> line of 30S-coding descent and whatever other genes co-evolved with
> that one gene. So "the" 3 domains is ambiguous depending on whether
> we're talking about the ur-karyote domain way back then or the
> eukaryote domain more recently.
>
>
>>>Evolution as we know it doesn't explain the *original* variation among
>>>and within the first column of pp,
>>
>>Sure it does. Why not? The only thing is that the amount of horizontal
>>transfer was, hypothetically, greater then than it is now.
>
> 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?
> Whatever variation there was
> between the different very-first-replicators, each of which arose via
> an independent abiogenesis event, was not generated by evolution as we
> know it, but instead was merely an artifact of the gazillions of
> different possible abiogenesis events, combined with the fact that each
> such actual event was in a different environment hence selected from a
> different subset of all possible abiogenesis events.
I think you are looking too far back in time here. 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. And
all that would have been way before any of the horizontal exchanges we
have any evidence of.
> We already know that complicated biochemistry starts very easily in
> reducing conditions such as Miller-Urey apparatus. What we don't know
> is whether over hundreds of millions of years in a natural ocean the
> biochemistry is likely to form a replicator. If so, then it's probably
> easy to form in not just one place but many places, and not in just one
> way but gazillions of different ways. So multiple independent
> abiogenesis events in different local environents seems likely to me.
> With each of them starting as a single auto-catalytic set, there's zero
> evolution-caused variation (initially) within a single such replicator,
> so 100% of the variation is between the different such events, none of
> which is caused by evolution. Then each such abiogenesis-generated
> replicator somehow evolves to some kind of linear digital genome, and
> all of that evolution is *not* anything like the kind of evolution we
> understand today. It's only after linear digital genome has appeared
> that evolution is even remotely like what we understand today.
>
> 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?
> (2) new variation that occurs during that early non-linear-genome
> "evolution" totally unlike what we understand today;
And why would you say this?
> (3) new variation that occurs during pre-DNA linear-genome, which is
> only slightly similar to today's kind of evolution;
And why would you suppose this sequence of events?
> (4) finally new variation that occurs during the DNA era.
I think we have evidence only for part 4. But what reason is there to
believe that variation in a pre-DNA genome is not similar in character
to variation in a DNA genome?
> Only part 4 and maybe 3 are explained by "evolution" as we currently
> understand it. That's a majority of the variation we see today, but not
> 100%.
I strongly doubt that contention.
>>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"?
Bob Jenkins
http://www.discover.com/issues/mar-06/cover/
which suggests that viruses are pared-down prokaryotes, and the nucleus
of eukaryotes is an engulfed virus.
After a bit more googling and scribbling on paper, I get:
Life appears
DNA viruses branch off, they hijack cells when they're eaten
Eocytes (and the rest of archaea) branch off
photosynthetic bacteria (algaes) show up
aerobic bacteria show up
And, sometime after eocytes branch off, some amoeba-like eocytes appear
capable of gobbling up useful cells and incorporating them in their
cellular machinery (endosymbiosis). They gobble up (in no particular
order, sometimes many times) viruses (the nucleus), aerobic bacteria
(mitochondria), and algae (chloroplasts). Amoebas continue to do
similar things today.
Bob Jenkins
found. Another approach is the virus taught the archaea how to do
endosymbiosis. Since the whole point of viruses is to co-opt other
cells, that seems a little more natural. It would predict that the
nucleus came before mitochondria or chloroplasts. Here's an article
related to that:
http://guava.physics.uiuc.edu/~nigel/courses/498BIO/498BIOonline-essays/hw2/files/rroy2.pdf
an...@sci.sci
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 fuck?? 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$24...@TSOFT.COM>
! 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.
.
John Harshman
>>The 30S subunit is the small subunit.
>
>
> Yes, that's correct. So now you will stop calling me a liar when I mention it?
I never did, so am unable to stop.
[snip many lines of you talking to yourself]
>>>"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.
Not really, unless there was all that much horizontal transfer on the
branch leading to eukaryotes. If so, then the eukaryote stem-lineage
begins after the last massive transfer event.
> 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.
True even if there was indeed no such massive transfer.
>>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.
It appears that every taxon without mitochondria so far examined does
contain remnants of mitochondrial genes in the nucleus. So you may not
actually need to resolve the phylogeny to learn about some of this stuff.
>>>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.
I have no guess, because we lack data on which to make such a guess. It
is useless to speculat in advance of the facts, as Mr. Holmes was wont
to say. I was asking what basis you had, if any, for presenting the
sequence you did. And I was asking specifically about the origin of
eukaryotes.
>>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!! :-)
[snip]
>>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.
You presented an argument. I'll give you that much.
> 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.
"Fight to the death" is an overly dramatic way to put it. There is no
reason to believe that separately originating replicators would be
similar enough in basic construction to merge genomes. If they didn't
merge genomes, stochastic processes could easily be enough to eliminate
one of them over time. At any rate, my argument is not one of lack of
plausibility, but of lack of evidence, when we would expect to see
evidence if an event had happened. Perhaps we wouldn't expect to see
evidence, in which case we have no basis for discussion.
>>>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.
OK. You mean differences not due to common descent. That's not the same
as saying they weren't do to evolution. And I don't think you can easily
separate "abiogenesis events" from evolution.
>>>(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.
Ah, by "linear" you mean that the genetic material is a linear polymer.
But I think that linear polymers, whatever they were, must have been a
very early development, long preceding DNA or RNA.
[snip]
an...@sci.sci
> Life appears
Presumably a simple auto-catalytic set with no polymeric genome whatsoever?
Or dislocation patterns in clay micro-crystals?
> DNA viruses branch off,
Huh?? You skipped a shitload of transitions between the above two points.
> they hijack cells when they're eaten
Well, after you fill in that shitload of missing steps, maybe this next.
> Eocytes (and the rest of archaea) branch off
> photosynthetic bacteria (algaes) show up
What the fuck do you mean by "algaes" there? Algaes are eukaryotes,
which can't exist until there's plenty of oxygen in the atmosphere and
water. Cyanobacteria (the photosynthetic bacteria that made the oxygen
by extracting it from water) are not algae.
> aerobic bacteria show up
Nope, aerobic bacteria made most of that oxygen.
Suggesting there were eukaryotes (which need molecular O2 to breathe)
before there were aerobic photosynthetic Cyanobacteria to make the
oxygen they need is as stupid as Genesis which has day/night cycle
three days before the Sun was created to make the daylight.
You haven't given any argument or evidence to support the idea of the
nucleus being from a virus, but that's moot with your whole sequence
messed up so badly, and that *huge* gap between the first and second
step.
.
Stanley Friesen
>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.
According to the information I have here:
Bacteria: Aquificales, Planctomycetes, and Thermotogales compete for
being the deepest (I have two alternate trees that disagree on this).
Archaea: the Korarcheota first, then the Euryarchota vs Crenarcheota
split, with the Nanarcheota probably very early also.
Eukarya: The Diplomonads are the deepest, followed by the discicristates
(acrasids + euglenids + trypanosomes).
[Interesting note: the *remaining* cellular slime molds are apparently
closely related to the syncytial slime molds close to the origin of
animals].