Re: Part 1 (of 3): What are major aspects of evolutionary theory?
- From: anon1@xxxxxxx
- Date: Sun, 1 Jan 2006 20:20:06 -0800
> I'm not talking in circles.
I ask you how to root the tree, you answer by using directed links.
I ask you how to decide which direction a link goes, you answer by
using the already-rooted tree.
I say that is talking in circles, you say it isn't.
> Perhaps I have not explained well enough.
In a few areas you have explained well, but your median is crappy.
> But you have no reason to be smug in your belief that all the
> scientists do everything wrong.
I have no such belief. I merely claim that the way scientists refine
their models of evolution, after already being 100% convinced the
prevailing theory of evolution is true, is no good at all for the task
of how to provide a concise summary of evidence for evolution.
> > In theory, it's impossible for a duplication to occur unless
> > some form of living thing existed prior to the duplication. So it is
> > *always* presumed that the true tree of life includes both the parallel
> > post-dup branches and the single set of pre-dup branches.
> No, it's not presumed. It never has to be presumed because it's
> irrelevant. Why bring it up at al
> (Yes, it's true that such branches exist or must at one time have
> existed. So what?)
So you claim it's true but all the professional scientists deny it?
You seem to be agreeing with me, while disliking how I worded it.
So how would you express the view that professional scientists take
toward the model that life must have existed before the duplication?
If somebody were to ask them whether they accept it as true, how would
they answer?? Would they refuse to take a stand on the issue because
it's not their job to express such an opinion?
> >>Classical systematists formed lots of groups based on distinctness.
> >>Some of them are monophyletic and some are paraphyletic.
> > Which puts us at square zero with no reliable data, at that point, as
> > to which of those are true clades (monophyletic) and which aren't.
> No, it doesn't.
How, in your opinion, does a mix of guesses, some true and some untrue,
with no way to distinguish the true from the untrue, give us any valid
starting point?
> But if it did, then we would have no way of rooting a tree and you,
> by your own logic, should be a creationist.
With nothing whatsoever to go on, except a bunch of ancient opinions
half of which are wrong, indeed there'd be no way to favor evolution
over creationism. Whenever I suggest some way to show evolution really
did happen, you say no that evidence is invalid, and the only thing you
have to replace it is circular arguments (use already-rooted tree to
establish direction along a link and use that to root the tree), so per
your criterion we have no evidence for evolution whatsoever.
> If so, then everything we know about phylogeny is built on sand.
No, everything we might have guessed about phylogeny prior to the first
fossil datings was built on sand. Now we have fossil datings, which
gives some starting point for phylogeny, but you deny that fossil
datings are of any value.
> For all we know, the root of the tree lies between Homo sapiens and
> all other species, or even within Homo sapiens. Hey, why not?
Fossil datings refute that hypothesis.
> Most groups are not in question, and nobody is looking.
Per the purpose of this thread, you're completely wrong here.
*every* philogeny is in question until we establish what evidence shows
any evolution happened at all.
You've proposed the argument that mere unrooted-tree distribution of
genotypes and/or characters is evidence for evolution. I showed a
washout model where unrooted trees don't correspond to any sense of
different times at different nodes. You didn't give any reason to
reject my model, so my model stands as a refutation to your claim that
every unrooted tree implies it has a root representing flow of time
from that point forward.
> I, however, am willing to believe that if all protists fall into one
> group on an unrooted tree, and all metazoans fall into another, that
> this means metazoans are monophyletic.
Given an unrooted tree Protist--Metazoa, there are several possible
interpretations:
- Root within protist, evolved over time to make metazoa.
- Root within metazoa, evolved over time to make protist.
- Root exactly between metazoa and protist.
- There's no root because there's no such thing as evolution.
I'm looking for evidence against that last one. Do you know any?
> You aren't willing to make that choice, which means that for you,
> Mammals are not a clade.
That's not correct. Fossils of mammals don't exist prior to about 150
million years ago. Other parts of the unrooted tree existed as long as
500 million years ago. Therefore the root, the UCA, if any, can't be
within the mammals.
> we may have some clue as to which character states are likely to be
> derived, because we know something about evolution.
For the purpose of this thread, showing evolution isn't just a joke, it
really happened, that's not a valid argument.
> If, for example, we suppose that life becan in the water, for which
> there seem reasonable arguments (even absent fossils, again),
Without a single fossil, what evidence are you claiming?
(Philosophical arguments not based on evidence are not allowed here.)
> then there is a presumption that terrestrial groups are monophyletic;
I am quite sure that terrestrial groups are *not* monophyletic.
First of all, at least two different oceanic groups evolved toward
living above the water line, so even at that point terrestrial groups
are two different clades.
Second, within at least one of those clades that got onto land, several
sub-clades have returned to water more recently, so the clade isn't
fully terrestrial nowadays, i.e. the terrestrial subset isn't a clade
at all, it's only part of a clade.
I think you mis-worded something so badly as to turn some idea into a
misspeak.
> thus the root of life cannot lie in the midst of any terrestrial
> group.
Truthful conclusion, flaky argument getting there.
> it's reasonable that multicellularity is not primitive for life.
Agreed, and irrelevant.
Consider this farfetched but possible scenerio, if fossil evidence ignored:
Simple replicator -> complex replicator -> simple pre-cells -> true
cells -> multi-cellular -> some clades revert to single cells.
Now suppose the first four stages have all gone extinct, replaced by
the next-to-last stage, then later evolution produced that last stage,
and only those last two stages are observed today, with LCA of all
extant life multi-cellular.
> Second, we may propose that too great a departure from a molecular
> clock is unlikely, so that if we are required to accept evolution
> proceeding thousands of times faster in some mammals than in others, we
> might perhaps reject roots that do so.
If we allow the genetic clock to vary by a factor of a thousand, but no
further than that, we may be able to eliminate root within mammals, but
the root could still be within other metazoa, such as sponges.
Farfetched mechanism to support the farfetched sponge-root hypothesis:
At one time sponges were the most advanced life, and several clades of
them were photosynthetic due to chloroplasts in their cells. Plants
handn't yet evolved, so there was no competion in that capability. The
Solar System was passing through a thick cloud that obscured sunlight
for years at a time, and allowed only dim light when thin parts of the
cloud happened to be between Earth and Sun. This gave advantage to
sponges, which could act as scavengers for all the bits of dying flesh
broken off all other forms of life (such as algae) during dark times,
just barely hanging on while nearly everything else died off, while
experiencing a growth spurt whenever light returned. Over time, sponges
totally dominated life on Earth, eventually driving all single-celled
life to extinction due to direct competition for scavenging during a
long cosmic-clump "meteor" shower which shattered anything except a
well built sponge, filling the ocean with abundent organic debris.
After the cloud finally passed, and the "meteor" showers ceased, life
began to diversify, with some planktonic larval stages of sponge
evolving to live independently in new habitats that became nice places
again. Mitochondria at that time hadn't yet lost their genes to the
nucleus, so they were capable of living independently if the
environment were suitable, if they could somehow escape their prison
inside eukaryotes. Indeed all it took was one chance lysis of one
eukaryotic cell to release one mitochondrion in just the right place
(among gazillions of similar releases under less favorable conditions)
to start the new prokaryotic branch of life. So now there was great
diversification of the three main branches of life: Continued metazoans
(from sponges), protists (from mutated larval sponges), and prokaryotes
(from that escaped mitochondrion). Eventually algae evolved to plants,
and we have the kind of life system we know today. Without any fossil
datings, how can you refute that?
> > That seems to be an argument for my position of discarding the
> > traditional taxonomy completely and starting from scratch using
> > inherent character polarity (SINEs DUPs etc.) to establish portions of
> > the tree as true clades and leave the root as unknown location within
> > the remaining part of the tree.
> If you want to do that, feel free. Do you really believe that?
Yes. I believe we don't yet know precisely where the root was, or even
whether there was a single root, although we have it (or them) narrowed
down quite a bit. But I haven't yet seen the solid evidence to support
all those narrowings, and you haven't helped much, so at this point I
can't show anti-evolution folks anything to convince them my belief is
better than theirs.
> Have I converted you into an evolutionary agnostic?
Huh?? I'm strongly in favor of evolution. I'm just root-agnostic.
> Hundreds of sequences exist for many genes.
I'm not sure what you mean by that sentence.
Do you mean:
- There are many genes, such that for each such gene hundreds of
sequences (i.e. homologous for that gene in hundreds of species) exist?
- There are hundreds of sequences, distributed among many genes,
perhaps only one or two different species per gene, for example 50
different genes, which is "many genes", each sequenced in 6 different
species, would yield 300 total sequences which is "hundreds of
sequences"?
> Is it sensible that life began with Metazoa, and that all other
> groups have emerged from within it?
No, but it's sensible tht life began with something other than Metazoa,
evolved to Metazoa, then degraded to Protozoa along some branches, just
as parasites have evolved degraded from fully-functional lifeforms.
Evolution isn't a one-way climb up the latter of complexity. It must
have originally started very simple, and then evolved to become more
complex, but there's no rule it can't evolve "backwards" to greater
simplicity, not following the same path in reverse, but nevertheless
following some other path that takes complexity back down many notches.
I bet that among the tens of millions of different species today,
there's at least one where an obligate symbiont is "just barely"
obligate, where it it tried to live outside its host it'd die, not
because it can't perform basic life functions, but simply because life
is too harsh outside the host, just as a baby kangaroo can survive just
fine outside mama's pouch, but it's just too dangerous there, so all
kangaroos at that age stay in the pouch for a few more months. When we
find such a species, I bet in the lab we can extract the symbiont and
raise it in a suitable media where it can survive and replicate
indefinitely, and then by varying the conditions we can force it to
evolve to become robust enough that it could survive out in the real
world. The very earliest mitochondria were like that, and if some
global catastrophe had happened just then to make it better for some
mitochondria to live outside the host, that could have happened.
> guesses at the polarities of many characters, ..., multicellularity
> terrestriality, wings, etc. Even if these have been lost from time to
> time (and they all have) or acquired independently from time to time
> (and some of them have), they can still be used to root portions of the
> tree of life.
Sure, all those sound reasonble, just as the pig bulding a house out of
straw seemed reasonable, until the big bad woof showed it to be a
mistake. Yeah, that's just a fictional story for children, but it has a
good moral point. Just because something seems reasonable at the time,
doesn't show it's actually correct. I want to present a checklist of
evidence and progressive logic to show evolution is very strongly
supported, not just that it seems reasonble as a guess. If I want to
establish a particular tree of life, which *really* happened, we are
very sure of that particular tree, and then as a side remark "obviously
evolution happened, not only did it happen but it happened in that
particular way I demonstrated", then I need solid evidence, not guesses
that seem as reasonable to us as a straw house seemed to the mythical pig.
> > Does the unrooted tree have all protists in one
> > branch and all metazoa in another branch, with a single link between
> > those two pseudo-clades, i.e. P--M in short form?
> Yes.
Good, then we have four choices (root in P, root in M, root between P
and M, no such thing as evolution in the first place so no root at
all). Do you have any evidence to eliminate that fourth choice? Do you
have any solid evidence to eliminate the second and third choices too?
> > Are you saying that among those few which *have* already been
> > sequencing, they fit into the simple P--M model, and you're predicting
> > the 90% not yet sampled will likewise fit that same model?
> I'm predicting that most of them will. There may be somewhere, somehow,
> and unknown "protist" that is really a degenerate metazoan, but even if
> there is, I don't see the problem.
In that case we'd have to re-define the word "Protist" not to mean any
single-celled eukaryote, or abandon the word totally, neither of which
is a problem in my opinion. If we invent new taxa (names) only for
firmly established clades, not any more "type names" as with the old
system, such as "Pisces" which is known very well not to be a clade,
I'll be satisfied.
> Given the data we have, relationships among the taxa we know about
> are clear in this case. Likewise, tetrapods are still monophyletic even
> if we know about snakes.
It depends on your definition of "tetrapod" of course. Actually I'll
use the technical name "Tetrapoda" instead.
<http://tolweb.org/notes/?note_id=471>
There is currently a debate concerning the definition of the taxon
Tetrapoda, which is part of a wider debate dealing with the definiton
of phylogenetic groups. ...
then it goes on to propose two cladistic definitions, the crown group
(smallest clade containing currently-living Amphibia and Amniota),
which is the least-inclusive reasonble definition, and the stem-based
definition (largest clade containing that crown group but not
containing sister groups such as lungfishes or coelacanths) which is
the most-inclusive reasonable definition. Then it goes on to show
problems with either definition, namely the least-inclusive definition
excludes many clear cases of land tetrapods with all the modern
characteristics definining such, whereas the most-inclusive definition
includes many clear cases of animals that are in no sense really
four-legged land animals.
IMO, the taxon "Tetrapoda" should be abandoned, just as "Aves" is being
abandoned, for a similar reason, replaced by new terms for each of the
crown group and the stem group.
Science -- Shubin et al. 304 (5667): 90
Consequently, we are unable to discern whether the new humerus is
referable to
Hynerpeton, Densignathus, or a third tetrapod taxon. ...
www.sciencemag.org/cgi/content/full/304/5667/90 - Similar pages
Hmm, looks interesting, but when I click on it:
YOU DO NOT HAVE ACCESS TO THIS ITEM:
The Early Evolution of the Tetrapod Humerus
Shubin et al.
Science 2 April 2004: 90-93
DOI: 10.1126/science.1094295
View Free Abstract
Need Help?
* Regain access to a Pay-per-view article >
* Can't get past this page? >
* Why don't I have access? >
But the abstract says merely that primitive fins were used for propping
up the body, before they evolved into separate lineages as different
kinds of legs. It says nothing about a "third taxon" of tetrapods.
<http://www.uky.edu/KGS/education/Devonian.htm>
Recent Findings Fishes with Legs, Devonian Times. Good summary of the
fossil evidence for the evolution of fish to amphibians. A table is
provided that includes the names of the known "transitional" tetrapods
(four-legged animals) with links to summaries and Web sites for those
animals. ...
Would you dismiss that evidence as you generally dismiss all fossil evidence?
The Fish That Was Not a Fish, Discover. A news report on the finding
of an apparent tetrapod fossil, Pederpes, which is older than
Acanthostega and Icthyostega, its two more famous cousins. More
information about this intriguing fossil and its relation to other
Devonian tetrapods can be found at the Evolution of Tetrapods and the
Closing of Romer's Gap.
-> <http://hometown.aol.com/darwinpage/tetrapods.htm>
... A good series of
specimens permit scientists to distinguish between ancestral and
derived characters, ...
That sounds like the kind of evidence you always dismiss as unreliable.
Hmm, of more general interest about methodology:
<http://www.pnas.org/cgi/content/full/98/19/10751>
A major issue in all data collection for molecular phylogenetics is
taxon sampling, which refers to the use of data from only^ a small
representative set of species for inferring higher-level^ evolutionary
history. Insufficient taxon sampling is often cited^ as a significant
source of error in phylogenetic studies, and^ consequently,
acquisition of large data sets is advocated. To^ test this assertion,
we have conducted computer simulation studies^ by using natural
collections of evolutionary parameters --- rates^ of evolution,
species sampling, and gene lengths --- determined from^ data available
in genomic databases. A comparison of the true^ tree with trees
constructed by using taxa subsamples and trees^ constructed by using
all taxa shows that the amount of phylogenetic^ error per internal
branch is similar; a result that holds true^ for the neighbor-joining,
minimum evolution, maximum parsimony,^ and maximum likelihood methods.
Furthermore, our results show^ that even though trees inferred by
using progressively larger^ taxa subsamples of a real data set become
increasingly similar^ to trees inferred by using the full sample, all
inferred trees^ are equidistant from the true tree in terms of
phylogenetic error^ per internal branch. Our results suggest that
longer sequences,^ rather than extensive sampling, will better improve
the accuracy^ of phylogenetic^ inference.
Any comment, honorable expert in the field?
> > If we restrict the data going into construction of our unrooted tree to
> > *neutral* sequences only, then I'd buy the clock hypothesis as a
> > reasonable way to calculate the odds. Unfortunately, prior to
> > whole-genone sequencing, most of the known sequences were genes that
> > code for polypeptides which have important biological functions,
> > correct?
> No. Certainly they are represented in a highere proportion than their
> proportion in the genome, but I wouldn't say "most".
Oh, so if I were to reject all cladograms based on expressed characters
that are probably selected, and insist only presumed-neutral DNA be
used, so that the contamination from selected sequences be reduced to
just that small part which is believed neutral because it isn't known
to code for anything but which unbeknownst to us actually is selected,
such restriction wouldn't throw out a majority of the data, so it would
be sufficient to generate meaningful cladograms? Has such an attempt
been made, any that you know of?
(Breaking reply here, will reply to rest of your article later...)
..
.
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