Re: Part 1 (of 3): What are major aspects of evolutionary theory?

> > OK, here's an unrooted cladogram, where branch lengths are
> > proportional to count of DNA base differences:
> > Portlandphyta Renophyta
> > | |
> > Salemphyta---+-------+----------------------+---+-Vegasphyta
> > | |
> > Chicagophyta---+----------Bostonphyta Hendersonphyta
> > Now without any timestamped nodes, and suspecting that different
> > branches evolve at different rates so you can't use branch length to
> > assign time durations, where do you place the root?
> No idea. But we don't work in a vacuum like this. There are many ways of
> rooting trees, and I will mention some of them: 1) by outgroup;

Which of the taxa in the above tree is the outgroup? How would anyone know?
Picking one at random seems to be a circular argument.

> 2) by midpoint (bad idea if the evolutionary rates are as different
> as you suggest here);

Agreed, bad idea, delete that method from the list.

> 3) by presumed character polarity, including ontogenetic criteria;

All species are equally well adapted to the modern environment. None of
them seem to be "primitive" in the sense of having major lack of
development of adaptive features compared to the others.

> 4) by assuming monophyly of two divisions of the tree

That seems to be a circular argument.

> -- that one needs explanation, so here's an example: if you are
> looking at a sample of galliforms and anseriforms, you can assume that
> each of these is a clade and that the root lies between them.

So just because there's a name for two parts of the unrooted tree, you
assume each is a clade separate from the other? Circular argument!
How do you decide which of the subsets of nodes in the unrooted tree
deserve a name hence presumably each define a clade?

> True. There is no way to root a naked tree with no additional
> information, except midpoint rooting, which assumes a clock. So? When do
> we ever lack all additional information?

When you use DNA evidence and/or character comparisons, without a
single reference to any dated fossil.

> The usual method is to ignore it when constructing and rooting the
> tree, which is commonly rooted by outgroup.

Which begs the question: How do you know which is truly the outgroup
relative to the rest? For example, suppose we consider a whale, a
termite, a human, a pigeon, and a kangaroo. Obviously the whale is the
outgroup, because it's ocean-dwelling, right? Or is the human the
outgroup because it's not really an animal, right? You and I know it's
the termite that is the outgroup, but how do we convince somebody of
that alleged fact based only on DNA and characters?

> > What other term would you propose me to use when I really mean
> > Intelligent Design (not tinkering)?
> Didn't I just suggest "separate creation", in the sentence immediately
> preceding your question?

"separate creation" is too ambiguous, and somewhat orthogonal to the
issue of intelligent design. If there was no intelligence whatsoever,
just magic, whereby each species was created to fill its role in
nature, no thought process, no design process, that would be "separate
creation" but not "intelligent design". If somebody carefully thought
out what species was needed, designed it, and designed a factory for
making individuals of such species, and built the factory, then pressed
the ON button and let it make ten thousand invididuals, then pressed
the OFF button, that might be separate creation of each factory but not
any kind of creation of the members of the species. If some
supernatural being created the Big Bang and then just let it run
naturally from then on, and on one obscure planet abiogenesis happened,
then evoluton happened, that'd be special creation of the Universe, but
not separate creation of more than one Universe, and not any kind of
creation of any life whatsoever, and it may or may not be intelligent
design of the Universe. When you make the lamebrained suggestion that
"separate creation" means the same thing as "intelligent design", am I
required to explicitly rebut it immediately? Can't I just ignore such
really stupid suggestions?

> > I'm not aware that the IDiots have
> > ever stated their definitions clearly.
> Yes. They are vague on purpose to promote their "big tent" strategy.

I think we need to drive a wedge between them. Here's an idea:
We build a fake religion or research organization, something that
postulates some belief very close to what one of the IDiots believes.
For example, in the case of Behe we might postulate that there's a
supernatural being whose name is "God" who designed each species
individually and then placed them on the Earth at various times, and
then when he was done with any species he released a deadly virus that
wiped them all out without affecting any other species. Then solicit
Behe to join that religion or other organization. Once he joins,
solicit others to join it too. If they resist, mention how Behe has
already joined it. If they still refuse, we have a wedge between those
who joined and those who resist joining. With a whole series of such
religions etc., each joined by only a few of the IDiots, we now have
them all separated.

Now suppose Behe resists because we didn't guess his belief closely
enough. So we then fudge our premise closer to his, until finally he
agrees with our premise and is ready to join.

> If, for example, you had a tree of all the amniotes, all you would
> need to root it is some non-amniote. And this requires onlyh the
> assumption that amniotes are monophyletic.

Do you understand how you're begging the question here? How do you
decide that your term "amniote" is a valid clade name, but the term
"fish" as used in the Bible is not, that whale-fish and tuna-fish are
totally separate from each other, separated by amphibians and reptiles
and mammals? Or how do you decide that the distinction between "man"
and "animal" as given in the Bible isn't the correct place to root the
tree (man one clade, animal the other clade, root between them)?

> rooting on a gene duplication

OK, now you actually have something. When you see two nearly identical
copies of a segment of DNA, the only reasonable hypothesis is that
there was originally one which got duplicated. So then if you have DNA
genomes sequenced for several different species, and you observe some
of them have just one copy while the rest have two copies, and those
two subsets of terminal nodes are situated within disjoint sub-trees,
then you can presume the sub-tree containing the duplication is a
single clade, so the root lies either between the two sub-trees or
somewhere within the non-duplicated sub-tree. Right? But what if the
exact same duplication seems to have happened in two different
sub-trees? What would you conclude from that situation?

Has anybody actually run a computer program that searches the entire
human genome (3.1 billion base-pairs) to find reasonable-sized
sequences that appear to be duplicates of each other, modulo reversal
of direction and complementary bases? If so, is there a Web page that
reports the statistics of such apparent duplications? Same question for
each of the other appx. 20 fully sequenced genomes to date?

> > just as we root human origins in Africa due to greater diversity there.
> Actually, an outgroup root is commonly used here too.

And again, how do we decide that some outgroup is such? If it's too far
from human genome, we can't make comparisons because we can't align
most of the genome, but if we pick something close to human such as
chimpanzee then how do we know for sure (without any fossils) that
chimpanzees aren't just a degenerate form within the overall clade of
humans? In fact given the greater diversity of genome in chimps
compared to humans, how do we know humans aren't a single clade within
chimps?

> I'm saying that we have several methods of rooting trees, of which
> outgroup rooting is by far the most common, and that this makes no use
> of stratigraphy.

And I'm saying that until you say how to decide among various taxa
which is the outgroup, you're begging the question.

> I root trees all the time. I root them using outgroups. What's the
> problem?

Do you just take it on faith that species number 47 is the outgroup and
species 1..46 and 48..307 are a single clade not containing 47?
My guess is you take it on authority. Somebody made the claim that
species 47 was a non-whatever and all the rest are whatever, and that
whatever is a valid clade taxon, and you just accepted that authority.
You never bothered to check for yourself whether whatever was in fact a
clade not including the species you're using as an outgroup.

> > So most early variation
> > already happened pre-Cambrian and won't ever happen again. Most
> > variation since then, i.e. within any single phylum, is either
> > late-development or biochemical pathways that don't affect develoment.
> That's an argument suggesting a mechanism for terminal addition. Since
> terminal addition is not a correct model, it's irrelevant.

No, not terminal addition, merely near-terminal amendment.
I did a Google search for that term just now, and came up with:
<http://www.sicb.org/meetings/2005/schedule/abstractdetails.php3?id=725>
<http://www.sicb.org/meetings/2005/schedule/abstractdetails.php3?id=27>
<http://gsa.confex.com/gsa/2005AM/finalprogram/abstract_97708.htm>
We argue that terminal addition, the process of addition of serial
elements in a posterior subterminal growth zone during animal
development, was the basal condition in Bilateria, and that
modification of terminal addition was an important component of the
rapid Cambrian evolution of novel bilaterian morphology.
where the phrase means neither what I claim nor what you seem to be
accusing me of claiming, but something quite unrelated in concept.

And many other places, including here:
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=4330056&dopt=Abstract>
it means something even more totally unrelated, adding molecular end-chain.

This Google search result:
Blackwell Synergy: Evol Dev, Vol 7, Issue 6, pp. 497-497: The end ...
This phenomenon is referred to as terminal addition (which should not
be confused
... Segmentation often renders terminal addition morphologically
explicit, ...
www.blackwell-synergy.com/ doi/abs/10.1111/j.1525-142X.2005.05054.x -
looked like it might clarify two usages of the term, but when I clicked
on the link
<http://www.blackwell-synergy.com/doi/abs/10.1111/j.1525-142X.2005.05054.x>
it gave me something entirely different that does not contain any of
the words "phenomenon" or "confused" or "Segmentation" or
"morphologically", so Google is not my friend here! Google search for:
Blackwell Synergy phenomenon terminal addition confused Segmentation morphologically
Blackwell Synergy phenomenon terminal addition Segmentation morphologically
turns up that bogus match as the very first result.

> Do you agree that a single, consistent, nested hierarchy results from
> analysis of disparate sets of phylogenetic data?

Just to protect myself from a trick question, I checked Google for
definition of the word "phylogenetic". Here's what I got:
* Pertaining to the evolutionary history of a particular group of
organisms.
www.edu.gov.nf.ca/curriculum/teched/resources/glos-biodiversity.ht
ml
* Pertaining to the evolutionary history of a group or lineage, or
the evolutionary relationships within and between taxonomic
levels; the relationships of groups of organisms as reflected by
their evolutionary history.
biology.usgs.gov/s+t/SNT/noframe/zy198.htm
* Concerning the relationships of evolutionary development
silicasecchidisk.conncoll.edu/LucidKeys/Carolina_Key/html/Glossary
.html
* based on natural evolutionary relationship.
www.umass.edu/biocomplexity/gloss.htm
* (Phylogeny) = pertaining to evolutionary history.
science.kennesaw.edu/~rmatson/Biol%203380/3380terms.html
* Based on common evolutionary descent (recency of common ancestry).
Now the preferred method because it has predictive value. Based on
shared derived characteristics. Phylogeny = the evolutionary
history of a group of organisms. Modern phylogenetic
investigations are based on molecular data, primarily nucleotide
sequences. Basically, the more closely related two organisms are,
the more nucleotide sequences (genes) they will have in common.
www.ualr.edu/~botany/systnotes.html
* of or relating to the evolutionary development of organisms;
"phylogenetic development"
wordnet.princeton.edu/perl/webwn

Well sure, if somebody tells you an evolutionary history, then of
course you can deduce a nested hierarchy from that. So if God tells you
the evolutionary history, you can construct a nested hierarchy from it.

But that's not the way scientists construct a nested hierarchy,
and that's not what we've been debating here.

It isn't phylogenetic data we use to construct a nested hierarchy, it's
phenotypical characters (of lifeforms either alive today or recently
deceased or found as fossils) and/or DNA sequences (of all but totally
mineralized remains) we use as input data. Even then we get multiple
solutions depending on which characaters or sequences we presume are
primitive vs. derived. DNA duplication events seem to be one way to
establish an arrow-of-time within unrooted trees to thereby narrow down
where the root really was. I claim (and you dismiss) that dated fossils
can also help narrow down where the root was, for example if a
particular character first appeared in the fossil record at a
particular time and appeared many times after that, and in fact where
that character appears in the unrooted tree is almost precisely a
single sub-tree, then we can conclude that new character is derived,
and that sub-tree is in fact a clade, and the root lies outside that
sub-tree.
..

.

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