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

anon1@xxxxxxx wrote:

>>>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.

Nobody would know because you made them up.

>>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.

This is not what character polarity or ontogenetic criteria mean.

>>4) by assuming monophyly of two divisions of the tree
>
>
> That seems to be a circular argument.

Only if you have nothing at all to go on, as, for example, if you had
arbitrarily made up a tree with fake taxa.

>>-- 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?

You don't start in a vacuum here, as you do with your made-up tree. We
do know something, or at least suspect something, about relationships
before going in.

>>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.

You understand that this means we can't ever reconstruct the phylogeny
of any group without a fossil record, or with one that's poor enough
that there might as well be none? And yet we do that all the time.
Perhaps there is something wrong with your reasoning. Perhaps all
systematists are not idiots, and what they actually do is not invalid.
Is any of that possible?

>>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?

That depends on who that somebody is, and whether they are reasonable or
not. Creationists (and, apparently, you) will never be convinced. And
yet systematists manage to convince both themselves and other
scientists. At bottom, it's a process of slowly assembling a foundation,
testing that foundation with new data, and using that foundation as a
basis for more hypotheses. We do know some groups, and know that other
taxa are outside those groups. That's all the start you need.

>>>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".

I don't think so. I think the word "creation" implies intelligence and
volition. And your preferred term is not evocative, and has the
disadvantage of having an existing, common meaning that differs
considerably from the one you want to give it.

> 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 never said anything of the sort. I said that separate creation means
what you (and nobody else) want intelligent design to mean. And you can
ignore my suggestion if you want to be really annoying, but not otherwise.

[snip]

>>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)?

You can do this because you are not working in a vacuum. Other people
have learned a few things before you. One of those things is that
amniotes are a clade, but fish aren't. If they hadn't previously learned
those things you would have to start somewhere else. But stratigraphic
data really are not helpful in doing this.

>>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?

No, you misunderstand. If you have a gene duplication that happened
before the time of origin of the group you are looking at, they will all
have two copies. These two copies will make two trees (which should be
identical), and the trees will be joined at some branch. That branch is
where the root must lie.

As for the same duplication happening twice, that's homoplasy, and it's
something we have to worry about with all data of any sort.

> 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?

Yes. It's on the UCSC genome browser, but it's not all that easy to read.

>>>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?

We make that assumption. One reason for that assumption is that when we
get a tree of all primates, human and chimp go together. Unless the root
just happens to be on the human branch, in which case all other
primates are degenerate humans, chimps are the closest outgroup to
humans. Again, we are not working in a total vacuum here, and
stratigraphic data just wouldn't solve that problem even if we were.

> 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?

Many reasons. Outgroup rooting of humans and chimps. Molecular clock
(which is good enough for this purpose at least). And all manner of
morphological data.

>>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.

Agreed. Fortunatly, we have ways to do that.

>>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?

No.

> 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.

You have a penchant for accusing people of being idiots. There are in
fact ways to test this, particularly by including additional outgroups.
But yes, I do rely on the notion that not everyone who preceded me was
an idiot too.

>>>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.

Wrong meaning of terminal addition for our purposes. Irrelevant. The
meaning relevant to Haeckel is the idea that new morphological features
are added to the end of an ontogenetic series, i.e. late in development.
Temporally terminal, not anatomically terminal. That's the necessary
condition for recapitulation to work.

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

> 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's certainly odd that you are able to tell me that I'm misusing terms
that I use every day in talking to other scientists. Phylogenetic data
is data we think might be useful in reconstructing phylogenies.

> 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.

And that's what phylogenetic data are. Really, this is common usage in
the field. Perhaps it's wrong; perhaps systematists are all idiots and
only you know the right way to communicate in the field.

> Even then we get multiple
> solutions depending on which characaters or sequences we presume are
> primitive vs. derived.

You are incorrect. Very few phylogenetic analyses make any a priori
claims to know what's primitive or derived. These are instead
conclusions gained from the trees.

> 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.

Not that reliable, at least in the way you have stated it, because
duplicates can be lost as well as gained. There are however some DNA
characters that are close to being self-polarizing. Look up SINE
insertions, for example.

> 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.

Yes, I dismiss it because, first, nobody does it that way (which should
be a clue for you), and, second, the reason nobody does it is that it's
very unreliable -- it depends on the perfection, or close enough to
perfection, of the fossil record, and we know that just isn't true.

.