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

anon1@xxxxxxx wrote:

>>>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.
>
>
> That's right. With no data except the character matrix or DNA
> sequences, you get an unrooted tree, but there's no way to know where
> to root it. You need some *other* kind of data to root it.

Which is what I've been saying all along, so I don't know why you made
that little demonstration.

>>>>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.
>
> OK, I'll try again, this time looking on Google to try to find the
> meaning of the jargon, instead of guessing what it means.
>
> <http://www.blackwellpublishing.com/ridley/a-z/Character.asp>
> Character polarity is the issue of the evolutionary history of a
> character: given two character states, which we call a and a' , we
> need to know whether a evolved from a' ' or the other way round.
> Discerning character polarity is a fundamental task of phylogeny.
> That begs the question. If you don't know where the tree is rooted, if
> all branches are unknown-direction, how do you magically know which way
> a trait evolved?

Yes, the best way is by looking at its evolution on a rooted tree.
Nevertheless, there are other ways used.

> <http://pw1.netcom.com/~wsavary/larvae.html>
> The outgroup comparison method for
> establishing character polarity (Maddison, Donoghue and Maddison 1984)
> clearly establishes transverse orientation as apomorhic.
> That begs the question. If you already know an outgroup, then the
> portion of interest is already rooted.

Yes, this method is not a way to establish polarity for the purpose of
rooting trees. There are of course other reasons you would want to
determine polarity.

> <http://www.sasb.org.au/TreeBuild/TreeBuilding2.html>
> Having determined the homology of the character states, the key to
> cladistic analysis is the distinction between derived character states
> and ancestral character states (character polarity). It is important
> to note that this is a local concept that applies only to a particular
> set of taxa. By this I mean that a character state is only considered
> to be derived relative to a specified ancestral state, and it may well
> be the ancestral state for a further derived state. As an example, for
> Again begging the question. You have no idea, within a portion of the
> connection (unrooted) tree, which is ancestral and which is derived
> until after already have found which direction (out which branch) the
> root is located.

You needed to read a bit further in that one: "The direct method (Weston
1988) states that:- if one character state is possessed by all of the
taxa that also possess the alternative state, and in addition it is
possessed by some taxa that don't possess the other state, then it is
postulated to be the ancestral state. For example, open gill slits are
possessed by all chordates in at least the embryonic stage, but in
tetrapod chordates these close early in development; thus, all chordates
possess open gill slits but only some possess both open gill slits
(early in development) and closed gill slits (later in development).
Consequently, possession of closed gill slits is hypothesised to be
derived relative to possession of open gill slits. This type of
argumentation can be applied to many types of characters (Nelson 1978;
Weston 1988, 1994), but it is probably of limited utility for molecular
data. However, Weston (1994) has pointed out that the direct method can
be applied to gene duplications (paralogy) to polarise the a and b
subunits of ATPase based on taxa from the archaebacteria, eubacteria and
eukaryotes, thus providing a "root" for the tree of life."

This is a form of the ontogenetic criterion. There are arguments against
it. In practice, polarity is almost always determined after the fact,
i.e. after rooting the tree by outgroup.

[snip]


> the one appearing lower in the stratigraphic record (paleontological
> criterion),
> Aha, just like I said, timestamps are useful for rooting trees!!

No, that's a criterion that has been used, but it has problems like all
the others. It's not commonly used by modern systematists, just like all
the other non-outgroup criteria are not commonly used.

> I said it directly: You use timestamps on fossils to establish
> direction among many of the branches. You said it indirectly, you use
> "character polarity" to root trees, but then I see that "character
> polarity" requires timestamps to decide which way they go.

No.

> or earlier in development (ontogenetic criterion).
> Aha, early-development-fixed late-development-fluid, which I stated
> within the past week but somebody said I was talking garbage, equated
> that idea to late-development-add-on as in the "recapitulates" lie.

Precisely. That's why this criterion is unreliable and is seldom used
either.

>>>>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.
>
> What if I use real DNA sequence data, but I don't tell you the name of
> the four species, so you can't just beg the question by already knowing
> their location in the TOL.

Like I've been saying all along, you have to bring additional information.

> Well you can cheat by looking up the DNA
> sequences in a database to find the species names, then beg the
> question. So what if I delete all base pairs which are identical in all
> four species, leaving only the SNPs, so you won't be able to simply
> search for them to find the species names? You have to work from the
> actual DNA data with no outside information? I bet with only the DNA
> data, no outside information, you can't root the tree.

That's right. As I've been saying all along. You don't listen.

>>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.
>
> That isn't going to convince an anti-evolutionist that your entire
> theory is based on circular argument. It also isn't going to correct
> you if your original suspicion is mistaken.

Systematists are not particularly concerned with convincing
anti-evolutionists. I really don't know what would convince an
anti-evolutionist. But you can in fact test your original suspicions by
bringing in more taxa. If, for example, you root the human tree by using
a chimp, you can test this by including a gorilla in a new analysis. If
humans still form a single group relative to the chimp when the tree is
rooted on a gorilla, the chimp as outgroup is confirmed. Still don't
trust that? Bring in more taxa. If you bring in all the primates and
still the humans form a single group, then either all other primates are
descendants of humans or humans are a clade. Now, you may consider both
these hypotheses equally sensible without fossil evidence. But I would not.

>>>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.
>
> For this purpose, I allow living bodies as "fossils" with zero million
> years before current as timestamp.

How would that help you at all? All the living bodies would have the
same time stamp, and you would have no way of telling which one was the
outgroup using your method.

> If you know of any species which
> went extinct and never left any evidence that it ever existed, and it's
> not simply an inferred species such as branch points on rooted trees,
> how do you know there ever was such a species? If the only fossils are
> so poor you can't tell what on Earth they might have been like, how do
> you know they aren't just pieces of some other species you already know
> about? How do you know they are an additional species not already in
> the system? How do you "do it all the time"??

All those questions make no sense. We're not talking about using fossils
at all here. Look again: you can determine the phylogeny about groups
with no fossil record. According to you this would be impossible. Yet we
do it anyway. How? Not the way you seem to think.

> As for philogeny of inferred species, that's easy. You use a few
> fossils you *do* have dated very accurately to root the tree, then you
> have the whole tree converted to a philogeny, including those other
> species that were only inferred.

Nobody is talking about inferred species, so I don't know what you mean.

>>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.
>
> How do you build that very first foundation, and be reasonably sure you
> got it right? My answer: With a few dated fossils from long ago.

You might think that's the way it should be. But that's not the way it
is. Do you understand that systematics has in fact not been done this
way? You are describing your own personal notion of how science should
have been done, but was not and is not.

> Fossils show that the fish group is not a clade unless the amphibians
> are included too, because the first fish were before the first
> amphibians, and even that's not a clade unless the reptiles are
> included too, because the first amphibians were before the first
> reptiles, and that's not a clade unless the mammals and dinosaurs are
> included too, because the first mammals and dinosaurs were both before
> the very first reptiles, and that's not a clade unless the birds are
> included too, because the first dinosaurs were before the first birds,
> but at that point you finally have a clade. Then working backwards you
> get the dinosaur+bird clade, the reptile+mammal+dinosaur+bird clade,
> and the tetrapod clade.
>
> But without dated fossils to show that fish predates the first
> amphibians, and yet lines of fish continued right in parallel with
> amphibians, hence amphibians are a sub-group within fish, how do you
> root the vertebrates? And how do you know vertebrates, without the rest
> of the chordates, are indeed a clade, without fossils of chordate
> non-vertebrates that pre-date the first vertebrates?

Considering that most of these judgments were made before we had any
such fossils, you might indeed wonder. The first fossils of chordate
non-vertebrates that I know of, for example, were found in the Burgess
Shale by Walcott, but were not recognized as chordates until much later.
Yet long before that the chordates had been recognized as a distinct
group. So were vertebrates, mammals, and so on, long before there were
fossils that might have been used to root a tree. How do you think that
was done?

> I'm to start from scratch in checking what evidence somebody accepts.
> There is no framework of evolution already. The person doesn't believe
> in evolution. The person says evolution is a joke, or a fraud, or a
> lie, or a religion, and there's no evidence that there's any evolution
> whatsoever. So without any framework a priori, how to establish the
> framework of evolution, directly from evidence, without any circular
> arguments, without any faith in evolution, etc.

If that's your goal, I'm afraid fossils will not root a tree unless you
have a touching faith in the completeness of the fossil record.

> If we try to root the tree of animals based on diversity, just as we
> presumed humans came from Africa due to largest diversity there,

You confuse two sorts of diversity. Genetic diversity within a single
species is not the same as species diversity within a clade. Nobody
would try to root a tree of animals "based on diversity".

> So what evidence, other than dated fossils, would refute that cladogram?
> (The correct root is between Porifera and the entire rest of the tree.)

Actually, the correct root apears to be within Porifera; at least there
is evidence suggesting that currently. And the tree is rooted by
outgroup; you pick a non-animal or three as outgroup. In this case, good
evidence suggests that choanoflagellates are the closest outgroup to
animals.

>>You can do this because you are not working in a vacuum.
>
> Wrong. I *am* trying to start from the very beginning, no knowledge of
> evolution whatsoever, only knowledge of the prerequisites such as
> crystal formation and isotopes and genetics (including DNA) and plate
> tectonics. What evidence is needed at the very start to show
> conclusively that evolution is a good theory to seriously consider.

In that case, you don't need to root the tree at all. An unrooted tree
is as good a bit of evidence for evolution as a rooted tree.

>>Other people have learned a few things before you. One of those
>>things is that amniotes are a clade, but fish aren't.
>
> Presuming there's even the concept of a clade, much less anything
> specific about fish vs. amniotes, already presumes the truth of
> evolution as a fact, creating a circular argument if we are to use this
> to show evidence for evolution, per the whole purpose of this thread.

You could avoid this by rephrasing, if you really want to. But you were
talking about rooting trees. If all you are trying to do is demonstrate
evolution, we don't even have to root the tree. Just the existence of a
tree is evidence of a phenomenon for which creationists have no explanation.

And your fossil criterion doesn't work, so if we believe you, then we
indeed have no evidence for evolution.

>>If they hadn't previously learned those things you would have to
>>start somewhere else.
>
> Yes, that's my purpose in this thread.
>
>>But stratigraphic data really are not helpful in doing this.
>
> What else gives clear evidence that something changed over time, that
> things now aren't the same as things long ago, not just day to day
> things like Kennedy born then assassinated, or century to century
> things like Rome built then fallen, or even Babylon founded, but really
> major things like a time when there were no humans whatsoever yet there
> was other life already, not just two or three days of animals without
> people, but hundreds of millions of years of animals without people,
> and not even remotely the same kinds of animals during various eras of
> that very long span of time?? Or ignore the absolute time span. Many
> mega-generations of different forms of animals over whatever span of
> time whether it be five years or five hundred million years,
> trilobytes, then dinosaurs, then mammouths and primates. A whole series
> of major changes in kinds of animals before the first human. Not just
> all the non-human animals and plants virtually simultaneously, then
> humans created specially apart from the rest. But all those major
> different kinds of animals in temporal succession.

There is a germ of truth in all that verbiage, but not the sort of thing
you think. We are all agreed that the Cambrian is a very different place
from the Jurassic, which is itself very different from today. And that
the biotae of one period are more similar to those of adjacent periods
than to those of distant periods. That, in a gross way, is evidence for
evolution, and rather good evidence at that.

But we were arguing about your claim that fossils, and only fossils, can
be used to root trees. None of that is true.

>>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.
>
> That assumes enough time has elapsed *within* the group of interest
> that every branch has "suffered" enough mutations to be sure of the
> branching of those copies. Indeed I agree if the two unrooted trees run
> parallel to each other, that's nice, and whichever pairs are most
> distant show them to be furthest from the root.

That's irrelevant.

> If there are two which
> are definitely closest, then the root probably is between them.

No, not true. You just don't understand what I'm saying here.

> But if
> there is one that is significantly closer than all neighbors, then it's
> not clear which branch from that one node has the root. Still it does
> narrow down the root to either one branch between two nodes or three
> branches from one node to its various neighbors. Assuming all the
> species are currently alive, and DNA is from living samples, All the
> species should be approximately the same distance from the root, so I
> would expected the unrooted tree to look something like this:
> A--------+-----+-------------+----E
> | | |
> B------/ | \--D
> \-----------C
> Assuming equal rates of evolution, the root might be just to the right
> of that central +, but we can't really be sure.

What you are describing here is just midpoint rooting. That has nothing
to do with what I'm talking about. Here, I'll draw a picture:

copy 1 tree copy 2 tree

A--------+------*--------+---A
| |
B-+-/ \--------+--------B
| |
C-----/ \-----C

You have two copies of a gene (or two related genes, whichever you want
to call it). You sequence both of the genes and it gives you 2 unrooted
trees. But put both copies into a single analysis and you get a single
tree, which you can objectively root somewhere on the branch connecting
them (*). This doesn't depend on any sort of clock or midpoint rooting,
and I have tried to show this by making the two genes not very
clocklike. Now do you get it?

[snip]

>>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.
>
> Is there *ever* a case where exactly the same segment of DNA is
> duplicated in two very different branches of life, with the copy
> landing at exactly the same new location both times, so it looks like
> the two branches are a lot closer than they really are? If so, what
> mechanism might do that?

Yes, there is. The shorter the segment, the more likely. There are
several mechanisms that might do that. Some regions are more prone to
duplication than others, and the boundaries of such regions are not
arbitrary. There may be hot spots for SINE insertions, making even those
not quite immune to homoplasy. That's why the best test of homology is
congruence of one character with another. No one character is the magic
bullet that makes a tree. You have to assemble a lot of them and compare
their mutual fits.

>>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.
>
> It's my understanding that the idea that a primitive species progresses
> to some point and stops, but an advanced species progresses to that
> same point but goes on another step, the "recaptulate" idea, what I
> understand by the term "terminal addition", is wrong.

You understand also that the definitions you had just given for
"terminal addition" were contradictory to your claimed understanding, right?

> But the idea that
> two closely related species share steps 1 thru 8 but differ at step
> number 9, and two species not quite so closely related share steps 1
> thru 7 but start to differ from 8 onward, what I call "terminal
> modification", is basically true.

I don't see the difference except that in the one case you are inferring
the adult condition in ancestors and in the second you are not.

> Feel free to correct me.

Sure. It's not true. It has enough resemblance to the truth to be
interesting, but the exceptions are too many. It is, for example,
considerably after the blastula stage that vertebrate embryos come to
resemble each other most closely. So they don't look alike at the
beginning but depart from that progressively. They look different in
early stages, come to resemble each other in the middle, and depart at
the end.

>>Phylogenetic data is data we think might be useful in reconstructing
>>phylogenies.
>
> That's not a definition at all. It's a circular piece of crap if you're
> trying to tell me which specific kinds of data you would consider
> useful for reconstructing phylogenies.

I'm not. Definitions don't have to do that. Definitions tell you how a
term is used. That's how the term is used. If you want to know
specifics, that's another matter.

[snip]

> When I ask what sort of evidence might help root an evolutionary tree,
> it doesn't help if you answer "Phylogenetic data", and when I ask you
> what you mean, you answer "anything that would help root a tree" or
> "anything that would help reconstruct a phylogeny" etc., because that's
> what I was asking in the first place.

Who knows what question I was answering? You have eliminated all context.

>>Very few phylogenetic analyses make any a priori claims to know
>>what's primitive or derived. These are instead conclusions gained from
>>the trees.
>
> But you have only unrooted trees until *after* you have decided where
> the root lies. It's a circular argument to use an already rooted tree
> to decide what's primitive and use that to decide how to root the tree.

And indeed this is not done. Like I said, trees are rooted by outgroup.

>>>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.
>
> If a duplication event occurs, the two copies will be nearly identical.
> After a period of evolution, they won't be the so similar any more. If
> then one of them is deleted, the two that existed just before the
> deletion won't be very similar at all. It's very easy to see the arrow
> of time in an unrooted DNA-segment tree like this (horizontal
> represents DNA base differences, vertical represents chain of
> time-related species):
> *
> *
> * *
> * *
> * *
> #
> *
> (# represents two nearly identical sequences, i.e. ** on single grid point)
> Can you see the arrow of time in that diagram? Does time go up or down?

The problem with this is that you don't have that information. You don't
have the ancestral gene, and you don't have any deleted copies. All you
have is whatever exists in the extant organisms. In light of this, none
of what you say above makes any sense. Try again, just looking at it
from the perspective of available data: species A and B have two copies
of a gene, while C and D have only one copy. With that information, can
you root the tree?

>>There are however some DNA characters that are close to being
>>self-polarizing. Look up SINE insertions, for example.
>
> Looked it up just now, some kind of spontaneous multiple repeats, can't
> figure out what's the difference between these and "tandem repeats".

No, SINEs are not multiple repeats in that sense. They are usually
inserted one at a time, though they can be inserted at many different
places in the genome, so in that sense they are multiple. The idea is
that the point of insertion is random, and that deletions are very
unlikely to exactly match insertions. So if you find a sequence in
multiple species that doesn't have a SINE inserted, and more species
with the SINE inserted at exactly the same spot, the insertion is
homologous and polarizes the tree: the species with the insertion are
more closely related to each other than to any species without the
insertion.

.