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Re: Was: Wukongopterus and Darwinopterus, now phylogenetics etc.

 For the moment you have complete knowledge of every living thing. You
 snap your fingers and POW the tree of life is assembled. That's the
 "right tree." Oops, there's a new taxon that just came to light,
 let's see it goes right here... voila. No change to the tree. In
 fact, that new taxon fills a gap left over from earlier. That's what
 I'm talking about.

That's intuitively obvious. And yet, it's wrong. That's because parsimony cannot guarantee correct results from incomplete data. It's not immune to things like long-branch attraction, for one.

(In fact, it can't even guarantee correct results from complete data. That's why it's called "parsimony" and not "proof". But I digress.)

>> Getting closer and closer to the The Truth should be the push.
>> That's not how science works.
> First of all, suppose you discover the truth. How can you figure
> out that what you've found is in fact the truth? By comparing it to
> the truth, which you don't have?
> Science is not a quest for truth, it's a quest for falsehood. It
> tries to eliminate all possibilities that are impossible, and then
> all those that are too improbable (unparsimonious); but there are
> just too many of those (including lots that nobody has ever thought
> of) for this approach by elimination to lead to a single answer
> with full certainty.

 Funny. I wish I could tell you all the people who did NOT first spy
 the moons of Jupiter, but what does that matter?

Tsk, tsk, tsk. The existence of those moons is a fact, not an overarching hypothesis or theory. Discovering a fact isn't science on its own; explaining the fact is science.

 I think you would be very entertaining company. We should room together at
 some upcoming convention.

I think you would be very exhausting company, because I'd have to teach you a lot of literature that you don't even know exists...

>> This complexity you're suggesting is another facet of fractals.
>> Avoid it or delve into madness.
> You can't avoid it if you don't want to get a hopelessly wrong
> answer. It's like thermodynamics: you can't win, you can't break
> even, and you can't quit the game. :-)

 Excellent. That's why I have studiously avoided philosophy and
 quantum mechanics. Let someone else invent warp drive.

I don't quite see where you're going with this.

>> All we're looking for are simple models for complex processes
>> taking millions of years and just as many generations.
> "Things should be made as simple as possible, but not any simpler."
>  -- Albert Einstein
> You advocate making them simpler than possible. Inevitably you get
> wrong answers. :-|

 Again with the unfounded insults! David, if you're going to tell me I
 get wrong answers, you have to point out which are wrong (and by
 inference, the rest will be right!)  Simpler than possible? Isn't
 that, by definition, "impossible"?

I mean it in the sense of "simpler than {as simple as you can possibly make it if you still want to get realistic results}". I thought that was obvious.

Also, I can't tell you which particular parts of the trees you've found are wrong, because they're not published.

>>> Presuming you mean everything should be unordered and ignored
>>> for correlations, there are quite a few manuscripts in the
>>> cladistics literature that suggest otherwise.
>> Posting your question back to you: how did they know they were
>> more right than wrong when they concluded?
> You should read more Systematic Biology and journals like that.
> Simulation studies to see if a method works are normal these days
> in biology. There are several papers in the June 2003 issue of JVP
> that explore the "problem" of missing data in phylogenetic analysis
> by simulation.

 I'm trying to avoid the abstract and concentrate on reality.

Every single one of these papers goes on, after the simulation, to work on concrete examples. You act as if you were the only person to ever think of the obvious.

> Except, if you don't publish for too many years, you'll get into
> trouble if you have or want an academic job. Better publish
> intermediate results every once in a while -- that's also a good
> opportunity to let others go over your matrix and point out
> mistakes to you.

 I see. Do they do that?

Not as often as they should, but it does happen.

 And, going back to an earlier thread, if
 someone finds three mistakes is that enough to "distrust" a matrix
 with 40,000 cells? That's reality, my friend.

"Distrust a matrix"? No, mistakes are a property of single cells, not of entire matrices. You correct all mistakes you can find and repeat the analysis. :-|

>>>> Please name any apomorphy that is not rare.
>> Ovoviviparity and viviparity in squamates...
>> "Viviparity has evolved almost 100 times among lizards and snakes." :
>> Shine and Gillette 1988.
> Color. On scales like tetrapod phylogeny, integument color has no
> phylogenetic signal whatsoever.

 Sounds like we're back to fractals. How to grade, judge and score
 color, patterns, etcs.

No, we're merely back to continuous characters. They take some time to deal with, but it's feasible (Wiens 2001).

> Body size. _Has_ a strong phylogenetic signal, but not as strong as
> it could be.

 Every tetrapod has "body size."  I'm making fun, but your line of
 reasoning is interesting. Hone and Benton 2007 Anurognathus and
 Quetzalocoatlus on a diagram, drew a straight line between them and
 came up with a Cope's Rule for pterosaurs.

That was a rather appalling paper, if I'm thinking of the right one: a linear regression that completely ignored phylogenetic inertia and stuff. Evolutionary biology without a phylogeny. <headdesk> Hasn't a response already been published?

BTW, it's not "my line of reasoning", it's a result by Laurin (2004, Syst. Biol.) and my unpublished Master's thesis.

> Warren 2007 fig. 10. Should I send you the pdf?


Will do.

 And by "ruin" I mean the movement of major branches.

The tree gets completely uprooted, and the major branches rearranged at random. It's incredible.

 And by sufficient size, I mean 50+ taxa and 150+ characters.

It's a little bit smaller.