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Re: Wukongopterus and Darwinopterus

 Every right tree we hypothesize will admit
 new taxa as they are discovered with no change to the rest of the
 tree topology.

No, why? I've seen back-and-forth changes happen with corrections, why shouldn't they also happen with addition of taxa? I can't think of a good example right now, but I think I've seen that happen, too...

 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.

 You're never going to figure out the perimeter of England because you
 come up against fractals.

But you can come close enough, either by mathematical tricks like integration, or (in theory anyway) by bumping against the fact that space is quantified (keyword: Planck's length).

 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. :-)

 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. :-|

> 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.

> However, low resolution does not mean a tree is "bad".  Sometimes,
> low resolution is the correct answer given the data at hand: it
> simply means that taxa cannot be differentiated in a repeatable
> manner according to the present data.  That may be the error-free,
> robust answer for a given dataset.

 Then get more data. It's always there.

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.

> Please name any apomorphy that is not rare.

Ovoviviparity and viviparity in squamates...

Color. On scales like tetrapod phylogeny, integument color has no phylogenetic signal whatsoever.

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

 Typos are to be avoided, but they don't ruin trees of sufficient

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