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Re: Popper and Palaeontology (was: Re: "running" elephants - locomotary analoges)

On Tuesday, April 29, 2003, at 06:21 AM, Jonathan R. Wagner wrote:

[quoting me]
But it is meant to model the >pattern< of evolution - otherwise no-one would bother doing it. By pattern of evolution, I mean the arrangement of the real characters in respect to clades.

Are characters real? Shall we dance?

Mistake. I meant to say: "the real arrangement of characters in respect to clades", which I hope makes a little more sense.

Actually, I hate to weasel, but I really don't have time to dance now.

"Weaseling out of things is what separates us from the animals... all except the weasel." {H. J. Simpson)

Obviously Dr. Simpson has an unique approach to phylogenetics - I would like to know more about his methods.... ;)

No one every asserted that they believe homoplaisy is UNLIKELY... I suspect that, as an estimator of phylogeny, parsimony is robust to a large proportion (ergo, likelihood) of homoplaisy. You should specify whether you are concerned specifically with the case in which homoplaisy is rampant, or the case in which homoplaisy is MORE LIKELY than synapomorphy. The former case appears to describe the situation in many datasets, and there is a case to be made for the utility of parsimony methods under those circumstances. Down the latter route lies madness. Seriously, there are some places science can't go... if homoplaisy is more likely than synapomorphy, and you have NO other data (e.g., branch length estimates), I think you can see that the odds of getting a useful result are pretty low.[...]

So we DO assume that homoplasies are less likely than synapomorphies.

Are you trying to say that, for parsimony analysis to be valid, the true tree must be the parsimony tree for all the data? I don't think anyone is under the illusion that this is the case, and I don't think anyone would insist it must be. Again, this the newtonian mechanics issue: we cannot ask for a method that WILL reproduce the correct tree, given all the data, we can only ask for a method that brings us closer to the true tree than all other competing methods.

You seem to be dragging in the issue of precision here, which is a separate. I'm arguing that the true tree must >approximately< match a parsimonious arrangement of data for a parsimony analysis to work. If no-one else is under such an "illusion", well so be it, I still don't see how it could be any other way.

If a parsimonious arrangement of data models a true tree, in what sense is that true tree not an approximate parsimonous arrangement of data?

Since, until recently, there was NO accepted method other than parsimony for discrete morphological data, parsimony wins by default. If you want to dethrone it, you need to come up with a new method.

I am not arguing against parsimony - I'm saying it makes assumptions about evolution which may well be correct, but are nevertheless glossed over.

To get back to the newtonian analogy - we have good reason to believe that newtonian mechanics is a good approximation of the universe - and that newtonian models will produce results close to the truth. A newtonian model applied to a non-newtonian universe will give results far from the truth.

Just as newtonian models assume that newtonian mechanics is a good approximation of the universe, cladistic parsimony assumes the true pattern of evolution will be approximately parsimonious.

John Conway, Palaeoartist & Protophilosopher

"Do I contradict myself? Very well, then I contradict myself, I am large, I contain multitudes." - Walt Whitman

Palaeoart: http://homepage.mac.com/john_conway/_palaeoart/
Palaeontology & philosophy discussion forum: http://clouds.proboards16.com/