Suggesting our differences are due to childish error on my part, in his Longisquama argument Darren Naish uses the ‘lots of others do it so it can’t be wrong’ ploy, with the implied insult that I’m too stupid to see it:
“And I will repeat what I’ve said in responses to John several times before: you may think, John, that there’s some sort of methodological problem behind the generation of cladograms, but you once again ignore the fact that there are biologists who both generate and use cladograms, and write the software involved.”
This from someone with no understanding of any methodological issues in anything technical. No-one has to “think” there are such problems with these cladograms – their flaws have always been obvious. My reply to his ‘others use cladograms so it must be all right’ argument – which he deleted – was this:
“Darren defends his unthinking faith in them [cladograms] by saying lots of biologists use them. Well, lots of people drive Formula-1 cars but that doesn’t mean any palooka is advised to try. The amateurish mistake is not to understand when not to trust cladograms. Some biologists use them only in situations were they can be trusted, while others are actually making the mistake of not avoiding those situations. And then there are some that don’t use them because they understand the problems. We KNOW they don’t work in numerous circumstances, and we often gets hints as to when those apply.”
(And we do know they don’t always work: the mammal cladograms built using bone shapes and molecules differed significantly, proving one of the cladograms was wrong.) He shows he’s completely failed to understand there most certainly is ‘some sort of problem’ with them: both in the answers they give, and in the unquestioned acceptance of them.
I didn’t “…once again ignore…” anything of course. I didn’t need my degree in the design and use of information systems to know what any worthwhile scientist would know. It just meant I couldn’t not know it.
Treating cladograms as gospel is exactly the kind of thing you do when you have no understanding of the technicalities behind them. And I don’t refer to the technical skill of writing the programs that make cladograms – I refer to the information science behind the interpretation of their output.
For the record, here’s why all that effort to examine cladograms, fully understand them and pronounce them unimprovable (ironically, on Popperian grounds), was doomed:
Cladograms were intended to deal with the evidence (the character matrix) in such a way that all the different possible cladograms (i.e. hypotheses) are all tested on the data matrix. Thus: hypotheses (“all of them”), and all tests, all in one. But not all the evidence and potential simplicity is actually considered since there are some patterns inherent in the data that aren’t taken account of in cladogenesis, and other data such as time and geography aren’t included at all; also adequate independence in the data is wrongly assumed, (and) homoplasy is wrongly assumed to be taken care of automatically, or to be unimportant. Cladograms thus cannot be taken to act as their own test and should be treated realistically as heuristic hypotheses that need independent testing. The approach of Kluge, de Queiroz, Poe, Cracraft, Wiley etc. would be exposed were it ever tested on realistic simulations but they never do that. Their detailed but flawed work in this area is why so many wrongly imagine a valid theoretical underpinning for absolute cladistics even under rampant homoplasy.
Anyway, if those workers missed the point, there’s no hope for dinobird palaeontologists to catch the mistake. And whatever good intentions are or were once claimed, they’re not honoured now. Padian, who does have a degree in biology but like all of them, nothing in anything informatic which is much more important, amazingly said on his website downloaded about 2003:
“Through a synthesis of phylogenetic, functional, and comparative morphological evidence, I try to assemble the best-supported evolutionary sequences available and to reconstruct the steps by which major adaptations, particularly flight, arise.”
Yes, that was “functional” you saw there. For new “experts” like Naish the word just triggers jeers of “Scenario” (see below) and “Just So Story”. But if you think Naish is just a blogger, and the professional strand holds itself at a distance, here’s Gauthier who launched his friend Padian into his Head of Integrative Whatever post at Berkeley, and, after G. S. Paul (1984), the first user of cladograms for dinobirds, taking a pavement lecture from Naish at SVP ’09:
Naish’s ignorance of the rest of science as a whole, and his insulting attitude to those who are familiar with it, can be assumed to be reflected throughout the Society of Vertebrate Paleontology, even amongst those more reticent.
If you’d seen Naish lying back on the grass that day holding court amongst those sitting around him, you’d know why feeding him criticism with a teaspoon would be pointless, and why you’d need to use a baseball bat. And why you’d want to.