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Re: Sci. Am. - present. [long]

John V Jackson wrote:
>and the most modern, elegant, unembarrassed by evidence and supported by
the >writer: 'Birds' Came First.)
        I would've said "unencumbered by evidence", myself...

>They cannot explain why Archy's near ancestors (strictly
>non-arboreal and non-flying or gliding, they say) lengthened the arm while
>numerous other lines shortened it.
        Use of the forelimb in prey collection. (or, perhaps, climbing, if
you believe in "trees down").

>Unfortunately this movement on its own moves the claws sideways,
>and would have to end with a conventional downwards movement for a strike. 
        Actually, experts seem to think that the hands weren't ever pronated
in theropods. The idea, as I take it, is the hands were whipped out and then
closed from side to side, in a sort of "clapping" motion. I may be off on

>The prey of animals which flick something out, is always taken by surprise
>while within range of the extension:[...] Dromeosaurs could not hunt by
>creeping up to within range of such a flick; for one thing it would bump
its >nose against the prey first.
        a) the nose could be pulled back in a beautiful s-curve
        b) the way a dromaey got into range was by running after its prey,
at least that's what I thought this scenario was about.

>As usual we see Greg Paul's Velociraptor skeleton laughing her head off at
>the folly around her - or maybe she's just panting in an effort to get past
>the Archaeopteryx in front and take up her proper place on the cladogram. 
        Actually, she is runnin very hard to find her generic identity
(_Deinonychus_). ;)

>Why must a media superstar like her always suffer the indignity of being
>placed ancestral to a creature 70 million years earlier?
        Aw jeez, here we go again. This has been discussed many times both
on this list and off. Summary:
        a) the terrestrial vertebrate fossil record is woefully incomplete
        b) the terrestrial vertebrate fossil record has not been 
                completely explored
        c) we don't really have the same exposure of Jurassic sedimentary rocks
                as we do for the relatively well known Late Cretaceous
        d) even then, there are possible troodontid teeth in the Morrison [sic?]
                Formation. Depending on whose phylogeny you use, this ranges
                from suggestive to decicive evidence against your point

>Because too much faith has been placed on the ability of cladistics to deal
>with unprepared input.
        In my limited experience with folks who don't appreciate cladistics,
"prepared input" means that you've had a chance to monkey with the data
until you are *assured* the result which you expected in the first place.
That is *not* scientific. The beauty of cladistics is that it minimizes a
priori assumptions. If you want to dabble in biasing your data, feel free to
do so, but I expect that the scientific community will not be amused.

>Objectivity is nice in science,
        Ok, stop right there. It is important in science to strive towards
objectivity whenever possible. "Nice" simply will not suffice!

>but some traits input into cladograms really are more equal than others,
        And who is to say which ones? I certainly don't feel qualified. Last
I checked, neither did Jaques Gauthier, Kevin Padian, Paul Sereno, Tom
Holtz, Catherine Forster, and a host of others. On this very list, if you
look, say, in Chris Brochu's latest work, you won't find him making this
call. So, then, who is to say?

>and can easily be swamped by multiple less significant features.
        Of course, the "more significant" features may have an unknown
functional importance which encourages homoplaisy. But you wouldn't know
that unless you interpreted them, just like you interpreted the ones you
think are less significant. Now your phylogeny is no longer based on a
fossilized skeleton (or several, adding layers of interpretation at every
turn), but on your interpretations of the significance of characters which
you have found.

>The dozens of flight-dependent
>characteristics such as arm length and feather symmetry change in a flash
>upon loss of flight and are way too labile to be used as a guide for
        This may be so. It does make me wonder then why some folks (George
Olshevsky, for instance) resits so strongly the idea that _Mononykus_ might
be a bird. Anyway, you cannot simply say that because something *could* have
happened that it actually *did*. Do you have any?

>They will always group fliers together.
        This is interesting... Then why are not pterosaurs and birds grouped
together exclusive of non-avian dinosaurs?

>By priming the cladistic process erroneously, for example by placing
special >emphasis on "flying" and "nectar-drinking", we can show bees are
related to
>hummingbirds, or even to shunting engines if we choose "humming" and "black
>and yellow markings" instead.
        True. However, I could just as easily publish a "traditional"
phylogeny showing the same thing. However, with the cladistic analysis, you
could go back, see that I had done a positively moronic job of selecting
characters, and rerun my study with better data. For the "traditional"
analysis, all you could do was poo poo me.

>The first toe in larger non-arboreal theropods was probably used for
scratching >(or preening), so it usually pointed forwards.
        Can you say "vestigial"? I knew you could. (That's for you Alan...)

In smaller arboreal forms when reversed, it could help
with stability on branches.

>Since we KNOW we have to use some common sense with cladistic input,
        I'm not saying you're wrong, but I'd appreciate an example. I can't
really come up with any...

>we must surely give features such as uncinate ribs, more weight.
        Why? Why? Whywhywhy?
        ON a different suject, is there current aggreement on the presence
or absence of uncinate processes on non-avialan dinosaurs?

>Surely a feature such as this is more significant than the
>highly variable 1st toe orientation?
        "Variability" depends on your *a priori* assesment of phylogeny. If
you were to group all theropods with a reversed hallux, then the character
is NOT variable at all. On the other hand, if you group them on other
criteria, it might be extremely variable. So then, is this an objective
evaluation, or a subjective one based on your a priori expectations for the
phylogeny of the group?

>A guiding principle in science is - look for the simplest explanation. 
        The explanation which best accounts for the data with a miminum of
untestable assertions and unsubstantiated assuptions. It's called parsimony,
and it is weapon of a cladist. Not as clumsy or random as tradtional
methodologies. An elegant concept, for a more reproducable result.

>Most people accept that bats and pterosaurs attained flight through an
>arboreal gliding stage. Gliding lizards ancient and modern are known, along
>with frogs and snakes but for some bizarre reason large numbers of people
>have found this route to flight in birds hard to accept.
        Perhaps this is because most gliding animals, and all those flying
animals believed to have gone through a gliding stage, have *patagia*..
There are several features of the flight apparatus which unite these animals
in a morpho-evolutionary class (to coin a clumsy phrase) exclusive of birds.
They have patagia, the patagia connect the fore- and hindlimbs, they do not
possess integumentary flight structures comparable to flight feathers, etc.
At least some of these characteristics are linked, of course, but many can
be theoretically tied to the development of flapping flight through gliding.
Indeed, this is a case where homoplaisy ("convergence") can actually aid in
our attempts to reconstruct evolutionary history.

>Despite earlier, famous supporters now having changed their minds, Padian
and         Changed their minds about what? Don't go putting words into
people's mouths now...

>Chiappe still think all those pre-adaptations miraculously suited to flight
>simply accumulated in flightless animals over 70 million years.
        In point of fact, many people who may or may not buy the "ground-up"
hypothesis also believe this... Indeed, the current evidence strongly
supports this position.

>Here's how they express their mistrust of the trees-down hypothesis:
        "Mistrust" is a rather strong word, don't you think?

[here John quotes the article]
>Archaeopteryx and its maniraptoran cousins have no obviously arboreal
>adaptations such as feet fully adapted for perching.
        See Sereno 1997 for a more charitable interpretations.

>Perhaps some of them
>could climb trees, but no convincing analysis has demonstrated how
>archaeopteryx would have climbed and flown with its forelimbs
        See Chatterjee's new book for a demonstration.

>and there were no plants taller than a few metres in the environments where
>archaeopteryx fossils have been found . 
        I seem to recall that Paul Davis' [sic? sorry dude!] work on
taphonomy at Solnhoffen suggested the bodies were laid down by storms. I may
be out on a limb here (pardon the pun), but if this is the case, the little
guys might have been blown in from anywhere. In any case, what does this
have to do with anything. Parsimony my keyster (forgive, oh Hennig on high)!
Is it so hard to believe that "shore-birds" might have evolved so soon after
the origin of birds (if it was truly so soon?). Just because it is the
earliest known confirmed bird does not oblige _Archaeopteryx_ to look and
behave just like the first flying dinosaurs.

>Even if the animals could climb trees, this ability is not synonymous with
>arboreal habits or gliding ability.
        Nor is an ability to run synonymous with strictly non-arboreal
habits (q.v. kangaroos and goats). Oh, yeah, one thing I'm quite tired of is
the knee-jerk association of the "arboreal theory of the origin of avian
flight" and an obligate gliding stage. The two are not necessarily linked.

>Most small animals, and even some goats and kangaroos can climb
>trees but that does not make them tree dwellers.
        Nor does it make them obligate cursors.

>Besides, Archaeopteryx shows no obvious features of gliders such as a broad
>membrane connecting forelimbs and hind limbs."
        See above on the obnoxious association of the arboreal theory and
gliding. Anyway, they are quite right on on this one. This may or may not
have a bearing on the origin of flight, but I'd say it's more damning than
the arboreal adaptations stuff. Then again, maybe I'm biased...

>That paragraph, which is unworthy of a professor or a respectable
        Perhaps you'd like to tell the authors this yourself. Out of
curiosity, how long have you been peer-reviewing scientific publications?

>Misuse of the cladistic process,
        Hmm? How should it be used? When is your book on the subject due
out? I'm sure that all of the above mentioned cladists, not to mention the
rest of the scientific community (who has certainly never heard the
objections you have raised so far) are looking forward to being set straight.

>total failure to explain the uncanny homing in of flightless forms towards
>bird-hood over most of the Cretaceous,
        Umm... wouldn't this (if it were a meaningful phenomenon, and not an
artifact of the fossil record) imply that birds evolved at the *end* of the
Cretaceous? Perhaps *you* should explain this phenomenon... ;)

>reliance on unjustified beliefs such as "the immediate theropod
>ancestors of birds were terrestrial",
        Not "unjustified", perhaps merely interpretated in a manner which
you think is inconsistant with logic. As for "beliefs", well, I hardly think
Padian and Chiappe pray to the Cursorial Proavian in the Sky every night.
Scientists usually consider themselves to be working in the realm of theory.
>and the apparent ignorance of the elegant and untroubled BCF theory,
        It is certainly unfettered by evidence. I think you will find,
however, that this is the reason "BCF" has not been adpoted, rather than out
of any petty spite or whatever. Indeed, it thrives quite nicely on being
entirely undemonstrateable. It truly is an elegant piece of work.
        However, if it makes you feel better to believe that you are
fighting the good fight against the oppression of professional orthodoxy, go
right ahead. I wouldn't go around making accusations, though... 

>go together to make a pretty dreadful piece of science writing.
        I am actually rather looking forward to the full scientific article.
I rather like Chiappe's work, whether or not I agree with all of his
theories (and I'm not saying I do or don't, mind you [hedge hedge]).

    Jonathan R. Wagner, Dept. of Geosciences, TTU, Lubbock, TX 79409-1053
              "I'm being nibbled to death by cats" - L. Molari