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The now very long Actual running Archie thread ... cladistics



John:

First off, let me apologize for not realizing how you viewed avian
evolution.  I didn't quite realize at the time I wrote that e-mail on
Friday night that you view the evolution of maniraptorans as coming
from birds and secondarily becoming flightless.  Do I have it right
now? =)  By the way, I like Larry Martin very much even though I don't
agree with his and Alan Feduccia's interpretation of the data, but
that's a bit off track.

Okay ... to continue:

We said:
"> What are you going to replace that methodology [cladistics] with?

What am I going to replace poking myself in the eye with a sharp
stick with,
now that I've decided it's not a good idea? :-)"

And further:
">And I by no means suggest that it [cladistics] will stay forever
or
>never be replaced by better methodology -- all I suggest is that
you
>cannot dismantle cladistics without a replacement.  If you don't
like
>cladistics, suggest something else.

It is not a general principle that everything that is bad needs
replacing.
(See the "sharp stick" argument above.)"

Yes, very clever. =)  The sharp stick argument.  I don't take you too
seriously on this one, but you do realize you have set up a false
analogy.  The false analogy is that the cladistical method is harmful
(unless poking your eye out with a sharp stick has some value) and
therefore not using cladistics is better than its use.  Perhaps it is
not a general principle that everything that is bad needs replacing,
but in science one cannot dismantle or disregard a theory or
hypothesis without offering a replacement for it -- otherwise, this is
"I win, you lose" kind of politics, and then no matter what I offer,
I'm always on the defense and you are on the offense.  How can you
possibly "lose" when I do all the work of coming up with examples and
you shoot them down without offering an alternative?  But, you offer
an alternative:

"I do however have an alternative."
[snip]
"For example, when guessing pack hunting in Deinonychus, shall we say
it is
an example of a reptile?...in which case we might generalise from
extant
examples.  Or is it an example of a plains carnivore predating much
larger
prey? ...in which case we might invoke African hunting dogs as the
example.
Or is it an example of a bird?  Of a flightless bird?  Of a
dinosaurian
predator?  Of an archosaurian predator?"

I assume you've seen my thread to MegaRaptor and others on the pack
hunting evidence in Deinonychosaurs.  This would be hard to argue with
you, as most dinosaur or fossil organism's behavior is largely in the
realm of speculation, and my giving an answer would only give the
impression that an understanding of fossil animal behavior is anyone's
guess, which it is in many circumstances.  This is the "who are you to
say so" argument.

However, would you agree that no matter how you look at evolutionary
biology, there is a hierarchical arrangement of organisms?  I do not
mean to suggest that this is so because of Linneaus, Darwin, or
whomever, but rather, most folks have noticed that certain organisms
appear to be more closely associated or related in form, behavior,
function, etc., to certain organisms than others.  Chordates have a
dorsal hollow nerve cord, a notochord, a postanal tail, an endostyle
(thyroid), and myomeres (segmented musculature).  Vertebrates share
these features with chordates, but also have cephalization, neural
crest cells, ectodermic placodes, and of course vertebrae surrounding
their notochords.  We can go on, of course, but the point is these are
not just random guesses picked out of nowhere.  Anyone can observe
them over and over again.

While we may not be able to predict exact behaviors, rituals, etc.,
in fossil animals, we can say some things about these organisms and
the way they made their livelihoods based on what we know about the
groups they're related to and the fact that they tend to follow
certain patterns of function and development.  While I can't tell you
if a Deinonychus was a pack hunter or not, I can tell you for sure
that it was a flesh eater, its arms and hands functioned in certain
ways to obtain prey based on the bone articulations, and perhaps
something about its basic mental nuts and bolts from an endocast --
after all, vertebrates (and I really mean the amniotes here) have 12
cranial nerves, each of which does similar things in all known living
animals.  While we could guess that Deinonychus had a great sense of
smell, we could look at its olfactory bulbs, note their size, and say,
"Yes, this animal probably had a sense of smell comparable to ..."

You said:
"If we go for parsimony, should we minimise the number of individual
changes?
Or maybe the number of niches or roles the creature was adapting to?
(eg
flight, or the elusive "activity X" that give rise to feathers, wings
etc
according to the popular view).  The latter might sometimes be more
reliable, but if it were, it would be harder to justify any
particular
quantitative treatment for it.  Another possible application of
parsimony is
of course in the stratigraphic sense - assume age indicates position
in the
tree unless very good evidence contraindicates this.
[snip]
"Another might be: If some vast suite of adaptations suddenly
appears
simultaneously, all of which are astonishingly perfectly suited in
great
detail to some particular role, again be very wary indeed of theories
that
say "coincidence: they just happened for reasons unknown". 
Statistical
justifications for this guiding rule might conceivably drawn up -
inadequate
to satisfy a disputant no doubt, but perhaps useful for believers."

I'm not sure I understand your use of parsimony.  For a non-dino/bird
example, we could talk about the development of the coelomic cavities
in vertebrates and other chordates during their early development.  In
most chordates and their close relatives the echinoderms, the coelomic
cavities develop by a process called enterocoely, in which the
coelomic cavitiy develops within the mesoderm when it pinches off from
the other tissue layers.  In contrast, most vertebrates (except
lampreys) develop their coelomic cavities by schizocoely, a process by
which the mesoderm starts first as a solid sheet which later pinches
off into the coelomic cavities.

Why do I mention this seemingly obscure reference?  Because, the
protostomes (earthworms, etc.) are the other group which has
schizcoelic development.  Are we to conclude that vertebrates and
protostomes are more closely related to one another than either is to
the chordates?  Or do we stick to the traditional account of
vertebrates coming directly from chordates?  Here's where parsimony
steps in.  Vertebrates share far more characters with chordates, and
even with echinoderms, than they do with protostomes.  The simplest
(least amount of steps) answer is that vertebrates secondarily
developed schizocoelic coelom formation from a chordate ancestor. 
While the other idea (protostomes are direct ancestors to vertebrates)
is perhaps a possibility, we consider this possbility remote because
it would take a quite uncanny amount of convergence for this to happen
(turn a ventral nerve cord into a dorsal one, develop a notochord,
develop a post anal tail, etc.).  This is parsimony writ large.

I don't know enough to make an argument for or against the trees
down, maniraptorans are flightless-birds hypothesis (or its variants).
 The point is, the cladistical method, and its use of parsimony to
sort out which phylogenetic trees are most likely based on the
evidence we have at present, is not a guess machine.  We must be
careful with the word theory.  A theory in science has testablility,
repeatability, falsifiability, and predictive power.  Used in casual
conversation, a "theory" is someone's guess or idea about something, a
thing very far removed from the scientific method.

You said:
"We do not live in a neat mathematical simulation inside a computer,
where
everything is certain.  We live in the real world where there are in
general, no rules except those we make up, but even those are liable
to
correction at any time.  Our best guesses are best inspired by a vast
expert
system than a fixed list of "laws".  The search for better rules for
generalisation is never ending."

I think some physicits and chemists would disagree with you here. 
There are laws of thermodynamics and physics, chemical bonding and
reaction rates.  These are not made up by us, but merely observed and
reported so repeatedly that they have become laws.  Keep in mind that
scientific theories, not laws, are the most powerful tools of the
scientist.  A scientific law is only a repeatable observation with no
explanation and no predictive power.  The law of gravity can be
observed over and over and over, but all we can say is that when an
object is dropped, it falls towards the ground at a specified and
unchanging rate of acceleration.  But that will not tell you why an
object falls to the ground or why it is at a certain rate of
acceleration.  Newton and then Einstein both gave us theories of
gravitation, and while they are not 100% certain and are certainly
falsifiable, few would say their theories were just guesses because of
their great explanatory and predictive powers.

While I am not attempting to compare cladistic methodology to that of
Einstein, I am asserting that cladistics is a powerful explanatory
tool that allows one to more accurately sort out and understand the
already hierarchical nature of evolution, and predicts when and where
certain evolutionary changes should occur, while being falsifiable. 
We don't just make up the rules -- there is a reality out there. 
Science is cumulative, and while some of our hypotheses and even
theories may eventually become falsified, I sincerely doubt that when
that happens, vertebrates will turn out to be protostomes, and birds
to be fish. =)

Sincerely,

Matt Bonnan
Dept. Biological Sciences
Northern Illinois University