This week's revolution. Was Re: paleonet Fossils/molecular data: Seeking Thread

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From: TomDeVrie@aol.com To: paleonet@nhm.ac.uk Date: Friday, September 13,
2002 01:13 AM
Subject: paleonet Fossils/molecular data: Seeking Thread


>I'm teaching a high school elective that compares the paleo record of whale
>evolution with that yielded by mtDNA sequences.  Students study modern
whale
>bones, examine an Oligocene mysticete in a nearby museum, use online and
>literature sources for paleo data, and isolate mtDNA (chicken proxies for
the
>techniques), run PCR reactions, manually sequence mtDNA fragments, and use
>Genbank sequences for aligning and building trees.
>
>I'd be grateful if someone could email the full thread (to date) of this
>discussion on paleo and molecular data (to me, not the listserve).  Even if
>the discussion is occasionally overheated, it will illustrate to students
the
>tension that arises from using different data sets to resolve a single
>problem.
>
>Tom DeVries
>


Hi Tom (and list) -

If no-one yet has, I can supply most of the thread.  I'll move gradually
towards outlining how important this week has been.

Yes, it is most valuable to introduce students early to all aspects of
science, and I applaud you for including even those which involve heated
tensions.

This often occurs when science is at its most interesting - where new
paradigms are being hacked out of the rock.  This is where the philosophy of
science comes to the fore:  you only really need it at important crossroads,
and since these rather seldom occur in most fields, and few scientists ever
get to be involved in one, let alone have the benefit of the experience of a
past paradigm change when encountering a new one, they don't see any point
in bothering about philosophy and knowledge engineering.  Even those that do
show interest mess it up.  A year or two ago Jere Lipps wrote a piece for
Palaeontologia Electronica about creativity in palaeontology which looked
into the process of theorisation.  Through reading his writings, and via
indirect report, I know in personal terms he's an excellent chap, and with
the most honest of intentions, but his piece started by mentioning a few
established tenets of sound theoretisation, and then descended via a parody
of the worst kind of Socratic dialogue into the most dangerous and
misleading conclusions, among them that new theories mustn't violate any old
ones!

If you want your students to make outstanding contributions to science, you
*have* to teach them to know their way around the edges of science, just as
top engineers explore the limits of engineering possibility, and successful
businessmen make their millions by flirting with bankruptcy, illegality and
immorality.  Any idiot can identify a form of scientific method that
deviates from the traditional in a field, but it takes something special to
discern a new crock of gold from a new pile of crap.  Yes, it does tend to
go with cleverness, but if it also had nothing to do with the habit of
thinking not along traditional lines, why does it so often seem to be those
employed outside a field who bring the most worthwhile novelty into it?

But major contributors need not just a sound enough appreciation of the
philosophy of science, you also a keen nose for bullshit, an understanding
of just how staggeringly high a percentage of an orthodoxy it tends to
comprise, and a willingness to ignore it in theorisation, but if necessary
stuff it back where it came from - "pour encourager les autres".

For example, already in this thread I have stressed how little the late
man-chimp-gorilla split advocated in "The First Chimpanzee" has been
considered in the scientific press.  Science should be the comparison of one
theory against another.

One reply to my postings said:
"...there always seem to be a few bad eggs who are convinced
that their way must be the only way to do things..."

He is thus accusing me of insisting that I am right, and claiming those who
write or edit long articles on palaeoanthropolgy are more open-minded, when
in fact they quite obviously are the ones presuming the late-split theory is
wrong without considering it, and I am only insisting on the right for this
obviously good candidate to be fairly heard.

His suggestion is sheer hypocrisy, and he augments it by adding that I
should...

"...try to be more constructive and work with a paleontologist on trying
to incorporate both fossil and molecular data."

... implying that the premature and unjustified rejection of the theory is a
result of my lack of cooperation.  I am only advocating that you explicitly
explore the good and bad points of the theory, dammit!  For the record, my
"main" line of work, which I will resume a soon as I have helped clear out
the dino-bird stable, is not molecules but thinking, natural and artificial.


Now Tom, if you want to show your students an example of science in the
making, you have a splendid oportunity going on at this moment right in
front of our eyes!  This week is the biggest week in the dinosaur sciences
since 1969, and possibly before that!  (But I've only been waiting for this
moment since 1988 :-) .)

As I wrote in my review of Paul's "Dinosaurs of the Air" in the Times Higher
Educational Supplement on 26th April:

"However frequent revolutions are in any science, the punctuations are still
the most revealing parts of the story.  One such is currently occurring in
dino-bird palaeontology, and it’s a triple-decker: the relationship of birds
with dinosaurs is again under consideration; the magic algorithm –
cladistics – for automatically generating family-trees of extinct animals
directly from the characteristics of their bones is being tested; and the
very nature of the scientific process will, for many in the field, be
brought into question."

Brewing since Greg Paul first mentioned it in a conference in1984 has been
the idea that many well-known theropod dinosaurs were flightless birds,
which has considerable significance for both the sequence of events in the
evolution of flight and for the phylogeny of dino-birds.  But it's the
sociology that's most fascinating.  This theory has been studiously ignored
in a water-tight blockade for a decade and a half by the "scientists"
involved and the editors of the major science journals and magazines.  In
all that time, the debate has been kept out of the public gaze, but has
raged on the internet, but this week, with the publication of the Czerkas'
book "Feathered Dinosaurs and the Origin of Flight"
 http://www.dinosaur-museum.org/featheredinosaurs/chapters.htm , and the
revelations within of highly significant fossils, it becomes impossible for
any reasonable thinker to deny at least the likelihood, and probably the
truth of the theory of secondary flightlessness.

Greg Paul himself puts the icing on the cake in a "must read":
http://www.cmnh.org/dinoarch/2002Sep/msg00255.html

(For an example of the desperate nitpicking of the losing theorist,
equivalent to a man lost in the desert, squirming his fingers about in the
wet sand where his last water has spilled, see Holtz :
http://www.cmnh.org/dinoarch/2002Sep/msg00203.html )

Why has an entire theory gone from birth to maturity without ever *once*
being properly revealed in a generally available journal or TV/radio program
by any responsible third party as an interesting thread in the fabric of
modern science?  The notorious paper shortage?  The ????  !  I just can't
think of any feasible excuses!

The truth is something your pupils Tom must be warned severely against more
than anything else: personal bias.  How can you expect any journal to air a
theory implying that cladistics is not the right and only approach, when a
senior editor in that field has nailed his reputation to the view that it
is?  When furry dinos were revealed a few years ago, this was taken
triumphantly as evidence that the cladists were right and the ornithological
old-guard were wrong.  Front cover - loads of articles etc etc.

Now that the evidence shows that simplistic cladistics is perfectly capable
of giving a completely and very seriously wrong answer, what do we get?
Absolutely nothing.  No mention of anything involved, in this week's Nature.
Check out next week's edition 19/9/02 to see if the report "Henry Gee proved
completely wrong - Felsenstein, Sober, Paul, Czerkas, Jackson vindicated!"
appears!

Like heck will it!  And while we're on the subject of Hecht, the reporter on
palaeontological subjects for New Scientist has also never once mentioned
this all-important theory, except for a brief mention of some obviously
ex-flying forms.  In his case it's even harder to understand the error.  I
can only think it's because the people supporting the theory are not
employed as palaeontologists, and the theories are not expounded at
conferences.  How stupid in the light of the history of science -
particularly evolutionary and dinosaur science!  That way though, the
journalist hopes to avoid any blame - and possibly a lot of effort trying to
work out if the theorists have a point.

Blame unfortunately cannot be avoided.  Whether you believe a scientist's
worth can be judged by his employment strictly within the field concerned,
or by the style by which they modify and further propagate memes which reach
them, people are a part of the scientific process, even when they are
journalists.  The same professional talent that caused the average man in
the street who knows anything about pteranodonts to believe they ate
shellfish even though the journalist responsible was warned before and after
that it was wrong to report the idea, and has never corrected it, has now
helped convince the world of the reverse of much of what was actually
happening with the post-Achaeopteryx maniraptorans.  Sometimes people have
to be criticised when they get it very very wrong having been warned
repeatedly.

Well OK, so dinosaur science doesn't count for much?  Then just give me 1%
of all the public money that's spent on it (to include a fair share of
subscriptions to New Scientist paid by people who expect a fair,
professional and unbiased digest of the discipline.)


I've been planning this email for weeks - just lucky the Czerkas book came
out now.

The book's main significance is that, as I've been saying over the last few
years, if two main lobes of the phylogeny of bird-like dinosaurs
(maniraptorans or whatever) both include flying forms, then either flight
evolved in both lines simultaneously (unlikely) or their last common
ancestor flew.

Even if you doubt the early troodont Sinovenator had flying ancestry, the
hard-to-deny flying ability of the dromaeosaur Cryptovolans, and the
oviraptorid (if people are right in accepting that it is) Omnivoropteryx
make the cladograms say flight evolved a surprisingly long way back and
included many groups.  At least one good cladist has now accepted this, but
I'm sorry to say the widespread neoflightlessness also makes the trees the
cladograms suggest very untenable.

As for the captions over the specimens at the Chinese feathered dino-birds
exhibition at the London NHM, they are now seen to be wrong, since  the
dinobirds mentioned in:

"The dinobirds prove that feathers evolved before flight",

and:

"The fossil dinobirds show beyond doubt that feathered dinosaurs were
the ancestors of birds",

all inherited their feathers from flying birds, exept Sinornithosaurus which
doesn't have flight-type feathers.  And while Greg would dispute this, my
theory that Sinornithosaurus also inherited it's flightless-bird type
feathers from types with gliding flight is far from refuted, so alternative
theories cannot be "proven" or even "beyond doubt".  (see
http://www.geocities.com/strangetruther/picphilos1.html )

In recognition of its importance to all of us involved with cladistics, I am
prepared to offer to deliver a sound, memorable and early (ie Monday
morning) review of the Czerkas book FREE OF CHARGE to any journal that
requests it - even New Scientist or Nature!


Cheers,

JJ