RE: Feathers are not magical things...

["Thomas R. Holtz, Jr." <tholtz@geol.umd.edu>]

> From: philidor11 [mailto:philidor11@snet.net]
>
> I think I understand:  it is possible for a 'scientific' idea to be proven
> factually wrong and for an idea which cannot be challenged directly to be
> 'unscientific'.

Ah, yes, precisely!!

For example, many aspects of geosynclinal theory (the American precursor to
continental drift/sea-floor spreading/plate tectonics) were certainly
scientific, derived from observations and tested against possible
alternatives.  Given much of the information at the time they seemed to hold
up.  However, introduction of new types and new lines of evidence forced a
rejection of this model.

Similarly, the idea that chocolate is better than vanilla is unscientific,
even if it is true (:-).

> And after a number of examples of ideas identified as not demonstrably
> wrong, but
> unscientific:
> <The short answer: no, I would not be "outright wrong"; however,
> I would be
> unscientific.  (These are different types of things).  It is,
> ultimately, a
> burden of proof issue.>
>
> Okay, I think I see it.  A scientific idea is ' a hypothesis backed by a
> self-consistent logical argument employing certain principles'.

Hmmm, perhaps, particularly if one of those certain principles is
falsifiability.


In the case of the discussion with Jura, I said that drawing _Velociraptor_
without feathers (or, in the previous posting in this thread, drawing
_Hesperornis_ without feathers) was unscientific.  That is, such a
reconstruction is at odds with our current framework of understanding of the
historical (aka phylogenetic aka evolutionary) distribution of feathers.
Further information could change that idea: here are some examples:
        *The best way: skin impressions of _Velociraptor_ showing only scales,
especially if multiple age groups were represented.  (Granted, this is
unlikely given the sediments in which most _Velociraptor_ specimens have
been found, but people do get lucky).
        *Another way: skin impressions of another advanced dromaeosaurid (say,
_Deinonychus_ or _Saurornitholestes_) showing scales instead of feathers
over the body.  This would demonstrate that, although all other information
points to the most recent common ancestor of dromaeosaurs and birds being
feathered, at least one advanced form lost that condition and it might be
that a larger clade (say, a lineage containing _Deinonychus_ and
_Velociraptor_ but not _Sinornithosaurus_) lost it as well.
        *Still another way: if a sufficient number of other maniraptorans (i.e.,
some oviraptorosaurs, some therizinosauroids, troodontids, maybe some basal
birds) which were demonstrated to have scales only, then we would have much
less confidence either that feathers evolved only once or that feathers,
once developed, were retained.
        *And (unlikely, but worth the mention) should someone demonstrate that
birds lie far outside of the traditional theropods and/or that the "feather"
impressions (which in the case of "Dave" and some others are identical to
those of birds in the same formation) are not integumentary structures, then
the whole framework of the argument is lost.

> You're
> asserting
> that no alternative argument is possible given these principles, and
> therefore a
> proposed alternative must be so poorly supported as not to meet the
> definition of a scientific hypothesis.  Also, that denying such a well
> supported
> idea must be subjective rather than analytic.

Actually, I wasn't asserting that as such.  There are degrees of confidence
of inference, though.  To use some evolutionary transformations, one can be
very confident that a fossil baleen whale (known only from the skull) lacks
hindlimbs, or that _Hesperornis_ had feathers, due to the consilience of the
data at hand.  On the other hand, we could support multiple equal
alternatives further down the respective branches of the tree: that is,
basal members of the cetacean lineage known only from the skull may or may
not have had hindlimbs, and theropods phylogenetically outside the
_Sinosauropteryx_-bird clade may or may not have had feathers.  In these
parts of the respective trees, one could argue either hindlimb or integument
case strongly, but without additional evidence we would not have confidence
in either alternative.

> You referred to one of the principles when you said:
> <In the sciences we choose the simplest explanation possible, since that
> criterion requires the fewest additional assumptions.>
> However, you are not arguing for just characters and simplicity.
> (I didn't
> realize this in a past discussion.)

Oh, my yes!  Searching for "parsimony" on the dinosaur list archives yeilds
403 matches.  Many of these will link you into previous discussions on this
list, involving many current and past list members.

>You do include:
> <*Models of adaptation and functional morphology
> *Patterns of biogeography
> *Evolutionary tempos and modes (e.g., Punctuated Equilibrium vs. Phyletic
> Gradualism; Red Queen matters, etc.)
> *And just about anything else that gets published in journals like
> Paleobiology and Journal of Experimental Zoology and the like.>
> So, anyone with a character list and PAUP would not necessarily be able to
> produce a 'scientific' cladogram.

Huh?  I don't see what you mean by that.  (Sorry, maybe I'm just being
dense).  If you are saying "you have to know how to operate the software",
then of course: you have to know how to operate the software.  However,
anyone who knows the principles of the discipline can produce a scientific
cladogram: if you think that I am saying only some "qualified Ph.D.s" should
due this, you are VERY VERY far from the truth!!!

> There are certain conclusions which can
> be dealt with by simplicity, such as the examples that you gave, but
> producing a hypothesis about a whole set of relationships involves
> application of a range of other knowledge.

True, but within each of those other disciplines, simplicity/parsimony is a
major criterion for choosing between alternatives.

> Your 'burden of proof issue' involves a whole complex of ideas.
>
> So, a scientific argument about relationships includes:
> - a number of shared characters judged sufficient to indicate that certain
> animals are
> related and few enough shared characters in animals outside the group that
> these
> animals can be excluded,

Not exactly.  It is the concordance (or consilience, or whatever similar
term you'd like) of the characters, not the number.  Certainly a higher
number of uniquely shared characters helps, but is not necessary (nor, in
fact, sufficient).

> - expectation that unknown characters will be consistent with
> others in the
> group, as in feathered velociraptors,

Yes. I also assume, without additional direct evidence to correct me, that
all dinosaur species had eyes, or that all descendants of the most recent
common ancestor of _Albertosaurus_, _Gorgosaurus_, _Daspletosaurus_,
_Tarbosaurus_, and _Tyrannosaurus_ had only two fingers on each hand.

> - expectation that evolutionary change in the group will be gradual and
> consistent
> (after all, if a large number of brand new characters suddenly appeared in
> the lineage,  the character similarity screen might fail to identify the
> animals as part
> of the group),

NO!  This assumption does not exist within phylogenetic methodology (or at
least morphological phylogenetic methodology).  The acquisition of large
amounts of new characters within a lineage are not a problem per se: they
will only add a long branch length to that particular (apomorphic) clade.

That being said, large scale transformations which "overwrite" a large
portion of the anatomy may obscure ancestral relationships, which is one
reason for trying to find new fossil taxa.

(Something distresses me in your above point: it sounds to me that you are
confusing phenetics (which clusters taxa based on some metrics of
similarities) with cladistics (which clusters based on the simplest
distribution of derived character states)).

> and
> - survival of the logically determined hypothesis after
> application of other
> theoretical
> constructs, including models of adaptation and functional morphology,
> patterns of
> biogeography and the other examples given above.

Not as such.  Certainly if you had a set of alternative equally
well-supported (on morpho or other tree-generating data) phylogenetic
hypotheses, and only one of these was well-supported by an
independantly-well-supported paleogeographic model, then this might help you
prefer that one tree.  Reciprocal illumination is common in lots of
sciences.

> As you've probably already seen, the issue that bothers me is that the
> simplicity
> pre-screening of hypotheses may not be consistent with the later applied
> theoretical
> constructs.  Suppose you could establish that PAUP gave a lower weight to
> punctuated equilibrium scenarios than to more gradualist models.
> Would that
> invalidate the algorithm?
> I realize that this must have occurred to other people; I'm
> asking because I
> can't
> solve it myself.

Interesting thought.  In the particular case in question, I think the whole
situation is flip-flopped.  I think the failure of resolution of the PE vs
PG question (which dominated a LOT of my classes as an undergraduate and
graduate, far more so than systematics) is that to effectively test models
of these two questions you need well-supported phylogenetic trees.  Even
better, to test some of the particular models you would need to account for
*all* the taxa within these trees.  Unfortunately, relatively few clades of
fossil invertebrates have been subjected to explicit phylogenetic analysis
at present, although some groups are getting addressed.  Within ten to
twenty years, I expect that enough of the relevant speciose and
individually-abundant taxa will be sorted out so that we can go back and
address many of the questions raised by Eldredge and Gould and Stanley and
company.  (Okay, some sooner than others).

> On the other hand, looking within arguments for ambiguities, unnoted
> assumptions, and arbitrariness is welcome.

As it is in other disciplines as well!

> Finally, you observe:
> <And this is where the difference between Platonic and Darwinian
> models come
> into play.  Platonic models of life says "the type is real;
> variations from
> the type represent oddities".  The Darwinian model says "the type
> is a human
> construct; variations (both within species and down along
> lineages, bringing
> with them their historical baggage) are the reality".>
> But you also said:
> <If you were drawing a "typical" dinosaur (whatever that means), go with
> scales.>

Notice the "whatever that means".

> In that sense, aren't feathers an 'oddity' among dinosaurs?

In precisely the same way that brow horns are an oddity among dinosaurs,
yes.  In precisely the same way that plates are, yes.  In precisely the same
way that a backwards-pointing pubis is, yes.

> And if there weren't strong similarities within lineages, wouldn't
> cladistics, etc. be
> impossible?  In fact, that consistency is the basis for your point about
> feathered
> velociraptors.
> Not disagreeing with the basic point about not being blinded by
> archetypes,
> but
> isn't it a bit hyperbolic to denigrate the degree of consistency?

No, it ISN'T hyperbolic, as seen in the (what I thought was a kind of
clever) example I gave last time: that is, if you were drawing a "typical"
mammal, you draw the hindlegs.  However, if drawing a "typical" baleen
whales, you better leave them off!  That is, evolution happens: what is
"typical" of a clade at one level of inclusiveness may not be "typical" at
another.

> Thanks for slogging through this lengthy explication and responding to my
> questions!

Hope this helps.

P.S. For anyone whose slogged through the bottom, if you are getting
unwanted messages from someone whose putting you on an "invisible Bcc:" you
might want to think about putting that individual on your "kill file".  I
myself do not use a kill file, but I realize that some people have objected
to being part of a mass mailing which is not part of this list.

                Thomas R. Holtz, Jr.
                Vertebrate Paleontologist
Department of Geology           Director, Earth, Life & Time Program
University of Maryland          College Park Scholars
                College Park, MD  20742
http://www.geol.umd.edu/~tholtz/tholtz.htm
http://www.geol.umd.edu/~jmerck/eltsite
Phone:  301-405-4084    Email:  tholtz@geol.umd.edu
Fax (Geol):  301-314-9661       Fax (CPS-ELT): 301-405-0796