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On science (phew, long)

Hi folks--
        I worry enough about the state of science education when my
undergrad biology students can't explain what a hypothesis is, but some of
the recent comments on science really get me concerned. I'm not sure if
people are taking time to think about what they're saying, or just spouting
out stuff, or maybe they're preoccupied while writing. I think some folks
should look at the bigger picture; step back from the dinosaurs and
cladistics for a second and think about science. However, for those who
can't leave dinosaurs behind for a second, I'll relate my comments to
dinosaurs where possible.

1) On truth: If the pursuit of an unattainable truth is irrational, then I
guess we might as well stop looking for fossils or cures for diseases,
studying the stars, or never try to do anything that is difficult.  We know
the fossil record is imperfect, yet we still keep looking.   A different
analogy: if your goal in life was to have all the money in the world, would
you rather have a billion bucks, or give up and have nothing?

2) On common sense:  I'd hate to live in a world where scientists proceeded
solely by common sense and without methodology, especially empiricism.
Should medical researchers just go by gut feelings in searching for medical
solutions?  Should the criminal justice system just let one guy's "common
sense" determine the fate of another?  Or do we need a methodological
structure?  Karl Popper may be dead and gone, but empiricism is a
fundamental component of scientific research.  Deal with it.  Keeping a
dewey decimal system of dinosaur genera is fine and dandy, but some folks
are interested in a broader picture than pigeonholing and counting taxa.
Evolutionary biologists today use evolutionary hypotheses derived from
methods and evidence.  The preferred approach is to put all of the data on
the table and let others assess the results through peer review and
reproducibility tests.  Falsifiability is the reigning paradigm, and I hope
that never changes.

3) On straw men: Man, will people please stop committing such foul
attrocities on poor defenseless straw men?  The intellectual battlefield is
already littered with their corpses. Some of the features attributed on
this list to cladists are just plain wrong. I do not know of one cladist
who thinks that his ideas are "the truth", not subject to change, better
than any other possible result, etc.  I do not know of any cladist who has
ever said that cladistics is better than any possible methodology.  The
reason journals like cladistics exist is to refine, discuss, and review
methods.  Cladistics has changed a lot since Hennig, but many basic
concepts remain. Cladistics will change further. Specific phylogenetic
hypotheses will be further refined, thrown out, or generally accepted. It's
the way science works. If it frustrates you then you might look into
hobbies/careers other than science and dinosaurs. Just leave the straw men
        I'm still waiting to hear an argument that is original and
constructive, or hasn't been voiced by cladists already. We're really a
pretty self deprecating and skeptical bunch, despite a few abusive
personalities. Heck, a fellow cladist told me the other day that he thinks
everything he's done is bullshit. Why does he continue using cladistics?
Because he knows it's the best thing going so far. I don't see why others
get so uppity and confused about it. After all, it's just science; there's
more to life.

4) A personal note: It really bugs me when people set up cladists as being
closed minded louts. When I joined this list ~2 1/2 years ago, I didn't
consider myself a cladist (or any category like that). I was wary of it,
but didn't have any plans to conduct cladistic analyses. No one at Berkeley
ever told me that I had to use it. I was left to make that decision on my
own. After a while (including an ill-fated attempt at ceratosaur
phylogeny), I accepted it as the best methodology available for formulating
phylogenetic hypotheses. Phylogenetic taxonomy came along with it.
Personally, I see the two as inextricably tied, but opinions do vary on
that one.
        I don't plan on doing cladistic analyses in the near future, but
it's crystal clear to me that if you're going to talk about evolutionary
patterns, you'd damn well better have a phylogenetic framework at hand.
Again, that's the way science is today, and I don't see that changing
anytime soon. Cladistics and other methods of phylogeny reconstruction may
change, but the importance of polarity (especially outgroups), parsimony
(which, by the way, is not restricted to cladistics; it's a basic
scientific precept), and monophyletic groups (ever try to do a study of
taxonomic diversity through time including paraphyletic groups?) will
almost certainly remain.  I have no desire and see no need to tilt at
windmills. Iconoclasm has its merits, but it's a silly approach to adopt by

5) To the critics: Please be consistent in your comments. I keep hearing
people in one post say "cladistics is bunk," and in another "well, it's
often correct."
 I've seen this in the literature, too; one author recently said that
cladistics is the best methodology in evolutionary biology, and then went
on a chapter-long tirade about its inadequacies. Sure it's inadequate. I
think we all agree on that; it's not perfect. Again, deal with it. Science
isn't done in a day; you can be patient and thorough and maybe make a long
term impact, maybe get falsified, or you can be impatient and speculative
and later get hosed and look like a real doofus.

Sorry about the negativity; nothing personal but some of this recent
shadowboxing and grandstanding is just tiresome. If you made it this far in
this post, I guess it wasn't that tiresome for you. Me, I'm off to teach
students about DNA manipulation techniques and cytokinesis. Have a good,
scientifically stimulating day.

                        John R. Hutchinson
                 Department of Integrative Biology
                  3060 Valley Life Sciences Bldg.
                University of California - Berkeley
                     Berkeley, CA 94720 - 3140
                      Phone:  (510) 643-2109
                      Fax:    (510) 642-1822