[Taxacom] Was Reproducibility of phylogenetic analysis

Richard Pyle deepreef at bishopmuseum.org
Wed Jan 27 15:34:16 CST 2010

Mike Ivie wrote:

> Historically, much of this series of arguments was rooted in 
> an insecurity as other areas of study became more obviously 
> and clearly "scientific"
> after the development of statistics, leaving the historically 
> progressive taxonomy/systematics/phylogenetics field to worry 
> if we got the respect we thought we deserved.
> I struggle with this all the time


I gave up that struggle when I was in my teens.  I made the decision to
follow the path of taxonomy not so much because I loved the idea of being a
scientist (I did then, and still do); but because I loved (and still love)
the idea of being a naturalist.

> How is exploratory discovery framed properly as good science?
> Any (positive) suggestions would be greatly appreciated,

I am increasingly convinced that the study of biodiversity is far and away
the most important endeavor in the history of humanity, certainly until now,
and very possibly into the future as well.  I say this not as a
self-proclaimed naturalist, but as someone who thinks objectively.  Future
humans will always be able to study physics and geology and chemistry.  But
what they won't necessarily always be able to study is history.  As we know
from our feeble attempts to interpret phylogenetic patterns among taxa (and
as is also well known by archaeologists and all other manner of historians),
the ability to infer history is highly dependant on the information that
transcends time.  The more of that information that is obliterated
(extinctions without fossilizations, grave robbers and other destruction of
archaeological sites, the burning of the Library of Alexandria, etc.), the
harder it is to reconstruct history with confidence.

So...what is the value of reconstructing history?  Well...there are the
obvious reasons, of course.  But whereas conventional history reaches back
over a few thousand years, and archaeology reaches back maybe a few tens of
thousands of years (or perhaps even a few hundreds of thousands of years),
evolutionary history spans some four BILLION years.  Human history, of
course, appears (at first glance) to be much more relevant to the current
and future well-being of humanity.  The stuff of past civilizations and
politics will certainly help guide us in our future efforts, so it seems as
though those thousands of years of human history trump the billions of years
of evolutionary history.  But this is very narrow-minded thinking, blinded
by anthropocentrism (there....I used an "ism" word, so now I'm a bona-fide
philosopher...)  We only assume this higher relevance because we are more
skilled at deciphering the threads of information available to us.  It's
analogous to a scholar who thinks that the only important poetry worth
reading is that which is written in the English Language, because English
happens to be the only language the scholar understands. Politicians come
and go. Countries come and go. Civilizations come and go. The human species
came, and will go.  But biodiversity spans almost the full scope of this
rock we live on (both in space, and in time).

We are at a major inflection point in human history because we are now,
finally, just beginning to grasp the basic aspects of the language of
genomics (and derivatives like proteinomics).  This is important, because
the largest library of information that will ever exist in this solar system
(maybe in this entire region of the galaxy) is largely written in this
language (it's also written in the way organisms interact with each other
and form ecosystems).  The information contained in this library is much,
MUCH more valuable to humanity than the historical insights it may give us
about evolutionary history.  Sure, that stuff is cool to us (we loves the
cladograms; especially the ones we have reason to be confident in).  But for
the rest of the (non-nerd) scope of humanity, it's the *practical*
information contained in that library that is of greatest value (especially
to those humans living a few decades to a few centuries from now, who will
actually know how to put it to practical use).  We can already guess at what
some of this practical information relates to (e.g., highly efficient solar
energy capture, highly precise and diversely useful nanotechnology; not to
mention the vast world of ecosystem services, etc., etc.)  But we probably
haven't even yet imagined the most valuable stuff buried in that library --
stuff we will only be able to fathom after we get past the "see spot run"
stage of our ability to read and interpret the information (and the crude
metrics of community ecology that we've had at our disposal so far).

And, of course, as we all know, the biodiversity library is burning.  If
what I read in the latest issue of Popular Science is reasonably accurate,
we destroy all copies of some 30,000 volumes in this library every year.
All that information, some fraction of it undoubtedly very valuable to
humanity and not written elsewhere in the library, gone forever.  One more
scroll from the Library of Alexandria that no future human will ever even
know existed, let alone have a chance to read and understand.  To most
people, this warrants little more than a shrug of the shoulders -- in much
the same way that a young child might shrug his or her shoulders when told
that the last copy of Homer's the Odyssey, or the Origin of Species, or
General Relativity, or the complete works of Shakespeare, or any of the
major religious tomes were destroyed and lost forever. We would look at such
a child as though they were incredibly naïve, in much the same way that
humans 100 years from now will look upon us as we try to justify the study
of biodiversity only in terms of what's important to a taxonomist.

So....to (finally) address Mike's question: "How is exploratory discovery
framed properly as good science?" When we do taxonomy and systematics, we
are doing much, much more than "good science". We are building the card
catalog for the most important library that has ever existed, and ever will
exist (at least from the perspective of humans). Taxonomy generates the
cards, and systematics organizes them in a useful way.  When we stomp
through the forests and swim over the reefs collecting our specimens, we are
gathering a few precious copies of those books and storing them in the
vaults of our natural history museums where (with luck and funding), the
information they contain will persist beyond the time when no more copies
exist in nature. Unlike physics; unlike chemistry; unlike geology; the clock
is ticking on our ability to capture this information before it's gone.

As Chris Thompson would say: "Oh, well...." (not sure if that counts as


P.S. Yes, I know this is a very long message.  And yes I know there are
people on this list to whom I owe things (I'm looking at you, Donat, Neal,
and many others).  Consider this my announcement that I have finally emerged
victorious from a two-month battle with my laptop, Windows 7, and our new
email server at the Museum.  It was a long, hard-fought war; and now I have
a mountain of backlog email to deal with.  But at least now I can actually
start dealing with it.

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