meanderings, riparian and philosophic

Richard Pyle deepreef at BISHOPMUSEUM.ORG
Mon Apr 5 23:07:44 CDT 2004

Curtis Clark wrote:

> Maybe. Dealing with lineages often requires inference, because we
> can never
> observe all the matings. A lineage split would result from members of two
> groups of potential parents never mating with one another. A
> consequence of
> this is that the distribution of homologies fits a tree better
> than it fits
> a network.

We seem to agree on a bunch of stuff, and where we disagree, I think we're
approaching mutual understanding. So this time, my responses are more

> I'll get metaphysical here...Linnaeus (for example) is physically
> dead, and
> never visited California, but in a sense he is here now. My point being
> that discreteness is often a fruitless thing to characterize, since it
> doesn't really address what's important. I suspect that our
> overemphasis on
> being discrete relates to our ability to "recognize individuals", which is
> a consequence of our being behaviorally complex social organisms.

Hmmm...not sure I follow. Sea slugs aren't particularly complex social
organisms, but they do somehow recognize and reproduce, and I can (usually)
see the discrete boundary between where the sea slug ends and the external
water begins. Linnaeus, as a person, was a discrete physical entity.  When
he died, many of his molecules disperesed via entropy (some of those
molecules may very well have ended up in California). None of them really
remained within the physical boundaries of his person; and so he, as a
discrete entity, ceased to exist not long after his corpse began to wither.
His ideas, and portions of his genome, on the other hand, may indeed
continue to perpetuate.

> But why does it matter, except to our ability to define boundaries?

I guess it matters because we sometimes fall into the trap of defining
discrete boundaries on entities which are not conducive to such definitions
(e.g., populations and taxa).  If we think of those sorts of entities in
ways that do not acknowledge their "fuzziness", we may be drawn towards
conclusions that lack merit under close scrutiny.

> It's the same as expert taxonomic opinion, but differs from "expert
> taxonomic opinion". The former is substantiated with data, the latter with
> authority.

I'll have to digest that one a bit more.

> >Well....I think we have our heads around the periodic table pretty well.
> And fortunately it seems to be the same now as it has been since a week or
> so after the Big Bang.

And I imagine that the phylogenetic relationships among extant organisms is
essentially the same now as it will be 30 years hence.  I'm just saying that
we'll probably understand it with much greater confidence then, than we do
now.  As for the generation of taxonomists a million years from
now....well...I suspect that will be well outside the range of my own
professional career.

> I agree totally. To me, the whole point is to craft elegant testable
> hypothesis that have no ego-investment at all, and then test them to
> destruction.

Sounds good to me.

>From another post in this thread:

> At 21:14 2004-04-05, Ken Kinman wrote:
> >I'm sure the chimpanzee genome will come first with a lot of fanfare, but
> >doubts will remain until orangutan whole genomes are available.
> Doubts will continue until there is an outgroup genome....

Indeed, doubts will continue until we've achieved the level of "intellectual
fortitude" (I just love that expression!) to fully extract the information
contained within those genomes....


And finally, on the other thread:

> What about water molecules that evaporate from one watershed and
> precipitate on another? Or that enter the water table and flow as springs
> into another? These are common occurrences.

I actually was going to use that exact point as a cross-analogy to lateral
gene flow, but I was spending too much time on Taxacom this morning, so
decided not to go there.  But my overall point has more to do with tracking
the path of something physical (like water molecules), compared with
tracking the path of something intangible (like information).

> I think "intangible" is here a value judgement. Sure, we can't physically
> touch it, but there are a lot of things we can't physically touch.

O.K., maybe "intangible" is too strong a word.  But genetic information is
certainly less tangible than water molecules, and therefore less trackable
(and, indeed, less "discrete").


Richard L. Pyle, PhD
Ichthyology, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at

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