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Re: Princeton Field Guide



A fun conversation here, even if it’s edging further into the philosophical.

David said:

        “I think the real problem is Linnaean nomenclature, which requires us
to shoehorn every organism into a species (and a genus) if we are to
put it into any kind of system at all.

If we ignore this requirement, and the PhyloCode will let us,
everything suddenly looks a lot different. For instance, "phylogenetic
species" turns out to be just a synonym of LITU (Least Inclusive
Taxonomic Unit = smallest recognizable clade; a term not used by the
PhyloCode, but fully compatible with it). Why use the separate term
"species" for it? There is no reason.”

I think there’s a lot of historical and cultural precedence for the
mere use of the term, as long as the definition is clear. Again: as
long as the definition is clear. And practicable in the field. “LITU”
won’t fly with an already science-illiterate public, either, so we
have to have some flexibility in our options. I’m OK with that.


        “Other species concepts, too, describe real entities. If you're
interested in gene flow between populations, the good old Biological
Species Concepts (both of them*) describe useful entities (ring
species included), laborious as they are to discover; they're just
often not congruent with ecological species, morphological species, or
phylogenetic species. All these concepts have nothing in common except
the _word_ "species". _There is no_ Platonic ideal of "species" that
these concepts approach, as so many people still seem to think.”

That’s exactly what I was getting at, actually. ;)

My point was that, with the phylogenetic species concept at the very
least, a pretty much airtight definition can be devised, one that
permits no fuzzy exceptions and which in principle applies equally
well to (essentially) all organisms. But that definition is so hard to
apply *in practice* to so many fields of biology (like ecology,
bacteriology, etc, as you imply) that it has virtually no use other
than in the abstract sense. This is of course largely because we can’t
identify in our limited time on Earth whether two modern populations
are truly on distinct and final evolutionary trajectories. So while
the exceptions may not be fuzzy in principle, they can’t be
distinguished in practice.


        “There is a definition of "genus". It's an extrapolation of the
Biological Species Concepts: if they (can) have fertile offspring,
they're in the same species; if they (can) have sterile offspring,
they're different species in the same genus; if they can't have
offspring at all, they're in different genera.

Unsurprisingly, almost nobody has ever tried to use this definition.
Like the BSC, it's impossible to use for anything but extant sexually
reproducing organisms, and very difficult in practice to apply even to
those; like the BSC, it would trigger a lot of lumping, in some cases
to the point that several traditional subfamilies would have to be
merged into a single genus; and in addition to ring species, we'd get
sphere genera.”

Following from my statement, this is the sort of thing that I mean by
not being able to define “genus” in a way that is logically sound. The
“definition” you mention fails not only for the important practical
reasons you describe, but also because it does not account for
anagenetic lineages (in which descendant would eventually be incapable
of reproducing with ancestor, due to genetic distance), horizontal
gene transfer, and the question of knowing when in the fossil record
genetic distance or other factors resulted in one genus splitting in
two.

More damning, all evolutionary lineages are part of a continuum that
(generally) branches forward in time and (generally) flows together
backward in time, and aside from divergence events, there is no kind
or degree of change that allows us to separate one portion of the
continuum from adjacent portions which is not also completely
arbitrary. Saying that one biological trait/suite of traits
(reproductive ability) defines a genus is ultimately no better than
saying any one other behavioral, physiological, or morphological
trait/suite of traits defines a genus, because no biological traits
have inherently greater or lesser value than other biological traits –
only greater or lesser value for subjective goals.

But I think we’re in broad agreement here.


        “The _name_ of the clade in question does this, not the _rank_ of
genus (or any other rank).”

Right, and by “genus” I meant an assemblage of names in the literature
that follow a specific formatting convention, not “genus” in any
metaphysical sense. Sorry for the confusion.


        “Problem is, there is no consensus, and the ICZN doesn't even try to 
help:”

Yeah, that was a rhetorical “*if* we agree” sort of statement.
Basically, I was saying that content in genera is subjective any way
you cut it, and that’s OK as long as everyone knows what’s being
talked about, because consensus aids stability in such a scenario.
That’s the matter in principle; obviously in practice it’s none too
clear.


        “Anyone can publish a classification that assigns however many
species to any genus as they damn well please. And then anyone else
can come along and publish a classification that contradicts it. And
to all eternity both are correct, and neither is wrong, provided they
keep the type species in their genera and obey priority.

(...Never mind that the mandatory suffixes for family-group ranks and
the mandatory formats for genus-group and species-group names
contradict Principle 2 rather blatantly.)

So, if I say "*Bufo*", do I mean the mid-20th-century *Bufo* which
includes all hundreds of bufonids that aren't too weird, or the much,
much smaller Frost et al. (2006) concept of *Bufo* which is limited to
a couple of Eurasian species, so that the cane toad is *Rhinella
marina*? The name alone doesn't tell you, and neither does the
(unchanged) genus rank of that name.”

Yep, which was my point about making definite claims from indefinite
concepts. People can bicker all day about content, but the underlying
reality does not change - and nomenclature should, as much as is
reasonable for the human mind, reflect that underlying reality.


        “We don't even need to agree. It's enough that the ICZN lets us.”

Regardless one way or the other of the ICZN’s relevance, I’m talking
about the utility of concepts to science, here or anywhere, for now
and forever, not what is or isn’t demanded by any particular human
institution.


        “There isn't a standard in the first place.”

There’s broad agreement, at this time in history and in those
particular sets of researchers, that the degree to which Greg lumped
species into single genera was unwarranted. Otherwise few would have
complaints worth responding to and he himself wouldn’t feel the need
to pressure the community to follow his lead.

That’s all I meant, not that there was anything formal and published
regarding supposed standards. A sociological commentary, if you will.


        “That consensus consists only of which species to include in which
genera of Mesozoic dinosaurs. There's not much, if any, of a general
concept behind it.”

See above. “Mesozoic dinosaurs” is what the book was published on, and
it’s all I’m discussing insofar as Greg’s involvement/primary
grievances are concerned.

The broader discussion is meant simply to clear the waters regarding
dinosaurs, but of course they aren’t the only organisms to which the
discussion inherently applies.


        “Really?”

In principle. I’m talking about definitions as sets of real
relationships that can by their nature be known and described, which
admittedly can be confused with the idea of definitions as human
*attempts* to describe those relationships. Things that do not have
relationships which can be empirically known and described have to be
either supernatural or nonexistent, and either way, they’re not too
relevant to science.

So yes, in my usage of the term, everything has a definition. Given
the size and complexity of the universe, we just don’t know what most
of them are.

(And math is the ultimate language by which all empirical phenomena
can *be* defined in four-dimensional spacetime. We just can’t apply it
on the scale or with the precision to do so, even though it’s possible
in principle.)


        “It's a continuum that our languages fail to express. Therefore,
where in the continuum we decide to draw the line is completely
subjective. Are viruses living beings? Depends on how we choose to
define "life". :-| If we want viruses to count as "alive", we'll
likely define "life" along criteria of information; if we don't want
them to count, we'll likely use things like independent metabolism as
defining. It's up to us.”

Right. And that sort of specifying the intent of the word is exactly
what I meant by “unloading” it first. Both definitions are also, as I
implied, what I consider “reasonable.” That is, since words have no
fixed meaning, their application is inherently incidental and/or
arbitrary, so “life” can be applied to a concept just as rationally as
any other word can apply to a concept. Choosing which concept to which
to apply the word is ultimately subjective, but as long as the word
conveys useful information, we can communicate meaningfully.

Incidentally, since we’re not talking about evolutionary change but
simply physiological structures, the existence of something like an
independent metabolism is in fact potentially relevant and useful in
devising a working definition, just as much as the form of limbs a
creature has defines its mode of locomotion or the type of teeth it
has defines its mode of feeding. Reproduction of information and
metabolism are both important concepts, so I’m not advocating one way
or another, but it’s a different kind of “continuum” than in
evolutionary lineages (more like a stepwise function, perhaps).


        “You are, thus, saying that, "philosophically, there's no such thing 
as" life.

I'm fine with that.”

Actually, what I was saying boils down to “A rose by any other name
would smell as sweet.”

Reality is what it is; phenomena are what they are. What we call them
doesn’t change that. The terms we apply to them are arbitrary – guided
by an intent to clarify through categorization, but arbitrary in and
of themselves. Human perception is at best an imperfect representation
of reality, so when I say “there’s no such thing as a battlecruiser,”
I mean there is no physical entity that actually *is* truly what any
given human mind perceives it to be.

Since perception is subjective, human minds only have definite access
to 1) sensory perceptions, which at best are imperfect translators of
reality, and 2) concepts, which don’t rely on purely sensory
perception to experience, and can exist independent of said, but which
have even less of a guarantee to actually reflect reality. Humans, in
their subjective nature, therefore only have access to 1) unfiltered,
unassigned, raw sensory data for those physical components of the
environment which we label “battlecruisers,” and 2) concepts of what a
battlecruiser *is supposed by the observer to be,* according to their
internal processing of the sensory data. No access exists to the
physical reality itself, assuming such even exists in the conventional
sense, so by default we’re talking about concepts. Concepts
incorporate interpretations of significance or the lack thereof;
physical phenomena do not.

My point, thus, was that – while battlecruisers exist as a concept –
the concept is not itself a material entity, and therefore does not
exist external to the mind. The thing that exists external to the mind
(I hope) can be referred to as a “battlecruiser” if we like, but we
are then using the concept as an imperfect stand-in; it is not the
empirical thing itself, which at best can be experienced only through
the senses.

So while I’m not a solipsist, that’s mostly because parsimony suggests
it’s a bad idea. ;p

(There’s some quote from a reasonably well-known ?19th-century
?geologist about the assumptions behind science being self-defeating,
and I recall it being admitted by philosophers to be unassailable by
logic despite the obvious success of science, but I cannot for the
life of me remember the exact quote or who said it. If anyone knows,
please, e-mail me.)


        “Phylogenetic nomenclature escapes this by using objectively
discoverable events to define clade names. Rank-based nomenclature
doesn't even try.

That's because rank-based nomenclature is deliberately theory-free.
Both Charles Darwin and Richard Owen, together with many others, are
among the authors of the 1842/3 Strickland code of zoological
nomenclature, so it's a worst-of-all-worlds compromise. It treats
organisms as battleships, battle cruisers and heavy cruisers.
Phylogenetic nomenclature, on the other hand, assumes evolution and
uses tree-thinking; this makes everything easier.”

Yes. And the formal need for “genus” as a distinct clade format falls
by the wayside as well . . . the point we’ve both been making in this
discussion.

No substantive disagreement here, I think . . . cheers. :D