[Taxacom] A Cladist is a systematist who seeks a natural classification
Stephen Thorpe
stephen_thorpe at yahoo.co.nz
Sat Apr 7 22:27:09 CDT 2018
Elena,
That really isn't the point. The point is that too many phylogenetists go on to say something along the lines of "the results of the phylogenetic analysis indicate that X is paraphyletic wrt Y, so we hereby synonymise X=Y". This makes little sense if the results of the phylogenetic analysis are merely a hypothesis.
Stephen
--------------------------------------------
On Sun, 8/4/18, Elena Kupriyanova <Elena.Kupriyanova at austmus.gov.au> wrote:
Subject: RE: [Taxacom] A Cladist is a systematist who seeks a natural classification
To: "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>, "taxacom" <taxacom at mailman.nhm.ku.edu>, "Kenneth Kinman" <kinman at hotmail.com>
Received: Sunday, 8 April, 2018, 12:57 PM
Therefore, what advantage does
cladistics/phylogenetic analysis have over any other method
for generating hypothesis, such as "taxonomic intuition"?
Sorry, I would really love to know what
these other methods for generating hypotheses, other than
cladistics/phylogenetic analysis and "taxonomic
intuition" are
Dr. Elena Kupriyanova
Senior Research Scientist
Marine Invertebrates
Associate Editor,
Records of the Australian Museum
Australian Museum Research Institute
1 William Street Sydney NSW 2010
Australia
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-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
On Behalf Of Stephen Thorpe
Sent: Sunday, 8 April 2018 7:04 AM
To: taxacom <taxacom at mailman.nhm.ku.edu>;
Stephen Thorpe <stephen_thorpe at yahoo.co.nz>;
Kenneth Kinman <kinman at hotmail.com>
Subject: Re: [Taxacom] A Cladist is a
systematist who seeks a natural classification
Ken said: "there is no problem with
cladistic analysis as an hypothesis generator"
Actually, I think that there is a
problem. A method for generating hypotheses does just that,
i.e. generates hypotheses, and nothing more. Now, it doesn't
actually matter where a hypothesis comes from (i.e. it
doesn't matter how it is generated). The (only) value of any
hypothesis lies in subsequent testing. Therefore, what
advantage does cladistics/phylogenetic analysis have over
any other method for generating hypothesis, such as
"taxonomic intuition"?
Stephen
--------------------------------------------
On Sun, 8/4/18, Kenneth Kinman <kinman at hotmail.com>
wrote:
Subject: Re: [Taxacom] A Cladist is a
systematist who seeks anaturalclassification
To: "taxacom" <taxacom at mailman.nhm.ku.edu>,
"Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>
Received: Sunday, 8 April, 2018, 1:23
AM
Hi all,
There is
no problem with cladistic analysis as
an hypothesis generator. The problem is that
phylogenetic systematists only formally recognize taxa
which are clades. By branding paraphyletic taxa
as unnatural
and refusing to recognize any of
them, they often fail to put in the added work of
incorporating divergence information into their
classifications when it would make them more stable
and usable (as advocated by Mayr, Ashlock,
Cavalier-Smith, and other evolutionary
systematists).
This is
especially true of higher taxa
(families to kingdoms). It is therefore no
surprise that it is at the level of Kingdoms, Phyla,
and Classes that the debate between evolutionary
systematists and phylogenetic
systematists is most
heated. Phylogenetic systematists have too often
generated instability at those levels, and thus
severely affecting usability.
That is
why Ernst Mayr called them
cladifications (not classifications). At the
level of species and genera, cladifications often turn
out to be good classifications, but the same is too
often not true at higher
taxonomic levels. The
worst case is the Three Domain cladification which was
(and continues to be) horribly simplistic. It is
people like Cavalier-Smith who is putting in the hard
work of attempting to construct more natural, stable,
and usable classifications.
--------------Ken
From: Taxacom
<taxacom-bounces at mailman.nhm.ku.edu>
on behalf of Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Sent: Saturday, April 7, 2018 1:01 AM
To: taxacom; John Grehan
Subject: Re: [Taxacom] A Cladist is a
systematist who seeks a natural classification
The issue
that I still haven't been able to get
a clear answer to is whether cladistics is just a way
of generating hypotheses for future testing (which, as
we all know, is ongoing and never conclusive), or
whether it somehow generates
something which can be more or
less thought of as a "fact", i.e. something which is
at least more likely to be "true" than not. My own
suspicion is the former, i.e. just a hypothesis
generator, based on various assumptions (such a s
parsimony) and given values
of certain variables
(weightings, etc.) which may themselves be quite
subjective.
Stephen
--------------------------------------------
On Sat, 7/4/18, John Grehan <calabar.john at gmail.com>
wrote:
Subject: [Taxacom] A Cladist is
a systematist who seeks a natural
classification
To: "taxacom"
<taxacom at mailman.nhm.ku.edu>
Received: Saturday, 7 April,
2018, 6:10 PM
Since there are at various times
some strong
opinions on cladistics and on
natural classification I have
pasted
below the text of a recent
article
that might be of interest to
some (some
typos may have crept in during
the
copy/paste).
Biol Philos (2018) 33:10
https://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1007%2Fs10539-018-9621-7&data=02%7C01%7CElena.Kupriyanova%40austmus.gov.au%7Ca8296606ea304383f56608d59ccb0f99%7C6ee75868f5d64c8cb4cda3ddce30cfd6%7C0%7C1%7C636587318368915357&sdata=y%2B6CxsAe2d11lHup48VafBHkoDbW6ffkpe3lGDkxcNQ%3D&reserved=0
David M. Williams & Malte C.
Ebach
A Cladist is a systematist who
seeks a
natural classifcation: some
comments
on Quinn (2017)
Abstract. In response to Quinn
(Biol
Philos, 2017.
https://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1007%2Fs1053&data=02%7C01%7CElena.Kupriyanova%40austmus.gov.au%7Ca8296606ea304383f56608d59ccb0f99%7C6ee75868f5d64c8cb4cda3ddce30cfd6%7C0%7C1%7C636587318368915357&sdata=%2FVgLke31Lm48sIrfxwLaU9%2BCuCX5Pul5125joI3eTgg%3D&reserved=0
9-017-9577-z) we identify
cladistics to
be about natural
classifications
and their
discovery and thereby propose to
add an
eighth cladistic defnition to
Quinn’s list,
namely the systematist who seeks
to
discover natural
classifications,
regardless of their
affiliation,
theoretical or methodological
justifications.
Derived from various
permutations of
phylogeny, biology, philosophy,
methodology, sociology, loyalty
etc.,
Aleta Quinn recently proposed
“seven
specific definitions that
capture
distinct contemporary uses” of
cladistics
(Quinn 2017, p. 1). Our own
efforts,
based on the same criteria,
yielded a
further seven, which we do not
intend
to bore our readers with here.
We are
sure more could be found and
more
people could be found who
subscribe/correspond to them.
Suffice
to say, one might find
definitions
for anything—and in any case,
Quinn
was clear about her motives:“I
do not
intend to classify individuals,
ideas,
or research programs. Rather, I
clarify distinct things that
speakers
mean by the term
‘cladist’” (Quinn
2017, p. 1). Depending on
one’s
outlook—philosopher,
historian, biologist,
even sociologist (Hull
1988)—the
definitions might help progress
their
subject. As biologists, we found
much
to think about but rather than
dissecting the minutiae, we seek
to
clarify by attempting to
simplify.
We need first to dispense with
one
misconception. Quinn draws upon
a
commonly preconceived notion,
namely
that systematics requires
evolution as
a prior condition:1
“What that theoretical
foundation may
have been [in reference to de
Candolle’s
view on characters] is not
relevant to
my points about contemporary
systematics,
whose conceptual framework
presupposes
the concept of evolution”
(Quinn
2017, footnote 11).
Consider the concept of a
cladogram,
which everyone might agree is a
branching diagram commonly
included as
part of the results of a
cladistic
analysis. One might derive from
this
diagram which taxon is more
closely
related to itself than to any
other.
One might explain this
relationship by
common descent. The cladogram,
however,
need not be constructed with
any
evolutionary assumptions in
mind;
rather, the evolutionary
assumptions
serve to explain why one taxon
is more
closely related to itself than
any
other.
The search for a natural
classifcation
was established prior to the
adoption of
any theory of evolution. In
fact
Augustin P. de Candolle’s had
a great deal
to say
on the matter, especially the
differences between natural and
artificial
classifications (Candolle 1913).
But de
Candolle was working some time
ago,
so what, if anything, might be
his
relevance today? Methods of
systematics
change as time passes. But all
methods
fnd cladograms, in the sense
that
the results yield sets of
relationships, either as a
branching diagram or
as a written classification.
Regardless
of method, which of these
relationships might be
considered to
reflect something that actually
exists, rather than a product
(an
artefact) of the method? How can
any
method achieve that without
knowing the
answer beforehand? Obviously it
can’t. One might play around
with
simulation studies to judge the
performance of any suite of
methods, or
one might delve into philosophy
to
create justification, but in the
court
of last resort all that remains
are
sets of cladograms that either
agree or
disagree to a greater or lesser
extent in terms of common
relationships
found. That is, they agree in
the
cladistic parameter, the
relationships
specified—that the signal to
noise
ratio is working in our favour,
as is
evident from classifications of
the
past. Here we might argue that
natural
classification is the result
derived
from several cladograms,
regardless as
to how they were arrived at;
artificial classifications are
derived
from a specific method, be that
Wagner parsimony, UPGMA,
maximum
likelihood and so on, or from a
specific
source of data (DNA,
ultrastructure, etc.), and so
on. Why are these
artificial? Because a method,
any
method, assumes the results that
are
required (the shortest tree; or
the
most similar taxa grouped
together; or
the most similar taxa grouped
together
via a weighted model of
character
change, etc.); for a data
source, they
assume those data are
privileged
over other data (DNA must be the
source
of ‘true’ relationships,
etc.).
Cladistics, in its most general
sense,
does not associate with any one
method, or any one data source.
It
applies to sets of
relationships—it is
the set of relationships. This
is
effectively what de Candolle
argued for,
and has been the basis of
systematics
for decades, if not centuries:
“For the last 50 years
and
more—even now continuing into
the realm of
nomenclature—in the name of
the
modern and the new, Visionaries
aim, as
it were, to confine the past to
a
dustbin of history, and to bolt
and lock
the
lid upon it. As if without it,
we be in
some way better, even born
again
more
whole-some; as if Carl Linnaeus
really
were among the last of the
Ancients,
and not, rightly, the first of
the
moderns, and so related to
us—of a group
inclusive of us” (Annual
Review of
the Linnean Society, 2001).
These words, not readily
accessible,
were spoken by Gareth Nelson
after
receiving the Linnean Gold Medal
and
re-cast above as part of the
2001
Annual Review of the Linnean
Society,
London. Linnaeus as the first of
the
moderns? Among other matters,
Linnaeus
spoke of the differences
between
artificial and natural
classification,
a subject taken up and developed
by
de Candolle (1913). One might
cast that
debate in very simple terms:
artificial classifications are
found by
imposition, natural
classification
is discovered. Imposition
implies some
method or motivation to erect a
particular classification, such
as a
field guide or handbook for
identifying specimens—today it
is
more likely those would be
websites, or
online interactive guides. There
is
nothing wrong with artificial
classifications. We both use
them all
the time, almost every day (
https://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.trilobites.info%2F&data=02%7C01%7CElena.Kupriyanova%40austmus.gov.au%7Ca8296606ea304383f56608d59ccb0f99%7C6ee75868f5d64c8cb4cda3ddce30cfd6%7C0%7C1%7C636587318368915357&sdata=U8%2BPeMIgalve2cDuEoerguLRMisn6iiK5M%2FuoBGoeFU%3D&reserved=0;
https://apac01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fnaturalhistory.museumwales.ac.uk%2Fdiatoms%2F&data=02%7C01%7CElena.Kupriyanova%40austmus.gov.au%7Ca8296606ea304383f56608d59ccb0f99%7C6ee75868f5d64c8cb4cda3ddce30cfd6%7C0%7C1%7C636587318368915357&sdata=b9qbuc4IMI1W9%2FUYuDgO6DE1yCez%2Bo5dq%2BPkUA0TZ2I%3D&reserved=0).
But
whatever merits they
have, and there are many, they
are created by acts of
imposition. We
ask our readers, then, if they
would
consider analysis of some data
with one
or another statistical program,
or
with one or another parsimony
program,
or with one or another phenetic
program, whether this is an act
of
imposition or an act of
discovery? We
see it as an act of imposition.
How
could it be otherwise?
Cladistics,
then, is about discovery, about
finding
repeating patterns,finding the
same
relationships, finding
relationships
that are not method dependent,
finding
relationships that are
reflections of
the world as it is:
“What, then, of cladistics in
relation to the history of
systematics? If
cladistics
is merely a restatement of the
principles of natural
classifcation, why has
cladistics been the subject of
argument? I suspect that the
argument is
largely
misplaced, and that the
misplacement
stems, as de Candolle suggests,
from
confounding the goals of
artifcial and
natural systems” (Nelson 1979,
p.
20).
For us, cladistics is about
natural
classifcations and their
discovery, an
activity
that occurs with or without
“knowledge of process”. Look
in museums,
herbaria,
universities and other
institutions
that still hire systematists and
you
will see:
Cladist (viii): A cladist is a
systematist who seeks to
discover natural
classifications.
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