[Taxacom] A Cladist is a systematist who seeks a natural classification

[Kenneth Kinman]

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://doi.org/10.1007/s10539-018-9621-7

 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://doi.org/10.1007/s1053
 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://www.trilobites.info/;
 http://naturalhistory.museumwales.ac.uk/diatoms/). 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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