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

Sat Apr 7 12:30:35 CDT 2018

I cannot find the macro key that I once I used to list 20 reasons why cladistics, phylogenetics, and molecular systematics were a scam, a grift, and a shuck, respectively. Read my books (available for cheap on Amazon) which explain in detail the above, with diagrams, aphorisms, copious bulleted lists, worked out examples, and interesting descriptive verbiage.

I think a cladist is a person who seeks to substitute a dichotomous tree for an evolutionary tree because that person l o v e s his or her computer, which only burps up dichotomous trees. Multifurcations are as cursed as is paraphyly.  Evolutionary theory be damned.

-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Kenneth Kinman
Sent: Saturday, April 7, 2018 7:24 AM
To: taxacom <taxacom at mailman.nhm.ku.edu>; Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Subject: Re: [Taxacom] A Cladist is a systematist who seeks a natural classification

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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