[Taxacom] A Cladist is a systematist who seeks a natural classification
John Grehan
calabar.john at gmail.com
Sat Apr 7 17:47:59 CDT 2018
"And those that are likely to be the result of convergence given little or
no weight."
There is no empirical way to do that. It is voodoo systematics.
" cladists too often want to formally name their hypothetical taxa too
quickly."
interested to know published examples with some statistical basis for
cladists being "too often" as opposed to non cladistist.
"The problem is the sheer number of possible clades, with little risk if
one is wrong, and it can be difficult to resist the lure of getting to
choose the name and getting your own name attached to it."
This can be a problem for anyone, regardless of their systematics approach.
John Grehan
On Sat, Apr 7, 2018 at 5:58 PM, Kenneth Kinman <kinman at hotmail.com> wrote:
> Hi Stephen,
>
> Well, taxonomic intuition also plays a role. Especially in giving
> more weight to some characters than others. After an initial cladistic
> analysis which weighs all characters equally, further analyses should be
> done by weighting some characters over others. And those that are likely
> to be the result of convergence given little or no weight. You never know
> what might result from additional analyses (hopefully more and better
> synapomorphies).
>
>
> And I agree that cladists too often want to formally name their
> hypothetical taxa too quickly. But unfortunately the desire to be the
> first to do so causes many to jump the gun. But that is not a problem
> confined to phylogenetic systematists. The problem is the sheer number of
> possible clades, with little risk if one is wrong, and it can be difficult
> to resist the lure of getting to choose the name and getting your own name
> attached to it.
>
> ----------------Ken
>
>
> ________________________________
> From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> Sent: Saturday, April 7, 2018 4:03 PM
> To: taxacom; Stephen Thorpe; Kenneth Kinman
> 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 a natural
> classification
> 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://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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