Tuesday, December 16, 2008

Death throes of Cladistics

I'm in the US on UK time, so this is probably a bad idea to write this, but the paper by Malte Ebach et al. ("O Cladistics, Where Art Thou?", doi:10.1111/j.1096-0031.2008.00225.x) in the latest Cladistics just annoys me too much. Rather than the call to arms that the authors intend, I think they've provided one more example of the death throes of cladistics (in the narrow parsimony is all, statistical methods are evil, molecular systematics is phenetics, barcoding is killing taxonomy sense).
Associations, such as the Willi Hennig society, and journals, such as Cladistics, were erected in order to tackle the growing problem of pheneticists, purveyors of overall similarity, clustering and divergence rates. Rather than challenge molecular systematists and their numerical taxonomic methods, we take part. Where is our integrity?
Gosh, maybe people realised that molecular data are useful, that molecular data benefit from statistical analysis, and that divergence rates (and times) were of great biological interest? Fancy that!
What happened to the Cladistic Revolution? Today, students appear to have no knowledge of that Revolution. They graduate as students did so before the Revolution, with a sound knowledge of phenetics, ancestor worship and a healthy dose of molecular genetics. What happened to taxonomy and cladistics?
I suspect the real drivers in the "Revolution" were: the development methods that could be implemented in computer software (I include parsimony in this); computer hardware that was becoming cheaper and more powerful; and, the growth of molecular data (i.e., data that was easily digitised). I don't mean to imply that everything was technologically driven, but I suspect it was a combination of a desire to infer evolutionary trees coupled with plausible means of doing so that drove the "revolution", rather than any great conceptual framework.
Such matters as the Phylocode, DNA taxonomy and barcoding, for example, have risen to prominence despite criticism of their many flaws and illogical conclusions. The attempts of these applied technologies to derail almost 250 years of scholarship are barely even questioned by our own peers with only a few taking a stand (e.g., Will and Rubinoff, 2004; Wheeler, 2005).
Barcoding is happening, get over it. There are technical issues with its ability to identify "species", but to object to it on ideological grounds (as papers published in Cladistics tend to do) is ultimately futile. If the authors dealt with bacteria they wouldn't bat an eyelid. Besides, I suspect that the ability to identify organisms, or discover clusters of similar sequences will be among the least interesting applications of barcoding. There will be a wealth of standardised, geotagged data from across life around the planet. People not blinkered by ideology will do interesting things with these data.
Barcoding is understood as a ‘‘solution’’ (to what, one might ask?), systematics journals are infested with phenetics and population genetics (cladistics has vanished), both, seemingly, directing the course and future of taxonomy. Where are the scholars?
Personally I use the term "phenetics" as a litmus test. If anybody says that a method is "phenetic" then I pretty much switch off. Almost always, if somebody uses this term they simply don't understand what they are talking about. If you describe a method as "phenetic" then that tells me that you either don't understand the method, or you're too lazy to try and understand it.

In some ways all this saddens me. I was an undergraduate student around the time of the heyday of the New York school, thought Systematics and Biogeography: Cladistics and Vicariance was a great (if flawed) book (and I still do), and did my first post doc with Gary Nelson at the AMNH. It was a great time to be a student. Phylogenetic trees were appearing in all sorts of places, and systematists were tackling big topics such as biogeography, diversification, coevolution, and development. There was a sense of ambition, and excitement. Yet now it seems that Cladistics has become a venue for reactionary rants by people unable to break out of the comforting (but ultimately crippling) coherence of the hard-core cladist's world view.

11 comments:

UPS Power Solutions said...
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Frank Anderson said...

Absolutely. I came to the revolution late, but was also trained as a cladist and instilled with a deep skepticism of all that was not parsimony. I grew out of it (though I still think parsimony is wonderful...for some things), and I've seen a number of colleagues do the same.

However, I know several people (and I'm sure you do, too) who to this day know virtually nothing about model-based methods -- they just know they don't like them -- and I am aware of graduate-level systematics courses at top-tier universities that largely ignore such methods, doing (I think) a great disservice to the students. It's fine with me if someone doesn't like, say, maximum likelihood, but they should probably understand it before rejecting it! Oh, well.

(also, I've have to admit that I'm curious about that deleted comment...)

Rod Page said...

The deleted comment was spam from somebody (or some bot) claiming to be UPS.I only delete spam (which seems to be an increasing problem on Blogger.

John S. Wilkins said...

The world, I suspect, divides into two: those who like binary taxonomies, and those who don't. It is not the case that one who takes a consistent phylogenetic approach is thereby what I once heard Dave Penny call "Capital K" cladists.

While I agree that fighting the wars of the 70s over again is unhelpful, it seems to me as an outsider that the wars were not won or lost so much as fought to a kind of weary standstill. The issues remain as live now as they ever were, for very good reason: the issues are effectively universal - do we classify by clustering or by etiology, by history or by pattern, by identity or similarity?

Parsimony is not the boogeyman some seem to think - it's basically a heuristic in all science. Likewise, likelihood is an operation of inference because Bayes rules all. It may not be that the versions in play in taxonomy are the best, but we really ought to talk about it.

I think that there are confusions arising from ambiguity. Much of what we call taxonomy is really typology - classifying according to types. These are constructed using similarity metrics, and as useful as they are, types are not taxa. It pays, I think, to maintain that distinction, even if we agree that rousing rhetoric is not going to clarify much.

Frank Anderson said...

The deleted comment was spam from somebody (or some bot) claiming to be UPS.I only delete spam (which seems to be an increasing problem on Blogger.

Phooey...I was hoping it would be a scathing retort!

Anonymous said...

Your post made me take a look at that Cladistics Letter to the Editor. Wow... That is sad. While I don't entirely agree with your response, it is a huge step in the right direction. I was particularly fond of the the phenetic point. This led me down a path to find their blog. You should take a look...

http://urhomology.blogspot.com/

Joe said...

"...I think they've provided one more example of the death throes of cladistics (in the narrow parsimony is all, statistical methods are evil, molecular systematics is phenetics, barcoding is killing taxonomy sense)."

Rod you forgot "alignment can only be done using POO, um, I mean, POY."

Mauro Cavalcanti said...

I do agree entirely with your comments. "Cladism" has become a kind of religion - and, as such, is embraced only by reactionaries. I personally do not like some of the interpretations that are made of molecular data (especially in biogeography), but to oppose the data themselves is to exaggerate. As you said, creative people may find interesting uses for them. As of the cladist neurosis of calling everything they do not like (or understand) as "phenetics", it is on the verge of the ridicule -- they also termed two quite successful research approaches (geometric morphometrics and spanning tree biogeography) as "phenetics" but this did not hampered the success of these approaches.

Roberto Keller said...

Rod you forgot "alignment can only be done using POO, um, I mean, POY."

I guess Joe here would agree that we should indoctrinate our students to stop questioning everything they do and just use the default options in PAUP.

Rod Page said...

Roberto,

Not sure that Joe would argue that. My own view is that I'd encourage students to look and play more than anything else. Look at the data, play with it, try different views of it. Look at the results, explore them, do they make sense? Can you see how you got them?

Regarding POY, I think it's a classic case of a method that is fine in theory, but can yield unsatisfactory results in practice. Unfortunately, some users don't take the time to look at the resulting ("implied") alignments critically. See doi:10.1080/10635150601156305 for an introduction to this debate.

P.S. Great blog!

Mats Envall said...

I love your argumentation Rod! Simple and sensible. Most of the herd of wilderbeasts that throwed themselves into the river to reach the Wonderland appear to have returned to the correct side of the river (except, notably, John Wilkins, who instead stubbardly continues to divide existence into only black and white). This was exactly what I tried to explain in the manuscript you turned down about 5 years ago without even sending it to referees. Cladistics (in its extreme form, cladism) is only a populistic simplification, and as such wrong per definition.