Such expressions as that famous one of Linnæus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications (Darwin, 1859, p. 413f).

Thursday, 3 April 2008

The Problem of Similarity

Systematics and Biogeography has a problem: similarity. Ever since Goethe, naturalists and biologists have been rejecting similarity. It is the foundation of artificial classifications, non-evolutionary groupings and the basis for many arguments against evolution (i.e., homology).

Similarity implies that organisms are similar and not the same, that is it remains silent about sameness. The difference between being similar and the same is astronomical. Any two things in the universe can be similar. It is not a discovery. It demands no explanation. It is a means unto itself. However, when two things are discovered to be the same, they require explanation. This is when the study of evolution begins. By denying sameness -- or ignoring it -- we remain in the realm of artificial classification.

So why, then, is similarity so popular? All methods in molecular systematics use "similarity methods", herein phenetics, in order to measure nothing more than similarity. No evolution is (or can be) discovered, nor even touched upon. Molecular trees are simply meaningless in the context of evolution. They tell us nothing about sameness and therefore demand no explanation whatsoever. Regardless of this fact, all molecular systematists seem to explain similarity as if it means sameness. A molecular tree is generated and not discovered. They are means unto themselves. The gargantuan task of sequencing, aligning and building trees to find similarity ends with nothing at all. We are by no means poo-pooing similarity methods (phenetics).

Similarity methods are vital for understanding in non-evolutionary fields, such as geology. The chemical composition of rock is important for classification and identification. The same is true for biological keys and other artificial classifications. They helps us identify organisms based on their characteristics. The key will still work if the characters are homologous, not homologous or a mixture of both. Similarity will never be able to show which is which. Phenetics is useful outside of systematics and biogeography and evolutionary biology as its popularity shows. But popularity alone will not validate phenetics, or any similarity, in evolutionary biology.

What do we do with all the data, the matrices and the trees, produced by phenetics? We hope that their owners have fluked it - actually found a meaningful evolutionary, that is a monophyletic group. The sad news is that they'll never know.

Of course, molecular data have meaning and we should not be understood as attempting to trash molecular systematics. We simply feel they have been sold short. Maximum likelihood, parsimony optimization, and so on, are all kinds of phenetics: they are similarity methods. They are useless in the pursuit of evolutionary patterns, namely homology and monophyly. Molecular systematists need to stand up and shake loose the shackles of similarity, realize that their data and their methods are two separate issues and question those that wrongly promote similarity methods as "evolutionary".


Dalton de Souza Amorim said...

Nelson Papavero used to comment some years ago that Chemistry is still in the Reign of Aristotle, i.e., in the domain of an essentialist sense of gathering. The table of chemical elements (which no doubt has an outstanding utility) actually has no utility to allow any kind of understanding of the history of particular rocks. It gathers within the same classes elements that are similar regarding to some properties (even though in many cases actually not being identical), regardless their age or place of origin. Like "triangle", an atom of "hydrogen" is anything that fits its definition. A historical classification of chemical elements may be of no practical use, but this is not the case of organismic history. Similarity, here, generates timeless sets of elements that are useless for evolutionary purposes.

Joe Felsenstein said...

"Molecular systematists need to stand up and shake loose the shackles of similarity, realize that their data and their methods are two separate issues and question those that wrongly promote similarity methods as 'evolutionary'."

If we have sequences, and two sequences share a C at a certain site, you call this "similarity". In your view parsimony and all other numerical phylogeny methods that use this similarity are "phenetic" and not "evolutionary". If we aren't to use those methods, what method do you have that we can use to discern whether the shared C is an homology. Have you got a method? I can't see one in what you have written.

René said...

I have a question for Malte and/or David.
I am reading your book, which I find extraordinarily interesting and clear.
However, there's a linguistic/historical point in your book that puzzles me.
You cite Owen 1849 as writing that it is difficult to understand what is the Bedeutung of general homology. I think I can understand what he is talking about, except that I need to refer to Frege, who distinguished the Sinn and the Bedeutung (the sens and denotation of Russell or the intension and extension of Carnap) only some years after (his very famous paper Über Sinn und Bedeutung is from 1892. Do you know why Owen used this very particular German word, or if the distinction between Sinn and Bedeutung had been discussed before?
thanks, and sorry if my comment is not in the right place...

David Williams & Malte Ebach said...

In his explanation for the use of the German word Bedeutung, Owen writes the following (On the Nature of Limbs, p. 1):

“A German anatomist, addressing an audience of his countrymen, would feel none of the difficulty which I experienced. His language, rich in the precise expression of philosophical abstractions, would instantly supply him with the word for the idea he meant to convey; and that word would be Bedeutung.”

Thus Owen uses Bedeutung for ‘signification’ and ‘nature’ to express ‘essential’ similarity. But his difficulty was introducing ideas relating to German anatomy. So this was his source.

Simon Mayo said...

Isn't cladistic analysis also based on similarity, i.e. co-occurence of the "same" feature in two organisms? It's just that you decide at the end of it to chuck out the similarities which conflict with the best nesting pattern. Cladistic analysis is just a different kind of similarity analysis which manipulates the matrix data in a particular way that happens to fit theoretical expectation from evolutionary theory. Isn't it just a distance method that happens to use 1-norm Minkowski distance?

Malte Ebach & David Williams said...

Some 'cladistic' methods are phenetic.

The problem lies in the definition and usage of the term 'cladistic'.