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, 29 November 2007

Artificial and Natural Classifications: A Clarification

It was not by accident that we referred to de Candolle (1813): "Naef's concern was with the discovery of natural, as opposed to artificial classification, a problem examined in detail by A. P. de Candolle (1813)".

This is what de Candolle had to say about artificial classifications:
"Others have as their essential goal to give to persons who know nothing of the names of plants an easy way to discover the names in the books by inspection of the plant itself. These classifications have been given the name of Artificial Methods."
"...there are those persons who want to study plants, either in themselves, or in their real relations among themselves, and to class them so that those plants most closely related in the order of nature are also those most closely related in our books. These classifications have received the name of Natural Methods."
De Candolle considers Systems and Methods.

A system is a key or classification based on a particular organ - leaf, flower, etc.

A method is a key or classification based on all of the organs of a plant; methods are sub-divided into artificial and natural depending on their purpose.

De Candolle again:
"classes that are truly natural, established on the basis of one of the major functions, are necessarily the same as those established on the basis of the other."
That is, congruence.

Bar-coding, based on "a particular organ", interpreted as a piece of DNA, is, in this sense, a system. It might be seen as an artificial classification as its purpose is to find the name of any given plant or animal.

Now, is molecular systematics a system or a method? It too is based upon "a particular organ", so it too might be considered a system. Now if considered a method, we see that there is no notion of congruence at all as no other datasets are given consideration. Molecular systematics as a form of measuring similarity constitutes a system, not a method.

Ancestors and other mechanical explanations are not of any concern in the debate between artificial and natural classifications. One does not decide on homology in advance. It is either there or it is not. Homology, as we understand, is a relation. A similarity such as 11, or AA, is not a relation. Thus, all molecular systematic studies are phenetic as they ignore relationship, that is, homology.


Joe Felsenstein said...

If we take a sequence alignment, perhaps an easy case such as an alignment of exon sequences of a gene, and then we run (say) a parsimony algorithm, and consider ourselves to be making an estimate of the unrooted evolutionary tree (perhaps later rooting it by outgroup), what do Ebach and Williams say of this? Some guesses:
* It is not inferring the phylogeny because this process is "phenetic"
* It is not making a classification so it is fine but not of interest to us.
* It should instead be trying to make a classification.
* It is making a classification but a "phenetic" one so not a good one.
Obviously I fail to understand their point of view.

It is hard for me to get a clear picture of what their attitude is toward methods intended to use sequence alignments to reconstruct evolutionary history. They are be called "phenetic" but what does that imply about their validity as reconstructions of phylogeny? Instead we get discussion of principles of classification which do not clear up this issue.

KZL Burington said...

I think I understand. If using only one gene is a "system", then if you use multiple points of homology, several or more orthologous genes, then perhaps the system would turn into a "method". The comparison to using only external leaf morphology to classify trees is apt.

Say we take Cytochrome Oxidase subunit I, but also several ribosomal subunits both nuclear and mitochondrial, and perhapse /other/ genes or regions of genes (those that code for tRNA for example), make separate comparisons between all those individually and then group those collectively on a matrix. This would be in my opinion very close to a morphological cladistic method, as there are multiple points of homology compared and coded separately and then compared collectively to formulate a topology.