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, 6 December 2007

Divisions: Who watches the philosophers of science?

There are a few things for the poor old philosophers of science to get over.

If Peter Lipton is right, namely that,
"Astronomers study the stars; philosophers of science study the astronomers. That is, philosophers of science—along with historians and sociologists of science—are in the business of trying to account for how science works and what it achieves" (Lipton, 2005: 1259).
then philosophers of science have to able to see beyond current trends and political avarice. After all who watches the philosophers of science?

The trend of embracing apparent dichotomies within systematics and biogeography rather than question them, is one of things that philosophers of science need to get over. Philosophers of science need to question, examine and assess such divisions and not blindly accept them as many seem to do.

Below we list the top 10 dichotomies in systematics and biogeography that philosophers of science need to get over:
  1. Morphology and Molecules
  2. Homology and analogy
  3. Homology and homoplasy
  4. Transformational and Taxic Homology
  5. Synapomorphy and symplesiomorphy
  6. Congruence and consensus
  7. Cladistics and Phenetics
  8. Simultaneous analysis and separate analysis
  9. Ecological and Historical Biogeography
  10. Dispersal and Vicariance

Just because scientists use these divisions does not mean they actually exist. Dichotomies often groups "us" from "them". Science is not immune from subjectivity or distortion of "the facts" through clever manipulation. Scientific decisions too are sometimes decided upon politics, personality and fashion.

Philosophers of science are there to make sure that fish caught last Sunday afternoon was indeed "that big". In believing, rather than questioning, the divisions between certain ideas that are made by scientists, philosophers of science are unable to for "account for how science works". For some philosophers of science, the one that got away was "ooh .. so big, bigger than anything you have ever seen".

Lipton concludes
"Indeed, one might go so far as to worry that if philosophy did have any impact on scientists, it would be pernicious, depriving them of the kinds of commitment and confidence upon which their practice depends" (Lipton, 2005: 1269).
Philosophers of science have already influenced science, based on some of the highly questionable divisions listed above, to the extent that that it has been fashionable to attribute the cladistics/phenetics "war" in systematics to real events rather than to a poor account of how science functions (i.e., Hull, 1988).

Hull, D.L. 1988. Science as Process: An Evolutionary Account of the Social and Conceptual Development of Science. Chicago: University of Chicago Press.
Lipton, P. 2005. The Medawar Lecture 2004: The truth about science. Philosophical Transactions of the Royal Society of London B, 360, 1259–1269.

Monday, 3 December 2007

Buddah: Look at the moon, not my finger!

Joe Felsenstein has suggested an analytical example, one he felt we might like to examine. The example is simple:
"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?"(Felsenstein in Comments)
Felsenstein kindly offers a few suggestions ("guesses") as to what we might think. These are as follows::
  1. It is not inferring the phylogeny because this process is "phenetic"

  2. It is not making a classification so it is fine but not of interest to us

  3. It should instead be trying to make a classification

  4. It is making a classification but a "phenetic" one so not a good one.
Felsenstein offers a view as to which of the suggestions ("guesses") is correct, opting for number 4: 'It is making a classification but a "phenetic" one so not a good one'.

Of course, we welcome helpful suggestions ("guesses"), as our desire has been (and hopefully will remain) the examination of the process of systematics, a complex field that develops and grows, as does all science. Thus, we crave his indulgence at our dissection of his suggestions in the interest of scientific endeavour.

First, we find it a little troublesome to deal with efforts that are thought ‘good’ or "bad" and do not really know what those words might mean in the context above. To us, phenetics is neither good nor bad. Consider the following. Linnaeus created the Sexual System of classification for plants, a system he acknowledged as artificial. That system still has its uses, when one is faced with a particular plant and needs to know its name, then (usually) that can achieved by working through the Sexual System. It is an Artificial Classification – it is neither bad nor good (Linnaeus knew that). It is inappropriate when wishing to investigate the natural system; it is appropriate when wishing to find a name.

Second, whether one is "inferring the phylogeny" or just exploring the distribution of homologies, any branching diagram that results can be made into a classification. Thus, points 1—4 above are without meaning.

In our (several) posts we noted that Natural Classification is investigated using homologies – and similarities, in and of themselves, are not homologies. Consider a matrix of characters, with either 1's and 0's or A's and T's ("…take a sequence alignment…"). What are they? Similarities. The matrix is, one might say, phenetic. The application of UPGMA, or Neighbor-joining, or parsimony, or…well, whatever, cannot change that fact. And, it would appear, that UPGMA, or Neighbor-joining, or parsimony, and so on, are all forms of weighting, regardless of whether one might believe that the 'model' is an accurate representation of the evolutionary process. Now as we noted, "Phenetics uses a method in order to generate a classification that mimics a natural group. The method for doing so can be useful in order to work out similarities between taxa, but the method is only a mimic." Thus, we might offer the following: much of the last 40 years of exploration of methods has, inadvertently, focused on ways one might modify or adjust a matrix of similarities.

We do not have, nor do we promote, any "favorite approach…". This is not a competition. Systematics (classification, phylogeny) is about homologies and their distribution.

The cladistic revolution of the 1960s was necessary because of palaeontology, its promises, its claims, and what it delivered. Palaeontology is reformed as a consequence, yet its effect on systematics, mostly detrimental, lasted 100 years.

Perhaps it's time for another revolution.