"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::
- 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.
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.
4 comments:
THE SOUND OF ONE FINGER FLAPPING: LUNACY OR NO?
I think that Ebach and Williams have answered "yes" but in a longer way. Yes, they are saying, the tree is in effect a classification, and yes, it is "phenetic", and yes that means it is not a good way to go. So my guess was correct. I am curious what method they propose that will do a better job. And how they're going to persuade everybody else that those people are all being pheneticists.
It is obvious that Felsenstein is not going to concede on the matter of classification. For him it is about values such as "good" and "bad" and competition, such as the "best method" versus the "worst method". It is sad that systematics and biogeography have been degraded to choosing "best" numerical methods when something far greater is at stake - the disappearance of natural classification.
This whole debate, for us at least, has been about the confusion between artificial and natural classifications. Felsenstein, a believer in the "it-doesn't-matter-very-much-school" of classification seems oblivious to the role classification plays in systematics. Inferring phylogenies, namely interpreting classifications, is a practice that stems back to Haeckel and before. However, as these naturalists knew, without classifications there will be no phylogenies to infer. We suggest that Felsenstein acquaint himself with the systematic and biogeographical literature of the past. We found it a rewarding experience.
Note: The title "Look at the moon, not my finger" refers to Buddah 'pointing the way' towards freeing oneself from suffering - the moon representing that goal. We are refering to those that have for centuries been pointing the way towards freeing ourselves from inference, teleology and mechanical explanations - the moon is, in this sense, referring to natural classification. It is not a crime to generate inferences and artificial classifications, but it is erroneous and misguided to assume that inferences and artificial classifications are somehow natural methods.
I reject the idea that I am simply looking for "good" vs. "bad" methods. The objective is to come and close as possible to reconstructing the phylogeny. "Good" and "bad" are to be interpreted in that light. Ebach and Williams consider a tree reconstructed by parsimony from a sequence alignment to be an "artificial classification" and their own preferred method to make a "natural classification". But they give no argument as to why the former will be inaccurate, and they do not explain their method, at least not in a way that allows me to understand its properties. If they will use a finger to point to the moon, I will happily look at it.
Looking at the moon is astronomy. Looking at the finger is science.
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