Sunday, February 26, 2006
Monophyly in Biology
For those of you not up on terminology, monophyly is a fancy way of saying "Universal Common Ancestry". This means that the variety of life can be viewed as one giant family tree. Polyphyly means that organisms had more than one root. Creationists believe in a polyphyletic system -- each "created kind" represents a uniquely rooted tree. Non-creationists can also believe in a polyphyletic system in two ways. (1) There were multiple starts to life, each resulting in a different branch of life today. This is usually thought of in terms of the three domains of life -- archaea, eukaryota, and bacteria. Another view is that there were numerous starts to life, but that in the past, horizontal transfer was the rule instead of the exception. Life started in many different ways according to many different paradigms, and then merged in different ways to establish the higher levels of taxonomy. The latter approach is the one examined by Gordon in this paper.
First of all, it was nice to see that my previous comments about common ancestry being the result of specific origin-of-life scenarios, not evoolutionary theory itself is backed up in the scientific literature. Even more so, when you remove the requirement that the origin of life must be naturalistic, you remove even the reasons for assuming that certain groups had ancestors in the first place.
Gordon shows the diverse functioning in the genome as essentially being built up from multiple ancestral lines which came together through lateral transfer. He argues his point by showing that very diverse organisms have very interesting patterns of gene sharing that aren't explainable by a monophyletic common descent, but are explainable in a very high lateral transfer scenario. However, this requires that (a) such degrees of lateral transfer is even possible, and (b) that it would have been so widespread. Another way of looking at the data, however, is in terms of design patterns. If you allow an intelligent designer, then I think that common design patterns is the most natural result of following this data. There are no direct evidences of ancestry, the monophyletic view isn't tenable, and the degree of lateral transfer required for Gordon's polyphyletic view has never been observed. However, design patterns are indeed exactly how designing intelligences go about the act of creating.
He distinguishes three levels of evolutionary differentiation:
- Micro-evolutionary differentiation (populational changes)
- Meso-evolutionary differentiation (genera and families)
- Macro-evolutionary differentiation (kingdoms, phyla, and classes)
He points out that monophyly works best for micro- and mesa- levels of evolutionary differentiation. Interestingly, this is exactly what creationists claim! Also note that interbreeding among species can adversely affect monophyletic assumptions in even these cases.
Another interesting thing about the paper is that he notes that the monophyly/polyphyly question affects the "perception of how many different kinds of organisms there are and have been". I hadn't thought of that, but indeed assuming monophyly would require a massive number of unseen transitionals, while for polyphyly these would not be necessary.
Also, he points out to a number of known cases of gene transfer, and that it occurs even between highly diverse groups of organisms -- even between kingdoms. This includes plasmid transfers, viruses incorporating their genomes into hosts, and host DNA into their genomes, and transposons which can be experimentally transferred between organisms in different lineages.
Personally, I think the ability for organisms to be able to incorporate DNA from other sources indicates (a) that life is based on a common, unified plan, and (b) that organisms can transfer DNA as a mechanism to help other organisms in the environment adapt to each other. However, these claims have not been investigated to my knowledge.
Anyway, here are some good quotes from the paper:
There is, however, no doubt that strong circumstantial cases have been made, based largely upon morphological evidence, for polyphyletic origins of a number of major groups of organisms.
Do traceable lines of descent exist that might ultimately permit characterization of the genomes of organisms basal to the clades for the highest categories? The answer to this question increasingly appears to be no. Recent work on genomic structures demonstrate that all living organisms are genetic composites: mosaics and chimeras composed of bits and pieces of multiple genomes derived from multiple sources.
The base of the universal tree of life appears not to have been a single root, but was instead a network of inextricably intertwined branches deriving from many, perhaps 100 or more, genetic sources. The traditional version of the theory of common descent apparently does not apply to kingdoms as presently recognized. It probably does not apply to many, if not all, phyla, and possibly also not to many classes within the phyla.
[about tetrapod evolution] everything we know is circumstantial and indirect, and what actually occurred remains unknown.
[concerning traditional analyses of phylogeny] Possible polyphyletic scenarios were methodologically and philosophically excluded as impossible [emphasis mine]
The crucial role that statistically inadequate sampling of Devonian faunas has played in the development of our perceptions must explicitly be acknowledged...The animals found represent only a small, stochastically selected, possibly quite unrepresentative, sample of the biodiversity that existed in these groups at those times. There is no way of knowing to what extent, if at all, those specific organisms were relevant to later developments, or what their relationships might have been to each other.
Th evidence cited and the arguments made in this essay indicate that the applicability of the concept of monophyly at the macro-scales of evolutionary differentiation increasingly appears to be severely limited. An operational definition of the concept does not seem possible at the macro-level. Indeed, the phenomena of a monophyletic origin for the universal tree of life probably did not occur.
It is also desirable to avoid restricting frameworks for the evaluation of relevant data to only cladistic models.
The author's hope is that this essay may contribute in a small way to the mitigation of the strong trend toward more and more reductionism that pervades much of modern biology. I think biologists should try to avoid what I call "physics envy." The search for the simplest, most inclusive explanations for biological phenomena certainly must continue. However, that search should be tempered with the realization that over-generalization (including efforts to force everything in entire fields of study into single conceptual molds, such as the cladistic mold in evolutionary biology) is also a hazard along the path to understanding of the natural world.
Sorry for the massive quoting. I'm too tired to summarize.