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).

Monday, 26 November 2007

The Curse of Complexity


The world is biologically complex. Scientists have always known this and it is not a new discovery. Rather than accepting complexity as an everyday wonder, scientists are surprised that the world is indeed complex and some are annoyed with those who describe complexity in simple statements or methods. Here are a couple of examples:
"Historical biogeography has recently experienced a significant advancement in three integrated areas. The first is the adoption of an ontology of complexity, replacing the traditional ontology of simplicity, or a priori parsimony; simple and elegant models of the biosphere are not sufficient for explaining the geographical context of the origin of species and their post-speciation movements, producing evolutionary radiations and complex multi-species biotas" (Brooks, 2005: 79).

"The problem can be reduced to deciding when a collection of trees—a 'forest'—is a better explanation for evolutionary relationships among a set of sequences than is a single tree" (Ane and Sanderson 2005: 146).
We see no problem with simplifying a complex world in order to communicate in the form of classifications. We know for instance that a cat is a highly complex creature. So complex in fact, that the term cat or Felis silvestris and the classification of the Felidae are satisfactory in communicating that we are in fact referring to a tabby and everything associated with its complexity. These terms and classification are not however sufficient in explaining the highly complex nature of cat behaviour, sexual reproduction or neural activity. Classification is not about explaining complexity - this is job of General Biology.

Classification, an integral part of comparative biology, attempts to convey what information we have (i.e., about cats) without having to divulge and detail all its complexity (i.e., sexual behaviour). The aim of classification is to summarize (not reduce*) a relationship based on known homologues without recourse to inference. That means, comparative biology is about "simplicity" not causality or interconnectivity (sensu reductionism). We can for instance classify all mammals based on their hair and vertebrates based on the presence of forearms. The more complexity we introduce, the less unique traits there are to compare (i.e., eye colour). Since comparative biology is about comparing and classifying, explicit unobserved explanatory mechanisms have little to do classifications. They are statements about a type of complexity reserved for general biology (i.e., physiology, behaviour, sexual reproduction etc.). Although such explanations are unique events (or a series of events) based on careful considerations of general biological laws and processes, they can however be represented by a single classification.

Let us say for instance that the trilobite Eoharpes guichenensis evolved from E. cristatus which then evolved into E. primus. This can be represented as an anagenetic event and drawn accordingly. Another person may object to this explanation and suggest that E. guichenensis evolved into E. cristatus and E. primus through cladogenesis. Another may see that both explanations have avoided the explanation that E. guichenensis evolved in E. primus and E. primus into E. cristatus.

Regardless of how these species of Eoharpes have evolved, the phylogenetic trees and be summarized or simplified as relationships in the cladogram: E. guichenensis (E. cristatus, E. primus). What is more, is that the nodes on the cladogram are not events, ancestors or morphotypes, but simply junctions supported by homologues. Rather than accepting the cladogram as means of communicating three or more different evolutionary scenarios, it is rejected as being too simplistic or as an explicit scenario (i.e. "cladification" of Mayr and Bock, 2002).

As systematists and biogeographers, that is comparative biologists, we study the shadows of the past. We are at best able to find gross relationships between taxa or areas. The ability to extract any pattern at all from the bits and pieces of information at hand is an extraordinary achievement, but for some this is not enough. A complex world it seems must be shown to be complex, as though this something that is not already appreciated. The ability to communicate and understand such complexity is impossible without "simplification", that is, classifications. Simplifying the complexity that surrounds us is not a crime but a way to understand the world and to communicate that information to others. Without classification, complexity becomes a curse, which leaves us dumbfounded in a sea of information.

*It is important to note that reduction is not simplification. Mechanical explanations for instance are reductions. The philosophy of reductionism revolves around causality and not natural classification.

References

Ané, C. & Sanderson, M.J. 2005. Missing the Forest for the Trees: Phylogenetic Compression and Its Implications for Inferring Complex Evolutionary Histories. Systematic Biology 54: 146 – 157.
Brooks D.R. 2005. Historical biogeography in the age of complexity: expansion and integration. Revista Mexicana de Biodiversidad vol. 76: 79- 94
Mayr, E. & Bock, W.J. 2002. Classifications and other ordering systems. Journal of Zoological Systematics and Evolutionary Research, 40, 169-194.

1 comment:

philbiosuigeneris said...

The same year that Dawkins published *The Selfish Gene*, he published a very obscure, but also a much *better* piece of work, "Hierarchical organisation: a candidate principle for ethology", Bateson PPG, Hinde RA, 1976 *Growing Points in Ethology*. Cambridge UP. This paper is actually quite impressive in its level of detail and insight re. hierarchy. [We are not a fan of *The Selfish Gene*.]
Here are two choice quotes:

This paper will not be a review of the literature, nor will it use hard evidence to convince anyone. It will be an attempt to arouse the imagination of those more accomplished in research than I am, to persuade them to look again at the idea of hierarchical organisation, and use it in the future. (p. 8)

Whether it is complexity of stored information, complexity of pattern in incoming data, or complexity of controlled output, hierarchical organisation provides a way of making complexity manageable. (p. 48)

Dawkins is admittedly talking about behavioral/ethological information (e.g., "neural input"), but his words have multiple resonances for those of us interested in classification and systematics. We leave the reader to draw her own conclusions re. "complexity management" in systematics.

---000---

Speaking of drawing conclusions, we would like to hear more about the distinction Ebach and Williams make between *comparative* and *general* biology. We do not see clearly where one ends and the other begins. Is comparative biology devoid of drawing any conclusions or inferences (besides the "best" classification/phenogram/tree/cladogram...)? Is general biology the only sort of biology that can make strong inferences?

We suspect that the two forms of biology are deeply intertwined. First we discuss how general is entwined with comparative, then how comparative requires general.

(A) General biology must also classify when it infers the basic "parts" and "processes" of neurophysiological or biochemical systems. And articulating this inventory is itself a theoretical exercise, requiring all sorts of sophisticated theories about biochemical, biophysical and developmental-physiological process giving rise to morphology. Isn't this classification "within" general biology? Is classification a practice or "style of research" (Ian Hacking) pertinent to every branch of science or does it stand on its own qua comparative biology?
Suggested conclusion: General biology inextricably involves comparative biology, both qua systematics (e.g., use homology to ground causal inferences) and qua classificatory practice within its own domain (to articulate a list, for example, of the similarities and differences, and causal effects, of all the protein-types pertinent to a system).

(B) Conversely, isn't general biology also an aspect of comparative biology?
1. Don't we use characters "inferred" or "abstracted" from all sorts of morphological parts, even physiological/cellular/genetic processes?
2. And is the abstraction and use of such characters completely primitive and, moreover, distinct from, and uninformed by, general biology?
Our answers: 1. yes, 2. no.

Olivier Rieppel and Maureen Kearney have a paper "The Poverty of Taxonomic Characters" (Biology and Philosophy, 2007, 22:95-113) in which they argue that we reify characters all the time. So, how can we know whether our reifications have objectivity? Answer: *Place them in a a causal context*, (i.e., in a "General Biology" context sensu Ebach and Williams)! Here is a final choice quote, this time from Rieppel and Kearney's paper:

What Richards (2002, 2003) put
his finger on is the trend towards an increasingly theory-free approach to characters, compensated for by an increasingly large number of characters to be used in phylogenetic analysis (Rieppel and Kearney, 2002). This research program results in what Wa:gele (2004, p. 109) called "phenetic cladistics: elegant analyses
with many sources of error." The problem with this approach is that an appeal to causal relations has been buried under the logic of numbers. But biology has a long tradition of doing much better: evaluating characters in a causal (developmental, functional) context. Such would indeed seem to be required if systematics is to play the foundational role in evolutionary studies that Sterelny and Griffiths (1999) request for it. (p. 109)

Richards R. 2002. Kuhnian values and cladistic parsimony. Perspect. Sci. 10: 1–27.
Richards R. 2003. Character individuation in phylogenetic inference. Philos. Sci. 70: 264–279.
Rieppel O. and Kearney M. 2002. Similarity. Biol. J. Linn. Soc. 75: 59–82.
Wa:gele K. 2004. Hennig’s phylogenetic systematics brought up to date. In: Williams D.M. and
Forey P.L. (eds), Milestones in Systematics, CRC Press, Boca Raton, FL, pp. 101–125.
Sterelny K. and Griffiths P.E. 1999. Sex and Death. An Introduction to Philosophy of Biology. The
University of Chicago Press, Chicago.

Perhaps systematists study the "shadows of the past" (previous post), but as in Plato's cave, there are ways to escape. Causal knowledge drawn from general biology can indeed serve as a torch, a beacon, starlight or perhaps even sunlight for comparative biology.

Conclusion: Contra Comte, Spencer and the generalized idea of the 20th century that classification is somehow primitive, prior to inference, and even inferior (!), we suggest that it is highly theoretical, requires causal knowledge, and is intertwined with all scientific activity.