TAXONOMY AS A CONTRIBUTION TO SCIENCE
By Patricia Barlow-Irick,
University of New Mexico, 1997
with added links July 2002.
The argument I am making here is simple: the descriptive science of taxonomy should rest on observable data, rather than interpretations, fads, and beliefs. Taxonomy describes the phenomenon of biological similarity among individuals and develops classification systems for the identification of these individuals. I suggest that as taxonomists we eschew the role of an unloved orphan of scientific heritage. The changing paradigms of scientific thought and cultural awareness offer the taxonomic community a respite from the perceived necessity to describe the world in physio-chemical terms. However this opportunity comes tied to a responsibility to discover, describe, and classify the world's biodiversity, efficiently and effectively, to meet the needs of science and society.
Philosophical Underpinnings: Variable and subjective beliefs about science.
Our assumptions color the attitudes and perspectives from which we view the world around us. Many of these assumptions are so deeply ingrained in cultural values and the contemporary worldview, that we may not realize that there are alternative ways to think. In this section I point out some subjective assumptions about the nature of reality, about the relationships among components of reality, and about the criteria for legitimate scientific endeavor. I do this in order to call attention to the underlying biases we bring to the task of describing nature.
Science is necessarily restricted to a perspective of the world as mechanistic. The classical approach to scientific problems identifies the system in which a phenomenon of interest occurs, decomposes the system into its functional parts, and identifies the causal and functional relationships between the parts (see Bechtel and Richardson 1993 for discussion). A rejection of the mechanistic viewpoint is typically precipitated by failing to find a more concise explanation of the original phenomena, not recognizing the bounds of the system in which the phenomena occurs, or approaching the problem at an inappropriate hierarchical level for decomposition to be successful. The only scientifically productive response to the failure of a mechanistic approach is to abandon decomposition and develop more adequate descriptions of the phenomenon, finally returning to decomposition after redefinition of the phenomena. However, the underlying reality of the world may or may not be wholly mechanistic. Fortunately, in order to be productive scientist, we are not required to hold a strictly mechanistic viewpoint. Among heuristic and productive anti-materialistic approaches to science are: epiphenomenalism (e.g. T. H. Huxley 1864), emergent materialism (e.g. R. W. Sperry 1980), psychological dualism (e.g. Eccles 1994) and teleomechanism (e.g. Karl E. von Baer) (Bechtel and Richardson 1993 p. 93). Adopting a position about the ubiquity of mechanistic processes is an act of subjective faith.
Hierarchical reductionism (Dawkins 1986) assumes that all phenomena can be explained at lower levels of organization. Not only does this philosophy assume that systems can be decomposed into constituent subunits, but also that the causal and controlling factors will be identifiable within this set of subunitss. The special danger of such a viewpoint in biology is that functionally integrated hierarchically systems may not be decomposable into independent units (Bechtel and Richarson 1993) and such a viewpoint will artificially constrain the elucidation of biological processes. Emergent properties are the result of functionally integrated hierarchical systems.
The concept of emergent properties in biology has a long history, being based at heart in the metaphysical traditions of the Germans (Harwood 1994), and being the only concept that eternally keeps biology from being considered a branch of physical science (Smocovitis 1992). Because this concept is difficult to conceptualize and test, it is often demeaned as "scientifically ineffective". Still emergent properties have been the subject of biological literature for more than fifty years (e.g.Jennings 1927). The study of systems complexity through computer modeling is now forcing biologists to revisit these issues. It becomes increasing evident that in some systems it is not the components of the system which are critical, but rather the organization and relationship between components, which produce emergent products (Kauffman 1995). Explaining the phenomena of diversity and identity of organisms may require a complex integration of processes at many hierarchical levels from molecular thermodynamics to ecosystems ecology, and may involve many levels of emergent properties which cannot be explained at lower hierarchical levels. There is a continuous gradation between the outlook of reductionism and holism, and one is not bound to any particular point along this axis by virtue of inherent or proven validity, therefore to adopt a holistic or reductionistic position is merely a subjective choice.
Some of my more positivist colleagues question whether classical taxonomy is a scientific activity. In his 1949 address, the president of the American Society of Plant Taxonomists said taxonomy could not truly be a science without having its fundamental unit, the species, defined (Raven 1974). The fundamental unit of genetics, the gene, remains ambiguously defined (Mahner and Kary 1997; Waters 1994). Furthermore, in the minds of many scientists, science can study only repeatable processes, and as a historical question the study of diversity of life on this planet is not even a valid scientific issue. From this perspective, the study of evolutionary processes is a legitimate question for science, but the resulting pattern is not. Taken to its logical conclusion, this perspective would eliminate from legitimate scientific endeavor all naturalist descriptive activities, from paleontology to cosmological astronomy. This is clearly a only a philosophical point of view, which no fundamental universal laws adjudicate.
Inarguably science depends on accurate and detailed descriptions of the phenomena that are to be explained. If descriptions are biased by underlying assumptions, this bias effects how the descriptions can legitimately be used to study phenomena. In particular, if a taxonomy is based on a conceptualization of the evolutionary process that theoretically produced a particular pattern of variation, then that taxonomy itself cannot be used to test the validity of the evolutionary process. Therefore it is advantageous to the study of evolution that taxonomy and phylogeny be distinct areas of study, allowing an unbiased taxonomy to be used to test phylogenetic hypotheses. I suggest that keeping taxonomies free of contamination by phylogenetic conjecture is of great value to the study of evolution and ecology. Furthermore, in order to identify the details neccessary to understand evolutionary processes, taxonomy must be the least reductionistic of all biological sciences.
Taxonomy: the task at hand.
A closer look at the current objectives of the community of plant taxonomists will provide a basis to evaluate the potential contribution which plant taxonomy can to make to the rest of science.
In 1994, the American Society of Plant Taxonomists, the Society of Systematic Biologists, and the Willi Hennig Society, in cooperation with the Association of Systematic Collections, and with financial support from the U.S. National Science Foundation, launched a global initiative to discover, describe and classify the world's species. This initiative is called Systematics Agenda 2000: Charting the Biosphere (SA2000). Produced from the input of 27 standing committees and over 300 scientists, the SA2000 report represents the current assessment and perceptions of the state of systematics, and so is used as the basis of this section's discussion of the objectives of taxonomy.
SA2000'S GLOBAL OBJECTIVE
"The global community of systematists, through Systematics Agenda 2000 (SA2000), proposes a clear scientific objective defined by the needs of the world's nations:
"To discover, describe, and classify the world's species."
(SA2000 1994)
The SA2000 report points out that with only 1.4 million species discovered, as "millions of species - perhaps even tens of millions - remain unknown to us", the objectives of descriptive biology are not trivial. Meanwhile we race against declining diversity, disappearing habitats, and escalating biological destitution to discover the unknown taxa before they are extinct. SA2000 delineates systematics, the science dedicated to the discovery, organization, and interpretation of biological diversity, as having three separate tasks: taxonomy, phylogenetic analysis, and classification. Taxonomy is defined by SA2000 as "the science of discovering, describing, and classifying species or groups of species," which echos the wording of the global objective for this project.
Four fundamental questions are identified as being at issue. First, what are the earth's species? Second, what are their properties? Third, where do they occur? And fourth, how are they related? SA2000 proposes to use the answers to these questions to organize a predictive classification and database. Their approach to these questions falls into three interrelated missions. The first mission is to discover, describe, and inventory global species diversity. The second mission is to analyze and synthesize the information into a predictive classification system that reflects the history of life. The third mission is to organize the information derived from this global program in an efficiently retrievable form that best meets the needs of science and society.
It is clear from the SA2000 literature that there is a pressing need to do basic taxonomic studies. Yet classical taxonomy has taken a back seat to phylogenetic analysis. Taxonomic questions are not held to be unworthy of scientific endeavor. To understand this denigration of descriptive biology, I turn now to the history of the subject.
How did we get here? : the history of taxonomic trends.
After publication of The Origin of the Species, evolutionary biologists (then called naturalists) became enamored with discovering the mechanism of descent rather than with the delimitation of species boundaries per se. This was precipitated by the realization that these groups called "species" were not immutable types, and whatever species boundaries might exist in the present, they are only temporary phenomena (See Darwin 1872, p.420). At the time there were monolithic taxonomic programs in progress to catalogue and describe New World organisms. This concept, that species were only snapshots of evolution in time, would eventually cast a pall over the dignity of taxonomic endeavor, reducing it to the domain of quarrelsome librarians (Stuessy 1990) and hobbyist-collectors.
Because the basic units of taxonomy are based on subjective judgements, there is a tendency for taxonomists to split groups into ever finer and finer units, to lump previously separated units, and to make revisions to prior taxonomies. This in turn muddles otherwise sound biological research by rendering the subjects ambiguous and obsolete. Some individual taxonomists over time have been, and continue to be, extremely insensitive to the need for nomenclatural stability. At the beginning of the 20th century as taxonomists tried to revise the incomplete and haphazard taxonomy of the earlier century, American taxonomy was extremely labile. F. E. Clements, working towards founding the new science of ecology in 1905 and obviously in need of a stable taxonomy, led a caustic attack on descriptive botany as an unscientific activity (Hagen 1984). By the 1930's the Rockefeller Foundation funding for evolutionary research was cut off (Keller 1990), and even the American Naturalist, was forced to consider changing to a genetics journal (Smocovitis 1992).
Biologists responded with a major shift of focus. Classical genetics became the center of the biological paradigm, not only because it seemed to be the system in which evolution occurred, but also because it was favored by the leading scintists and institutions of the times. The Unity in Science Movement of the 1920's had set to purge science of anything tainted by the metaphysical, and to align all sciences with similar methods under a mechanistic paradigm (Smocovitis 1992). The leading proponent of Mendelian genetics, Thomas Hunt Morgan, declared other approaches to the study of evolution, such as embryology (always seen as some what metaphysical, to be invalidated and antiquated (Gilbert et al. 1996). The statistical methods of Fisher, Haldane and Wright became powerful heuristic tools to understand evolutionary genetics. Quantification put biology in the same playing field as physics and chemistry (Smocovitis 1992). According to redefinition by Theodosius Dobzhansky, evolution wasn't adaptive change; more quantifiably it was a change in allele frequency. The Atomic Energy Commission developed an interest in the effects of mutations, providing Dobzhansky and his numerous graduate students with an unprecedented level of funding (Gilbert et al. 1996). Fueled by competition for financial resources, the politics of evolutionary studies moved from an open forum, wherein all concepts could be discussed on their merits, to one where intellectual turf-building and maintenance of the orthodoxy, gutted descriptive fields such as developmental biology and physiology. Over time this sharply restricted research and publication to papers consistent with the evolutionary genetics paradigm. This was a self-feeding cycle once initiated. As graduate students turned into authors and decision makers, spread through academia and became ubiquitous, all alternative hypotheses were suppressed (personal observation).
Taxonomists responded to these changes by refocusing their studies on population structure, origins of populations, races and subspecies, and the conditions leading to divergence. Mendelian genetics underscored the promise of finding the locus of evolution to be at the hierarchical level of the "gene". Clements spurred the development of experimental taxonomy among California botanists such as Jens Clausen, William Heisey and David Keck (Hagen 1984). This coalition of experimental taxonomists, called The Biosystematists, refined a view that the genotype was more fundamental than the phenotype and published "The New Systematics." At the same time, the equally displaced paleontological community brought forth The Society for Study of Speciation. Ernst Mayr coalesced these two communities into one with his energetic Bulletins, gradually taking control of the direction and tempo of the whole discipline of taxonomy (Smocovitz 1996).
Biosystematists donned the hats of population geneticists to validate their profession, but this did not resolve some of the bigger issues in the evolution of diversity. The population genetics approach is committed to explaining macro-evolution in terms of immediate selective advantage to individual organisms. In the end, this area has become highly controversial with proponents and opponents alike arguing from conviction rather than evidence. In considering the merits of the population genetics approach, the fundamental issue is how much biological significance generalizations, resulting from a statistical/probabilistic approach, have when the evolutionary fate of each individual, under a model of determinism and historical contingency, is unique.
As the "locus of evolution", population genetics swamped out any competing memes by virtue of its simplicity, its tractability for research, and its power to defend evolution against the Creationist factions (Gilbert et al 1996). Some of the heterodox concepts which were rightly or wrongly suppressed at one time include non-randomness of mutation, directionality to evolutionary change due to internal biases, non-chromosomal inheritance, and relative importance of the roles of mutation and selection (Briggs & Walters 1969). Molecular studies of the genetics of evolution has since reinstated each of these once heterodox views (Nei 1987, chapter 14).
Taxonomists may have simply welcomed molecular biology as a source of new and excitingly fundamental characters, but the effect of the new approach to biology has profoundly affected all aspects of the study of life. Initially appearing as ultimately and extremely reductionistic, this molecular approach seemed to suggest that life should be redefined to simple possession of an active genetic code. But this reductinistic perspective gave way to a view of the complexity of the evolutionary process. The molecular evidence shows that biological phenomena and processes are complex, diverse, historically contingent, and hierarchical in character (after Mayr 1990). The implications for systematics is enormous. The evidence says that there are numerous situationally dependent pathways of evolution, that the probability of convergence much higher than suspected, and that perhaps, population genetics makes sense only for regulatory genes. To me this suggests that although molecular biology is a powerful tools for understanding evolutionary processes, it may not necessarily provide any way to objectify taxonomic decisions.
Despite all the changing paradigms and historical contingency, we must strive to keep our focus. The taxonomic endeavor is simply to discover, describe, and classify organisms in the biological world. We can neither leave this task for garden clubs and orchid collectors, nor let ourselves be distracted by the seductiveness of high-tech characters, nor waste our productive lives arguing endlessly about species concepts. The task of alpha taxonomy lies before us.
Literature cited
Bechtel W, and R. C. Richardson. 1993. Discovering Complexity: decomposition and localization as strategies in scientific research. Princeton University PressBriggs, D. and S. M. Walters. 1969. Plant variation and Evolution. McGraw-Hill, New York
Darwin, C. 1872. Origin of the species 6th ed. 1988. New York University Press, New York.
Dawkins, R. 1986. The Blind Watchmaker: why the evidence of evolution reveals a universe without design. W. W. Norton & Co., New York.
Eccles, J. C. 1994. How the Self Controls its Brain. Springer-Verlag, Berlin.
Gilbert, S. F., J. M. Optiz, and R. A. Raff. 1996. Resynthesizing evolutionary and developmental biology. Developmental Biology 173(2): 357-372.
Hagen, J. B. 1984. Experimentalists and naturalists in 20th century biology: experimental taxonomy. 1920-1950. Journal of the History of Biology. 17(2)249-270.
Harwood J., 1994. Metaphysical foundations of the evolutionary synthesis: a hitoriographical note. Journal of the History of Biology 72)1):1-20.
Huxley, T. H. 1864. On the Hypothesis that Animals Are Automata, and Its History. Collected Essays Vol. 1.
Jennings, H. S. 1927. Some implications of emergent evolution. Science 65: 19-22 Kary, C. E. 1990. One causal mechanism in evolution: one unit of selection.Philosophy of Science 57: 290-296.
Kauffmann, S. 1995. At Home in the Universe: the search for laws of self-organization and complexity. Oxford University Press, Oxford. Keller, E. F. 1990. Physics and the emergence of molecular biology: a history of cognitive and politacal synergy. Journal of the History of Biology 23(3): 389-409.
Mahner, M. and M. Kary. 1997. What exactly are genomes, genotypes and phenotypes: and what about phenomes. Journal of Theoretical Biology 186(1): 55-63.
Mayr, E. 1988. Toward a New Philosophy of Biology. Harvard University Press, Cambridge.
Morgan, C. L. 1923. Emergent Evolution. Williams and Norgate, London.
Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.
Raven, P. 1974. Plant systematics 1947-1972. Annals of the Missouri Botanical Garden. 61:116-178.
Systematics Adgenda 2000. 1994.Charting the Biosphere: a global initiative to discover, describe and classify the world's species. American Museum of Natural History, New York.
Smocovitis, V. B. 1992. Unifying biology: the evolutionary synthesis and evolutionary biology. Journal of the History of Biology 25(1): 1-65.
Sperry, R. W. 1980. Mind-brain interaction: Mentalism, Yes; Dualism, No. Neuroscience 5: 195-206.
Stuessy, T. 1990. Plant Taxonomy: the systematic evaluation of comparative data. Columbia University Press, New York.
Waters, C. K. 1994. Genes made molecular. Philosophy of Science 61: 163-185.
Wheeler, W. N. 1911. The ant-colony as an organism. Journal of Morphology, 22: 307-325.
Useful Links
The Meaning of Evolution. by Stephen C. Meyer and Michael Newton KeasInterpreting the Homeobox: Metaphors of Gene Action and Activation in Development and Evolution. by Jason Scott Robert, PhD
Lifelines: biology without determinism. by Steven Rose