Andrew Aberdein. Scientific Thought: In Context. Editor: K Lee Lerner & Brenda Wilmoth Lerner. Volume 1. Detroit: Gale, 2009.
“All science is either physics or stamp collecting,” declared New Zealand—born English physicist Ernest Rutherford (1871-1937). While Lord Rutherford jokingly sought to deprecate areas of science other than his own, he conveyed a valuable insight. Stamp collecting is not merely amassing stamps: The conscientious collector imposes order, whether by date, nationality, subject, shape, or other factors. Analogously, much scientific inquiry imposes order on the world.
There are many sciences of classification: Astronomers classify stars; geologists, rocks; physiologists, diseases; meteorologists, storms; and chemists, molecules. Social scientists classify human behaviors—even mathematicians classify. But the most developed classification systems have arisen in biology to classify the natural world.
Classification is essential for rational thought. All language imposes a classification in the assignment of words to objects. Even animals classify, when, for example, they use different alarm calls in response to different threats. So classification may be safely attributed to the earliest human societies. However, the reflective articulation of such knowledge, the discipline of taxonomy or systematics, has a more recent history.
Historical Background and Scientific Foundations
The pioneer of taxonomy, and of many sciences, was the Greek philosopher Aristotle (384-322 BC). He sought to catalog all known species of animal into higher categories, some of which are still used. His approach was distinctive in its methodology and its ambition. He recognized that not every species could be identified by a single distinguishing feature or characteristic. This permitted him to correctly classify problematic creatures such as the bat, with its anomalous ability to fly among otherwise mammalian features. Aristotle’s disciple Theophrastus (c.372-287 BC) extended this method to plants.
Herbals and bestiaries proliferated in medieval Europe, the former based mostly on the Greek physician Pedanius Dioscorides’s (c.AD 40-90) first-century book De Materia Medica, the latter on the Roman scholar Pliny the Elder’s (AD 23-79) Naturalis Historia of the same period. Despite the passage of time, however, these works were not always as sophisticated as Aristotle’s. Even late examples, such as the English clergyman Edward Topsell’s (1572-1625) Historie of Foure-footed Beasts (1607) and its model, Swiss naturalist Conrad Gesner’s (1516-1565) Historia Animalium (1551), are arranged alphabetically and include mythical beasts.
English naturalist John Ray’s (1627-1705) Methodus Plantarum (1682) broke with this tradition. Ray anticipated the modern definition of “species” as populations (potentially) capable of breeding fertile offspring. But he also regarded species as fixed and unchangeable. This may explain the eclipse of his definition by essentialism, the definition of species by their resemblance to an archetype. Ray’s definition was revived by the German-American systematist Ernst Mayr (1904-2005), who also emphasized the importance of reproductive isolation, capturing the Darwinian insight that substantial variation occurs within, not just between, species.
Swedish botanist Carl Linnaeus (1707-1778; also known as Carolus Linnaeus or Carl Linné) set taxonomy on a modern footing with the establishment of binomial nomenclature. Prior to Linnaeus, plants and animals were referred to either by frequently ambiguous common names, or by descriptive Latin names. The latter aimed to identify all distinguishing characteristics, and thus were often long and unwieldy. Initially developed as a practical shortcut, Linnaeus introduced the binomial system still in use today. Every species can be identified by the conjunction of two names: its generic name, no two of which are the same, and its specific name, which may be safely reused.
Linnaeus grouped genera into orders, classes, and kingdoms. More recent taxonomists have expanded these ranks to eight basic levels: domain, kingdom, phylum (division in plants), class, order, family, genus, and species. These are sometimes further divided into suborders, superfamilies, and so forth. Species is the only rank that has objective definition (that of Ray and Mayr).
Scientific and Cultural Preconceptions
Classification poses a philosophical problem: How can individuals be both one—members of the same category—and many—unique individuals? This question recurs throughout the history of philosophy. Three answers are particularly important to taxonomy: Platonism, Aristotelianism, and nominalism.
For Aristotle’s teacher Plato (427-347 BC), our world is merely a reflection of the world of “forms.” The objects that we perceive are imperfect duplicates of these forms, which we cannot know directly, but whose properties we may intuit. For instance, all dogs are copies of the form of the dog.
Plato influenced taxonomy more than his metaphysical extravagance may suggest. The concept of species as perfect, immutable forms died hard. Some nineteenth-century naturalists were more upset by Charles Darwin’s inconsistency with Plato than his inconsistency with the Bible.
However, Aristotelianism was more directly influential. For Aristotle, forms do not exist independent of their objects: They comprise a common essence (a word originating in Aristotelian metaphysics). Hence the form of the dog is found within each individual dog: an essence of “dogness,” which explains why all dogs are dogs. Aristotle’s goal, and that of many subsequent taxonomists, was to describe the essence of every species.
Nominalists such as the English philosopher William of Ockham (c.1288-1347), denied the existence of forms. In this view, dogs are all dogs because they are all called dogs. Thus, for nominalists there are no true categories in nature, only in human convention. This abandons the ambition to carve nature at the joints, as Plato expressed it, that is, to construct a natural classification.
Logic has also influenced taxonomy. Plato introduced definition by dichotomy: zeroing in on a specific subject from a larger class through successive binary divisions. Since each division is between a property and its negation, the species resulting from a dichotomous classification are guaranteed to be exclusive and exhaustive: that is, they have no members in common, and no members of the larger group are omitted. Some logicians have argued that all classifications should be dichotomous.
Evolutionary thought transformed taxonomy. The widespread acceptance that species were not created separately but emerged from earlier species established a new principle for organization. Henceforth, many taxonomists sought to capture the phylogeny of the species they classified, that is, its history and development.
At taxonomy’s core is the recognition of similarities between species being compared. This is as true today as it was for Aristotle. However, the concept of “similarity” has undergone substantial refinement. Not all similarities indicate a genuine relationship: Dissimilar species can evolve similar characteristics independently, in response to similar environmental factors. For example, flight has emerged independently in many species, including insects, birds, bats, and pterosaurs. The wings of these different animals are inevitably similar since they serve the same purpose, but they are sufficiently distinct to suggest independent origins.
Modern taxonomists distinguish these two different sorts of similarity as homology and homoplasy. Homologous characters are due to a common ancestry, whereas homoplasious (or homoplastic) characters are independently derived. This distinction by the presence or absence of shared descent is explicitly phylogenetic, and therefore presumes the mutability, or evolution, of species. This distinction was first drawn by the English naturalist Richard Owen (1804-1892), an antievolutionist for whom homologies were evidence of common design.
Several novel approaches to taxonomy emerged in the twentieth century. The most influential was cla-distics, devised by the German zoologist Willi Hennig (1913-1976). Hennig further refined the understanding of similarity, subdividing homologies into synapo-morphies, symplesiomorphies, and autapomorphies. An autapomorphy is a character exhibited by only one of a range of species. A symplesiomorphy is a character common to the whole range, part of the species’ shared legacy, although some may display it to a greater extent than others. Conversely, a synapomorphy is a character shared by only some of the species. The central contention of cladistics is that careful tracking of synapomorphies can reveal the underlying phylogenetic relationships between species, whereas autapomorphic and symplesiomorphic characters can be of no use.
To see why, let us return to stamp collecting. Suppose you were sorting some stamps into smaller groups. Any properties shared by the whole collection—perhaps they are all rectangular—will be of no use. Nor would properties exhibited by only one stamp, perhaps a lone airmail issue. Useful properties will be those present in more than one, but fewer than all the stamps under consideration: the synapomorphies. This distinction is relative to the scope of the study: if some triangular, or other airmail stamps were added to the collection, then these properties would become synapomorphic too.
Cladism’s exclusively phylogenetic emphasis conflicts with other taxonomies. For cladists, the only measure of closeness between categories is recency of common ancestors. Hennig distinguished between monophyletic, paraphyletic, and polyphyletic groups, of which only the first are true clades, or natural groups. In each case, group members share a common ancestor, but only in monophyletic groups are the ancestor and all its descendents members of the group. Paraphyletic groups contain a common ancestor, but not all its descendents; and polyphyletic groups have no common ancestor within the group. For example, birds comprise a clade, the class Aves, since the most recent common ancestor of any two birds will always be a bird, and all the descendents of such ancestors are also birds. But crocodiles have a more recent common ancestor with birds than they do with tortoises. Hence reptiles do not comprise a clade, unless the birds (and mammals) are also included.
Cladists show phylogeny using the cladogram. Hennig believed that speciation would divide populations in two, and occur discretely. Hence an optimal (fully resolved) cladogram will be a dichotomy. This means that adding new species will always require the addition of an extra grade of classification, a poor fit with conventional Linnean terminology. Some cladists employ ever-more-finely qualified quasi-Linnean grades, others use numbering systems or leave some grades unlabelled.
Influences on Science and Society
As an abstract discipline, taxonomy can seem remote from the practical applications of science. However, there have been many important scientific breakthroughs that turned on taxonomic insight. For example, although it had been long believed that malaria was spread by mosquitoes, effective control measures were handicapped by the confusion of several closely related but geographically distinct species, not all of which spread the disease. Only when an accurate taxonomy of these insects was determined were control measures successfully deployed. Similar considerations apply in other fields of classification as well. For instance, much recent progress in the treatment of cancer has turned on more accurate taxonomy, since superficially similar tumors can respond to very different therapies.
There is a complex relationship between taxonomy and the formal study of language. As observed above, all language implies some form of classification. Of course, most such classifications are hopelessly naive in the light of conscientious systematics. Some individuals have sought to remedy this problem through the construction of artificial languages intended to reflect the natural order of the world. For example English naturalist John Ray (1627-1705) collaborated with English clergyman and mathematician John Wilkins (1614-1672), the first secretary of the Royal Society, on the latter’s An Essay Towards a Real Character, and a Philosophical Language (1668), an attempt to construct a new scientific language in which ambiguity would be impossible.
Conversely, the classification of languages into families, such as German orientalist and philologist Max Müller’s (1823-1900) Lectures on the Science of Language (1861), provided a model of how biological species might be classified, if it were conceded that they were mutable. Languages change clearly over time, and their boundaries are often vague, yet they can still be distinguished and their interrelations tracked.
Taxonomy has also been linked to embryology, especially through the slogan “Ontogeny recapitulates phylogeny.” That is, the development of the fetus resembles the phylogenetic sequence of the organism’s ancestry. This was first observed by the German embryologist Karl Ernst von Baer (1792-1876) and pushed too far by another German scientist, zoologist Ernst Haeckel (1834-1919). Haeckel’s view, that each individual passes through the same stages as its species, is demonstrably false: Human embryos may resemble fish, but they are not actually fish. Baer explained the phenomenon more effectively: early embryos are less specialized and exhibit more of the primitive, that is symplesiomorphic, features of their group.
Taxonomy is one of the principal sources of conceptual originality and explanatory force in biology. Not only would other branches of the discipline be unable to proceed without the classification of their data, in many cases they are also indebted to systematics for their theoretical innovations. For example, understanding the concept of species has come largely from taxonomists, as have the foundations of ethology, the study of animal behavior, and biogeography, the study of the distribution of plants and animals.
The last of these is an essential ingredient of the science of conservation, in which taxonomy has played a crucial role, both in assessing the magnitude of the task and exploring the feasibility of possible methods. Fewer than 2 million species are known, but estimates of the total number are much larger, although they vary wildly from 10 million to 100 million and beyond. The arguments behind these estimates appeal to taxonomic reasoning.
One of the most controversial aspects of taxonomy is the place of our own species and its subdivision. Ancient and medieval classifications included man within a “chain of being” that ran from inanimate objects up to God. Taxonomists such as Linnaeus, for whom species were fixed, often acknowledged the similarities between men and apes. Indeed Linnaeus exaggerated them, mistakenly placing the orangutan among the genus Homo. However, the spread of evolutionary ideas meant that this resemblance spoke not to a similar design but to a shared origin. This was much more controversial: Darwin largely overlooked the place of man in On the Origin of Species (1859), postponing the subject to The Descent of Man (1871). The Welsh naturalist Alfred Russel Wallace (1823-1913), who independently proposed natural selection, could never bring himself to accept the human brain as a product of the process of which he was the codiscoverer.
An even more controversial subject has been the classification of the different races of humanity. In the nineteenth century evolutionists were divided: Did the human race have a single origin, or were the separate races descended from separately evolved (or created) ancestors? Polygeny, the latter view, was particularly well supported in the United States, where it helped lend spurious legitimacy to the practice of slavery. Monogeny ultimately prevailed, but it in turn provoked the question whether race actually had any biological significance. The identification of taxonomic ranks below that of species has become controversial in itself. Some systematists argue that multivariate analysis of the many traits unevenly distributed within a species population is more valuable than the pursuit of ever more fine-grained subspecies, which may mask important properties of the species. But it is not clear that the differences among humans are sufficient even to satisfy conventional definitions of subspecies.
The use by governments of race concepts has a particularly sorry history. Prejudice against minorities in general, and anti-Semitism in particular, can be traced back to medieval Europe. But the expression of this prejudice in racial terms is much more recent. This characterization underpinned the Nuremburg laws of 1935 that led to the Nazi Holocaust. Elsewhere, the classification of races has had equally tragic consequences. Between 1950 and 1990 the government of South Africa classified its citizens by race, denying all but whites full property and legal rights. The United States government has tracked the racial composition of its population since the early nineteenth century, primarily through the census. This practice reinforced the “one-drop rule,” which classified individuals as black if they had any black ancestry. The 2000 census was the first to permit more than one racial box to be checked: If one of those boxes was white, however, the individual was counted as a member of the other race only. This is a conundrum, since omitting racial categories could make compliance with civil rights legislation impossible to enforce.
Modern Cultural Connections
A famous passage by the Argentinian writer Jorge Luis Borges (1899-1986) questions the very idea of classification. Borges imagines a certain Chinese encyclopedia entitled Celestial Empire of Benevolent Knowledge. In its remote pages it is written that the animals are divided into: (a) belonging to the Emperor, (b) embalmed, (c) tame, (d) suckling pigs, (e) sirens, (f) fabulous, (g) stray dogs, (h) included in the present classification, (i) frenzied, (j) innumerable, (k) drawn with a very fine camel hair brush, (l) et cetera, (m) having just broken the water pitcher, (n) that from a long way off look like flies. The sheer implausibility of this list draws attention to the contingent and nominalist aspects of all classifications.
The French philosopher Michel Foucault (1926-1984) took this passage as the starting point for his own genealogical investigation of the history of classification, The Order of Things (1966). Where Borges sought to undercut all classification, Foucault set out to expose its secret history. He observes that the ways in which we classify things are such fundamental aspects of our conceptual furniture that we mistakenly presume they could not be otherwise. That is, they form part of what he calls an epistemé: a very general system of thought and knowledge, independent of specific disciplines but tied to their historical context. Foucault’s widely influential work has provoked a growing interest in classification in the humanities and social sciences.
The explosive growth of the World Wide Web, and particularly of user-generated content, has also heightened the importance of classification. As the quantity of data grows, the more difficult it becomes to find things without a catalog. Cataloging the enormous data sets found online would be prohibitively time consuming and expensive. But if individuals place tags on items sharing features of interest to them, the resultant structure can facilitate searching by others. The American information scientist Thomas Vander Wal has proposed “folksonomy” to describe this process.
The enormous expansion of knowledge about biological species and their taxonomy in recent decades has also produced unmanageably vast quantities of data. Perhaps unsurprisingly, there is no single catalog of life on Earth; the information is diffused over thousands of libraries and archives. The growing political focus on biodiversity, however, and the accelerating growth of computer networks, has made a remedy to this oversight a feasible project.
At the March 2007 G8 meeting (France, the United States, the United Kingdom, Canada, Germany, Italy, Japan, and Russia), the environment ministers of the member governments announced the Potsdam Initiative—Biological Diversity 2010. One objective was to facilitate a global species information system to gather and make available information on all known species as a tool for both public information and enhanced scientific cooperation. This project has begun to take shape as the Encyclopedia of Life. The organizers, a consortium of natural history museums, hope to have catalogued the 1.8 million known species by 2018.
For biologists, one hope for the project is that the application of powerful data mining techniques will bring to light hitherto unsuspected patterns. Hence the encyclopedia will facilitate the practical application of biodiversity, one of the motives for its creation. More decisively, it will enhance our moral and aesthetic appreciation of the complex structure of the natural world, an essential prerequisite for conservation that only systematics can provide.
Primary Source Connection
The following article was written by Peter N. Spotts, a science and technology writer for The Christian Science Monitor.Founded in 1908, The Christian Science Monitor is an international newspaper based in Boston, Massachusetts. The article describes efforts by the national Science Foundation, in light of accelerating rates of species extinctions, to catalogue all species of life on Earth into a “family tree.”
CATALOG FOR LIFE ON EARTH
With 30 percent of species likely to disappear by 2050, mapping the family tree finds new urgency.
Not since an asteroid smacked into Earth to end the reign of the dinosaurs 65 million years ago has the evolutionary future of life on the planet been rewritten as extensively—or as suddenly—as it is being rewritten today.
By the middle of this century, many biologists estimate, human activities—from urban sprawl and deforestation to overfishing—will have erased up to 30 percent of the species inhabiting the planet.
Millions of those plants, animals, insects, and microbes never will have mushroomed under a field researcher’s microscope. Their potential value—for the ecological role they play or the useful chemicals they produce—and place in history will go unassessed.
This prospect is adding urgency to a new effort to build a comprehensive “family tree” of life on Earth—from bacteria to whales and all their fossilized ancestors. In the process, researchers hope to pull together an Internet-based catalog of Earth’s existing species.
An exhaustive “tree” establishing the evolutionary relationships of organisms, and a catalog placing them in their ecological niches, are expected to become powerful tools for guiding conservation efforts, discovering new chemical compounds for human use, and even investigating suspected acts of bioterrorism.
Researchers add that the tree of life will yield new insights into evolution itself, answering such questions as how often photosynthesis emerged, and whether life evolved only once. And, they say, the prospect of being able to address these questions marks a new chapter in the life sciences.
“We are at a historic turning point in biology,” says Harvard University entomologist Edward Wilson.
He explains that biologists until now have been reductionists, probing organisms down to the level of individual genes. This has culminated in various projects to map and sequence the genomes of organisms ranging from bacteria to humans.
Looking for the forest, after years of trees
“Now biology is entering its synthesis phase,” he continues. “We’re trying to put it all back together. This puts the emphasis on complexity, on self-assembly, on interdisciplinary work, and on the lateral spread of studies of an organism” among scientists worldwide.
This interdisciplinary approach is one of the distinguishing features of the new tree-of-life effort, says Quentin Wheeler, director of the environmental biology division at the National Science Foundation in Arlington, Va.
“Until now, this sort of work has been done piecemeal, with individual scientists slogging on their own,” says Dr. Wheeler.
The NSF is spending up to $10 million this year and is seeking $12 million for next year to begin the process of mapping “significant branches of the tree,” he says. The agency’s tree-of-life initiative, which could expand into an international effort following meetings with biologists in Europe later this year, could take up to 15 years to complete.
Although humans and their ancestors have long been classifying organisms out of eat-or-be-eaten necessity, scientists moved into the field in a major way following Darwin’s publication of “On the Origin of the Species” in 1859.
Yet only in the 1960s, when scientists standardized their approach to organizing organisms, did tree-building take off, according to Joel Cracraft, an ornithologist at the American Museum of Natural History.
Today, “out of the 1.7 million species we know of, up to 70,000 have been looked at,” Dr. Cracraft says. “Eighty percent of what we know of the history of life, we’ve learned in the last decade.”
And plenty of work remains to be done. Biologists estimate that from 10 million to 15 million additional species await discovery.
“There are huge areas on the tree we know nothing about,” laments Terry Yates, a University of New Mexico biologist who is widely acknowledged as a prime mover behind the current tree-of-life effort.
Some of those areas lurk in museum drawers
Oliver Zompro, a graduate student at the Max Planck Institute for Limnology in Plön, Germany, was studying a sticklike insect preserved in a collection in London. He established that the specimen, which came from Africa, represented a new insect order that dates back at least 45 million years. He reported his findings in April in the journal Science.
Two trends have converged to open the possibility of building a comprehensive tree of life, researchers say.
One is the emergence of the affordable computing horsepower needed to compare and find patterns in large amounts of data about, for instance, habitats, fossil information, and physical characteristics.
The other is the growth of molecular tools to help establish relationships among organisms. These would have eluded scientists focusing primarily on what creatures, plants, or microbes look like, or the features they share.
Prominent among these is biologists’ ability to sequence entire genomes of organisms. Researchers have learned to use sequences of DNA, which carry the genetic blueprint, and RNA, the molecular contractors that take DNA’s information and begin the building process, to help establish evolutionary relationships between and among organisms. For example, such techniques have helped establish that as a group, fungi are more closely related to animals than to plants.
The use of molecular techniques to help establish lineages can be a matter of life and death, scientists say.
During a recent conference on “Assembling the Tree of Life” at the American Museum of Natural History, one biologist noted that the efficacy of antivenin for bites from Australian brown snakes depends on how closely related the antivenin’s source is to the species that did the biting. The various species of brown snake are hard to distinguish at a glance, he said.
Researchers are quick to note some of the social and economic benefits they hope to derive from building a comprehensive tree of life.
“Nature has provided us with billions of years of free R& D,” Dr. Yates says. The tree would allow scientists “to make an intelligent search for very specific products,” from new pharmaceuticals to “natural” bug repellents.
But over the long term, a tree’s greatest value may lie in its potential for guiding conservation strategies as the international community strives to preserve the planet’s biodiversity in the face of what some researchers term the planet’s sixth extinction event.
Unchecked, human activities are conducting an enormous, uncontrolled evolutionary experiment, say biologists Andrew Knoll of Harvard University and Norman Myers of Oxford University in England.
Humans “are ‘deciding’ on evolution’s future in virtually a scientific vacuum—deciding all too unwittingly, but effectively and increasingly,” the two scientists have written.
The fossil record suggests that it takes roughly 5 million years for earth’s biosphere to recover from a major extinction event, they say. While no one can forecast what may happen to a given species at the end of that period, the two add that biologists can provide a sense for how reduced diversity could affect the broader course of evolution.
For example, they suggest that large mammals, which have relatively slow reproductive cycles, could give way to species that adapt more quickly to changes. This could lead to an increase in the number of ecosystems dominated by organisms that today we would consider pests and weeds. In addition, diversity could be expected to increase among species that thrive in human-affected ecosystems.
In total, while evolution certainly would continue, it could yield a more homogenized set of ecosystems with much less diversity overall than exists today.
Conservation efforts that once focused on high-profile species have largely shifted toward projects that preserve ecosystems inhabited by endangered species.
Yet, researchers say, conservationists may need to take yet another conceptual leap by designing projects in ways that preserve “the evolutionary processes at risk.”
Figuring out what to save as time runs short
Drs. Myers and Knoll posit that it is more important to maintain the “potential for diversity generation” and the “functional groups that increase the potential for recovery” than individual species.
“What do we save that preadapts the world to rediversify?” asks the NSF’s Wheeler.
He suggests that the importance of preserving old-growth forests in northern California may rest at least as much on preserving his “favorite poster child”—a group of primitive wingless insects known as bristletails—as it does on preserving the spotted owl.
One species of bristletail in particular was known only from fossils and was thought to have been extinct for millions of years. Then in the 1960s, Wheeler says, live specimens of these insects were found in the old-growth forests of northern California’s coast.
New molecular analyses suggest that the “fossil” species is the sister to the line that begat all 800,000 winged-insect species known today. The creature may represent an evolutionary branching point that could in the future repeat its diversification.