Online research in philosophy

Biologists and philosophers that debate the existence of the species category are split into two main camps. Some believe that the species category does not exist and that the term ‘species’ should be junked. Others believe that given new biological insights and the application of philosophical ideas, we can show that the species category does exist. This paper charts a position between skeptics and defenders of the species category. That position holds that the species category does not exist, yet those taxa we call ‘species’ do exist. And, despite skepticism over the species category, there are pragmatic reasons to keep the word ‘species.’ This approach to the species category is far from new, for it is the one that Darwin suggested. Hence it is dubbed ‘Darwin’s solution to the species problem.’.

I argue for accepting a pluralist approach to species, while rejecting the realism about species espoused by P. Kitcher and a number of other philosophers of biology. I develop an alternative view of species concepts as divisions of organisms into groups for study which are relative to the systematic explanatory interests of biologists at a particular time. I also show how this conception resolves a number of difficult puzzles which plague the application of particular species concepts.

College of Medicine, University of South Alabama Mobile, AL 36688-0002, USA wbp501{at}jaguar1.usouthal.edu ' + u + '@' + d + ' '//-->   Abstract Recent work in viral genomics has shown that bacteriophages exhibit a high degree of mosaicism, which is most likely due to a long history of prolific horizontal gene transfer (HGT). Given these findings, we argue that each of the most plausible attempts to properly classify bacteriophages into distinct species fail. Mayr's biological species concept fails because there is no useful viral analog to sexual reproduction. Phenetic species concepts fail because they obscure the mosaicism and the rich reticulated viral histories. Phylogenetic species concepts, even when extended to take into account reticulation, fail because there is no non-arbitrary distinction between recombination events that create a new viral species and those that do not. There is good reason to think that bacteriophages, arguably the Earth's most abundant biological agent, evolve without forming species. Introduction The Biology of Viruses 2.1 Bacteriophage life cycles 2.2 Mechanisms of HGT The Species Problem and Species Concepts 3.1 Phenetic species concepts 3.2 The biological species concept 3.3 Phylogenetic species concepts 3.4 The ecological species concept 3.5 Homeostatic property cluster species Viruses and Species Taxonomy Reticular Phylogenies Conclusion CiteULike     Connotea     Del.icio.us     What's this?

A natural starting place for developing a phylogenetic species concept is to examine monophyletic groups of organisms. Proponents of “the” Phylogenetic Species Concept fall into one of two camps. The first camp denies that species even could be monophyletic and groups organisms using character traits. The second groups organisms using common ancestry and requires that species must be monophyletic. I argue that neither view is entirely correct. While monophyletic groups of organisms exist, they should not be equated with species. Instead, species must meet the more restrictive criterion of being genealogically exclusive groups where the members are more closely related to each other than to anything outside the group. I carefully spell out different versions of what this might mean and arrive at a working definition of exclusivity that forms groups that can function within phylogenetic theory. I conclude by arguing that while a phylogenetic species concept must use exclusivity as a grouping criterion, a variety of ranking criteria are consistent with the requirement that species can be placed on phylogenetic trees.

I analyze a number of widespread misconceptions concerning species. The species category, defined by a concept, denotes the rank of a species taxon in the Linnaean hierarchy. Biological species are reproducing isolated from each other, which protects the integrity of their genotypes. Degree of morphological difference is not an appropriate species definition. Unequal rates of evolution of different characters and lack of information on the mating potential of isolated populations are the major difficulties in the demarcation of species taxa.

Many phylogenetic systematists have criticized the Biological Species Concept (BSC) because it distorts evolutionary history. While defenses against this particular criticism have been attempted, I argue that these responses are unsuccessful. In addition, I argue that the source of this problem leads to previously unappreciated, and deeper, fatal objections. These objections to the BSC also straightforwardly apply to other species concepts that are not defined by genealogical history. What is missing from many previous discussions is the fact that the Tree of Life, which represents phylogenetic history, is independent of our choice of species concept. Some species concepts are consistent with species having unique positions on the Tree while others, including the BSC, are not. Since representing history is of primary importance in evolutionary biology, these problems lead to the conclusion that the BSC, along with many other species concepts, are unacceptable. If species are to be taxa used in phylogenetic inferences, we need a history-based species concept.

Species concepts for bacteria and other microbes are contentious, because they are often asexual. There is a Problem of Homogeneity: every mutation in an asexual lineage forms a new strain, of which all descendents are clones until a new mutation occurs. We should expect that asexual organisms would form a smear or continuum. What causes the internal homogeneity of asexual lineages, if they are in fact homogeneous? Is there a natural “species concept” for “microbes”? Two main concepts devised for metazoans and metaphytes have been applied to bacteria. One is the Recombination Concept, a revised form of the Biological Species Concept in which the homogenizing mechanism is the sharing of genome fragments, somewhat akin to sexual recombination. The other is the Ecological Species Concept, in which the ecological niche is that which maintains lineages as cohesive. In this paper I will discuss these two concepts, and offer an underlying model that conjoins them, and consider the implications for species concepts in general. In short, my argument is that asexual species are instances of the most primitive and underived notion of species, which I will call “quasispecies”, following Eigen, and that sexual species are merely one derived kind of species. Moreover, I will argue that there is a continuum of recombination from simple viral models in which each strain is a clone, through to obligate recombination of 50% of the parents’ genome, and that consequently there is no sharp division between “microbial” and more familiar species.

Difficulties with the typological concept of species led biologists to reject the "typological" presupposition of an archetype which is manifest in each member of a species. The resulting concept of species, which is here called the phenotypic species concept, is considered as implying that biological species are not real. Modern population thinking has given rise to the concept of a species as a gene-pool. This modern concept is contrasted here with the phenotypic concept in light of some general criteria for evaluating species concepts and is shown to be more satisfactory. Finally, it is held that to ask if a species is real is to ask whether the species grouping arrived at by applying the principles involved in the species concept corresponds with groups of organisms amongst which important biological relationships exist. It is argued that in this sense species, as defined by the gene-pool concept, are certainly real.

Marc Ereshefsky argues that pluralism about species suggests that the species concept is not theoretically useful. It is to be abandoned in favor of several concrete species concepts that denote real categories. While accepting species pluralism, the present paper rejects eliminativism about the species category. It is argued that the species concept is important and that it is possible to make sense of a general species concept despite the existence of different concrete species concepts.

The correct explanation of why species, in evolutionary theory, are individuals and not classes is the cladistic species concept. The cladistic species concept defines species as the group of organisms between two speciation events, or between one speciation event and one extinction event, or (for living species) that are descended from a speciation event. It is a theoretical concept, and therefore has the virtue of distinguishing clearly the theoretical nature of species from the practical criteria by which species may be recognized at any one time. Ecological or biological (reproductive) criteria may help in the practical recognition of species. Ecological and biological species concepts are also needed to explain why cladistic species exist as distinct lineages, and to explain what exactly takes place during a speciation event. The ecological and biological species concepts work only as sub-theories of the cladistic species concept and if taken by themselves independently of cladism they are liable to blunder. The biological species concept neither provides a better explanation of species indivudualism than the ecological species concept, nor, taken by itself, can the biological species concept even be reconciled with species individualism. Taking the individuality of species seriously requires subordinating the biological, to the cladistic, species concept.