Phylogenetic trees are meant to represent the genealogical history of life and apparently derive their justification from the existence of the tree of life and the fact that evolutionary processes are treelike. However, there are a number of problems for these assumptions. Here it is argued that once we understand the important role that phylogenetic trees play as models that contain idealizations, we can accept these criticisms and deny the reality of the tree while justifying the continued use of trees (...) in phylogenetic theory and preserving nearly all of what defenders of trees have called the “importance of tree thinking.”. (shrink)

A common view is that species occupy a unique position on the Tree of Life. Evaluating this claim requires an understanding of what the Tree of Life represents. The Tree represents history, but there are at least three biological levels that are often said to have genealogies: species, organisms, and genes. Here I focus on defending the plausibility of a gene-based account of the Tree. This leads to an account of species that are determined by gene genealogies. On this view, (...) an exclusive group is a group of organisms that forms a clade for a higher proportion of the genome than any conflicting clade. Taxa occupy a unique position in what can be called the ‘primary concordance tree’. But each gene has its own historical ‘Tree of Life’. I conclude by arguing that both organismal pedigrees with their corresponding Tree as well as gene genealogies and their trees are objectively real and play important, but different, roles in biological practice. (shrink)

Phylogenetics is the study and reconstruction of evolutionary history and is filled with numerous foundational issues of interest to philosophers. This paper briefly introduces some central concepts in the field, describes some of the main methods for inferring phylogenies, and provides some arguments for the superiority of model-based methods such as Likelihood and Bayesian methods over nonparametric methods such as parsimony. It also raises some underdeveloped issues in the field of interest to philosophers.

The project of this paper is to understand what a phylogenetic tree represents and to discuss some of the implications that this has for the practice of systematics. At least the first part of this task, if not both parts, might appear trivial—or perhaps better suited for a single page in a textbook rather than a scholarly research paper. But this would be a mistake. While the task of interpreting phylogenetic trees is often treated in a trivial way, their interpretation (...) is tied to foundational conceptual questions at the heart of systematics—questions whose answers are hotly disputed. I have previously argued that widely shared ideas about the meaning and interpretation of phylogenetic trees are inconsistent with species concepts other than some genealogical version of a phylogenetic species concept (Velasco 2008). Here I rely on a similar approach and concentrate on the implications of the necessary conditions underlying the inferences that we make using phylogenetic trees. I argue that common practices for the interpretation and use of trees are in conflict and that unacceptable principles about species as units of phylogeny must be given up. According to the view that I will develop, all phylogenetic trees depict the history of populations. The branches on trees represent collections of population lineages through time and the splits represent population lineage splits. This is true regardless of whether the tips of the trees are themselves populations, or are species or higher taxa. Although this conclusion might be paired naturally with a view that species must be monophyletic groups, this population-centric view of trees is independent of that view of species. If we still want to have species that are paraphyletic groups of populations, this is permissible as long as we also do not treat species as the units of phylogeny. This population-centric view opposes a species-centric view of phylogeny and might be called a “rank-free” approach since it entails that we do not need to determine which groups are species (which is partly a ranking question) in order to build a tree. This conclusion and the argument for it are meant to be consistent with, but not require, acceptance of the conclusions of Velasco (2008) regarding species. (shrink)

In this article, I discuss and critique how metaphysicians of race have conceived of and defended racial realism according to how biologists use “race”. I start by defining “racial realism” in the broadest accepted way in the metaphysics of race. Next, I summarize a representative sample of recent attempts from metaphysicians of race and biologists to defend racial realism and the main criticisms against each attempt. I discuss how metaphysicians of race have defended racial realism according to how ordinary people (...) use “race” in Part II. (shrink)

Some astronomers believe that we have discovered that Pluto is not a planet. I contest this assessment. Recent discoveries of trans-Neptunian Pluto-sized objects do not require that we exclude Pluto from the planets. But the obvious alternative, that classificatory revision is a matter of arbitrary choice, is also unpalatable. I argue that this classificatory controversy — which I compare to the controversy about the classification of the platypus — illustrates how our classificatory practices are laden with normative commitments of a (...) distinctive kind. I argue that the “norm-ladenness” of classification has philosophically significant ramifications for how we think about scientific disputes and debates in the metaphysics of classification such as the monism/pluralism debate. (shrink)

The nature of science is a primary goal in school science. Most teachers are not well-prepared for teaching NOS, but a sophisticated and in-depth understanding of NOS is necessary for effective teaching. Some authors emphasize the need for teaching NOS in context. Species, a central concept in biology, is proposed in this article as a concrete example of a means for achieving increased understanding of NOS. Although species are commonly presented in textbooks as fixed entities with a single definition, the (...) concept of species is a highly discussed one in the science and the philosophy of biology. A multitude of species concepts exist, reflecting both the views and interests of researchers and their utility in different organism groups. The present study serves to address the following questions: How do textbooks in Norwegian primary and lower secondary schools present the concept of species? Can inquiries into the concept of “species” serve to highlight aspects of NOS? A review of the available literature on species and species concepts in school is also performed. In the schoolbooks, the biological species concept is commonly used as the main definition, whereas the morphological species concept is represented by additional remarks of similarity. The potential and pitfalls of using the species concept for teaching NOS are discussed, with NOS being discussed both as a family resemblance concept and as a consensus list. Teacher education is proposed as a starting point for inducing a more sophisticated view of biology into schools. (shrink)

The relation between method, concept and theory in science is complicated. I seek to shed light on that relation by considering an instance of it in systematics: The additional challenges phylogeneticists face when reconstructing phylogeny not at a single level, but simultaneously at multiple levels of the hierarchy. How does this complicate the task of phylogenetic inference, and how might it inform and shape the conceptual foundations of phylogenetics? This offers a lens through which the interplay of method, theory and (...) concepts may be understood in systematics, which, in turn, provides data for a more general account. (shrink)

Here, I consider the recent application of phylogenetic methods in historical linguistics. After a preliminary survey of one such method, i.e. cladistic parsimony, I respond to two common criticisms of cultural phylogenies: that cultural artifacts cannot be modeled as tree-like because of borrowing across lineages, and that the mechanism of cultural change differs radically from that of biological evolution. I argue that while perhaps remains true for certain cultural artifacts, the nature of language may be such as to side-step this (...) objection. Moreover, I explore the possibility that cladistic parsimony can be justified even if is true by appealing to the inference pattern known among philosophers as ‘Inference to the Best Explanation’. (shrink)

This article examines crop varietal standardization in the United States. Numerous committees formed in the early twentieth century to address the problem of nomenclatural rules in the horticultural and agricultural industries. Making shared reference to a varietal name proved a difficult proposition for seed-borne crops because plant conformity tended to change in the hands of different breeders. Moreover, scientific and commercial opinions diverged on the value of deviations within crop varieties. I review the function of descriptive difference in the seed (...) trade and in the framework of evolutionary theory before examining the institutional history of varietal standardization. Pimento peppers are used to represent how vegetables were treated differently than cereals. Lack of stability within a popular pimento variety caused problems for food packers in middle Georgia, which public breeders addressed by releasing new peppers. To conclude, the article questions the role of taxonomy in intellectual property, as breeding history and yield became defining attributes for making varietal distinctions. (shrink)

We argue for a new conventionalism about many kinds of evolutionary groups, including clades, cohesive units, and populations. This rejects a consensus, which says that given any one of the many legitimate grouping concepts, only objective biological facts determine whether a collection is such a group. Surprisingly, being any one kind of evolutionary group typically depends on which of many incompatible values are taken by suppressed variables. This is a novel pluralism underlying most any one group concept, rather than a (...) familiar pluralism claiming many concepts are legitimate. Consequently, we must help biological facts determine grouphood, even when given a single grouping concept. (shrink)