In earlier work, I predicted that we would probably not be able to determine the colors of the dinosaurs. I lost this epistemic bet against science in dramatic fashion when scientists discovered that it is possible to draw inferences about dinosaur coloration based on the microstructure of fossil feathers (Vinther et al., 2008). This paper is an exercise in philosophical error analysis. I examine this episode with two questions in mind. First, does this case lend any support to epistemic optimism (...) about historical science? Second, under what conditions is it rational to make predictions about what questions scientists will or will not be able answer? In reply to the first question, I argue that the recent work on the colors of the dinosaurs matters less to the debate about the epistemology of historical science than it might seem. In reply to the second question, I argue that it is difficult to specify a policy that would rule out the failed bet without also being too conservative. (shrink)

Phylogenies are increasingly prominent across all of biology, especially as DNA sequencing makes more and more trees available. However, their utility is compromised by widespread misconceptions about what phylogenies can tell us, and improved tree thinking is crucial. The most-serious problem comes from reading trees as ladders from left to right - many biologists assume that species-poor lineages that appear early branching or basal are ancestral - we call this the primitive lineage fallacy. This mistake causes misleading inferences about changes (...) in individual characteristics and leads to misrepresentation of the evolutionary process. The problem can be rectified by considering that modern phylogenies of present-day species and genes show relationships among evolutionary cousins. Emphasizing that these are extant entities in the 21st century will help correct inferences about ancestral characteristics, and will enable us to leave behind 19th century notions about the ladder of progress driving evolution. (shrink)

Despite the iconic roles of coelacanths, cycads, tadpole shrimps, and tuataras as taxa that demonstrate a pattern of morphological stability over geological time, their status as living fossils is contested. We responded to these controversies with a recommendation to rethink the function of the living fossil concept. Concepts in science do useful work beyond categorizing particular items and we argued that the diverse and sometimes conflicting criteria associated with categorizing items as living fossils represent a complex problem space associated with (...) answering a range of questions related to prolonged evolutionary stasis. Turner defends the living concept against a variety of recent skeptics, but his criticism of our approach relies on a misreading of our main argument. This misreading is instructive because it brings into view the value of three central themes for rethinking the living fossil concept—the function of concepts in biology outside of categorization, the methodological importance of distinguishing parts and wholes in conceptualizing evolutionary phenomena, and articulating diverse explanatory goals associated with these phenomena. (shrink)

Can we be realists about a general category but pluralists about concepts relating to that category? I argue that paleobiological methods of delineating species are not affected by differing species concepts, and that this underwrites an argument that species concept pluralists should be species category realists. First, the criteria by which paleobiologists delineate species are ‘indifferent’ to the species category. That is, their method for identifying species applies equally to any species concept. To identify a new species, paleobiologists show that (...) interspecies processes, such as phenotypic plasticity, sexual dimorphism, or ontogenetic diversity, are a worse explanation of the variance between specimens than intraspecies processes. As opposed to operating under a single or plurality of species concepts, then, paleobiologists use abductive inferences, which would be required regardless of any particular species concept. Second, paleobiologists are frequently interested in large-scale, long-term morphological patterns in the fossil record, and resolving the fine-grained differences which result from different species concepts is irrelevant at those scales. I argue that this claim about paleobiological practice supports what I call ‘indifference realism’ about the species category. The indifference realist argues that when legitimate investigation is indifferent to a plurality of concepts, we should be realists about the category those concepts pertain to. (shrink)

A series of recent studies on extant coelacanths has emphasised the slow rate of molecular and morphological evolution in these species. These studies were based on the assumption that a coelacanth is a ‘living fossil’ that has shown little morphological change since the Devonian, and they proposed a causal link between low molecular evolutionary rate and morphological stasis. Here, we have examined the available molecular and morphological data and show that: (i) low intra-specific molecular diversity does not imply low mutation (...) rate, (ii) studies not showing low substitution rates in coelacanth are often neglected, (iii) the morphological stability of coelacanths is not supported by paleontological evidence. We recall that intra-species levels of molecular diversity, inter-species genome divergence rates and morphological divergence rates are under different constraints and they are not necessarily correlated. Finally, we emphasise that concepts such as ‘living fossil’, ‘basal lineage’, or ‘primitive extant species’ do not make sense from a tree-thinking perspective.Editor's suggested further reading in BioEssays Tree thinking for all biology: the problem with reading phylogenies as ladders of progress Abstract. (shrink)