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)

The origins and evolution of the Archaea, Bacteria, and Eukarya remain controversial. Phylogenomic‐wide studies of molecular features that are evolutionarily conserved, such as protein structural domains, suggest Archaea is the first domain of life to diversify from a stem line of descent. This line embodies the last universal common ancestor of cellular life. Here, we propose that ancestors of Euryarchaeota co‐evolved with those of Bacteria prior to the diversification of Eukarya. This co‐evolutionary scenario is supported by comparative genomic and phylogenomic (...) analyses of the distributions of fold families of domains in the proteomes of free‐living organisms, which show horizontal gene recruitments and informational process homologies. It also benefits from the molecular study of cell physiologies responsible for membrane phospholipids, methanogenesis, methane oxidation, cell division, gas vesicles, and the cell wall. Our theory however challenges popular cell fusion and two‐domain of life scenarios derived from sequence analysis, demanding phylogenetic reconciliation. (shrink)

ABSTRACT Darwin claims in the Origin that similarity is evidence for common ancestry, but that adaptive similarities are ‘almost valueless’ as evidence. This second claim seems reasonable for some adaptive similarities but not for others. Here we clarify and evaluate these and related matters by using the law of likelihood as an analytic tool and by considering mathematical models of three evolutionary processes: directional selection, stabilizing selection, and drift. Our results apply both to Darwin’s theory of evolution and to modern (...) evolutionary biology. _1_ Introduction _2_ The Likelihood Framework _3_ A Sufficient Condition for a Similarity to Favour Common Ancestry over Separate Ancestry _4_ The 1/p Criterion and Its Limitations _5_ Directional Selection versus Drift _6_ Stabilizing Selection versus Drift _7_ Going beyond Two Taxa _8_ Conclusions Appendix. (shrink)

This article proposes a new interpretation of mutual information. We examine three extant interpretations of MI by reduction in doubt, by reduction in uncertainty, and by divergence. We argue that the first two are inconsistent with the epistemic value of information assumed in many applications of MI: the greater is the amount of information we acquire, the better is our epistemic position, other things being equal. The third interpretation is consistent with EVI, but it is faced with the problem of (...) measure sensitivity and fails to justify the use of MI in giving definitive answers to questions of information. We propose a fourth interpretation of MI by reduction in expected inaccuracy, where inaccuracy is measured by a strictly proper monotonic scoring rule. It is shown that the answers to questions of information given by MI are definitive whenever this interpretation is appropriate, and that it is appropriate in a wide range of applications with epistemic implications. _1_ Introduction _2_ Formal Analyses of the Three Interpretations _2.1_ Reduction in doubt _2.2_ Reduction in uncertainty _2.3_ Divergence _3_ Inconsistency with Epistemic Value of Information _4_ Problem of Measure Sensitivity _5_ Reduction in Expected Inaccuracy _6_ Resolution of the Problem of Measure Sensitivity _6.1_ Alternative measures of inaccuracy _6.2_ Resolution by strict propriety _6.3_ Range of applications _7_ Global Scoring Rules _8_ Conclusion. (shrink)

This paper proposes a new interpretation of mutual information (MI). We examine three extant interpretations of MI by reduction in doubt, by reduction in uncertainty, and by divergence. We argue that the first two are inconsistent with the epistemic value of information (EVI) assumed in many applications of MI: the greater is the amount of information we acquire, the better is our epistemic position, other things being equal. The third interpretation is consistent with EVI, but it is faced with the (...) problem of measure sensitivity and fails to justify the use of MI in giving definitive answers to questions of information. We propose a fourth interpretation of MI by reduction in expected inaccuracy, where inaccuracy is measured by a strictly proper monotonic scoring rule. It is shown that the answers to questions of information given by MI are definitive whenever this interpretation is appropriate, and that it is appropriate in a wide range of applications with epistemic implications. (shrink)

We show that as a chain of confirmation becomes longer, confirmation dwindles under screening-off. For example, if E confirms H1, H1 confirms H2, and H1 screens off E from H2, then the degree to which E confirms H2 is less than the degree to which E confirms H1. Although there are many measures of confirmation, our result holds on any measure that satisfies the Weak Law of Likelihood. We apply our result to testimony cases, relate it to the Data-Processing Inequality (...) in information theory, and extend it in two respects so that it covers a broader range of cases. (shrink)

ABSTRACT ‘Modus Darwin’ is the name given by Elliott Sober to a form of argument that he attributes to Darwin in the Origin of Species, and to subsequent evolutionary biologists who have reasoned in the same way. In short, the argument form goes: similarity, ergo common ancestry. In this article, I review and critique Sober’s analysis of Darwin’s reasoning. I argue that modus Darwin has serious limitations that make the argument form unsuitable for supporting Darwin’s conclusions, and that Darwin did (...) not reason in this way. (shrink)

In this paper, I discuss several temporal aspects of paleontology from a philosophical perspective. I begin by presenting the general problem of “taming” deep time to make it comprehensible at a human scale, starting with the traditional geologic time scale: an event-based, relative time scale consisting of a hierarchy of chronological units. Not only does the relative timescale provide a basis for reconstructing many of the general features of the history of life, but it is also consonant with the cognitive (...) processes humans use to think about time. Absolute dating of rocks, fossils, and evolutionary events (such as branching events on the tree of life) can be accomplished through the use of radiometric dating, chronological signals extractable from fossil growth patterns, and the “molecular clock.” Sometimes these different methods of absolute dating, which start from largely independent assumptions and evidentiary bases, converge in their temporal estimates, resulting in a consilience of inductions. At other times they fail to agree, either because fossils and molecules are giving temporal information about different aspects of nature and should not be expected to agree, or because of flawed assumptions that give rise to an inaccurate estimate. I argue that in general, despite the fact that it can be difficult to integrate disparate kinds of evidence, the principle of total evidence should be applied to the dating of evolutionary events. As a historical science, paleontology studies past events we cannot observe directly. This raises questions of epistemic access, meaning that due to the fragmentary nature of the fossil record we may find ourselves without access to the relevant traces to adjudicate between rival hypotheses about the past. The problems and prospects of epistemic access are explored through a case study of the reconstruction of the colors of dinosaurs. The paper closes with a reflection on the Darwin- Lyell metaphor of the fossil record as a highly fragmentary history book, and a call for a reconsideration of the book metaphor in favor of a systems view of the geologic and fossil records. (shrink)