Stephen Jay Gould argued that replaying the “tape of life” would result in a radically different evolutionary outcome. Some biologists and philosophers, however, have pointed to convergent evolution as evidence for robust replicability in macroevolution. These authors interpret homoplasy, or the independent origination of similar biological forms, as evidence for the power of natural selection to guide form toward certain morphological attractors, notwithstanding the diversionary tendencies of drift and the constraints of phylogenetic inertia. In this paper, I consider the implications (...) of homoplasy for the debate over the nature of macroevolution. I argue that once the concepts of contingency and convergence are fleshed out, it becomes clear that many instances of homoplasy fail to negate Gould’s overarching thesis, and may in fact support a Gouldian view of life. My argument rests on the distinction between parallelism and convergence, which I defend against a recent challenge from developmental biology. I conclude that despite the difficulties in defining and identifying parallelism, the concept remains useful and relevant to the contingency controversy insofar as it underscores the common developmental origins of iterated evolution. (shrink)

Scientific models are often said to be more or less general depending on how many cases they cover. In this paper we argue that the cardinality of cases is insufficient as a metric of generality, and we present a novel account based on measure theory. This account overcomes several problems with the cardinality approach, and additionally provides some insight into the nature of assessments of generality. Specifically, measure theory affords a natural and quantitative way of describing local spaces of possibility. (...) The generality of models can be understood as the measure of possibilities to which the models apply. In order to illustrate our view, we consider the example of structural genomics, the ongoing project of building three-dimensional models of biological macromolecules like proteins. Using measure theory, we interpret the practice of homology modeling, where such models are understood to apply widely but imperfectly to the space of possible proteins. (shrink)

This paper argues that besides mechanistic explanations, there is a kind of explanation that relies upon “topological” properties of systems in order to derive the explanandum as a consequence, and which does not consider mechanisms or causal processes. I first investigate topological explanations in the case of ecological research on the stability of ecosystems. Then I contrast them with mechanistic explanations, thereby distinguishing the kind of realization they involve from the realization relations entailed by mechanistic explanations, and explain how both (...) kinds of explanations may be articulated in practice. The second section, expanding on the case of ecological stability, considers the phenomenon of robustness at all levels of the biological hierarchy in order to show that topological explanations are indeed pervasive there. Reasons are suggested for this, in which “neutral network” explanations are singled out as a form of topological explanation that spans across many levels. Finally, I appeal to the distinction of explanatory regimes to cast light on a controversy in philosophy of biology, the issue of contingence in evolution, which is shown to essentially involve issues about realization. (shrink)

The reference class problem arises when we want to assign a probability to a proposition (or sentence, or event) X, which may be classified in various ways, yet its probability can change depending on how it is classified. The problem is usually regarded as one specifically for the frequentist interpretation of probability and is often considered fatal to it. I argue that versions of the classical, logical, propensity and subjectivist interpretations also fall prey to their own variants of the reference (...) class problem. Other versions of these interpretations apparently evade the problem. But I contend that they are all “no-theory” theories of probability - accounts that leave quite obscure why probability should function as a guide to life, a suitable basis for rational inference and action. The reference class problem besets those theories that are genuinely informative and that plausibly constrain our inductive reasonings and decisions. I distinguish a “metaphysical” and an “epistemological” reference class problem. I submit that we can dissolve the former problem by recognizing that probability is fundamentally a two-place notion: conditional probability is the proper primitive of probability theory. However, I concede that the epistemological problem remains. (shrink)

Biologists in the last 50 years have increasingly emphasized the role of historical contingency in explaining the distribution and dynamics of biological systems. However, recent work in philosophy of biology has shown that historical contingency carries various interpretations and that we are still lacking a general understanding of historicity, i.e., a framework from which to interpret why and to what extent history matters in biological processes. Building from examples and analyses of the long-term experimental evolution (LTEE) project, this paper argues (...) that historicity possess three essential conditions: (1) multiple possible pasts, (2) multiple possible outcomes at a given instant, and (3) a relationship of causal dependence between these two sets. These criteria can be further specified in two general forms of historicity: dependence on initial conditions and path dependence. More attention is devoted to developing a rigorous account of the latter, which captures the type of historicity displayed by stochastic processes. This paper also highlights that it is often more productive to adopt an instant-relative approach and think in terms of degree of historicity instead of trying to maintain a rigid and absolute dichotomy between historical and ahistorical (completely convergent) processes. (shrink)

The paper provides a new characterization of the concepts of necessity and contingency as they should be used in the historical context. The idea is that contingency (necessity) increases in direct (reverse) proportion to sensitivity to initial conditions. The merits of this suggestion are that it avoids the conflation of causality and necessity (or contingency and chance), that it enables the bracketing of the problem of free will while maintaining the concept of human action making a difference, that it sanctions (...) tendencies without recourse to teleology, and that it recasts the controversy between historicists and anti‐historicists in less dogmatic language. (shrink)

In “Spandrels,” Gould and Lewontin criticized what they took to be an all-too-common conviction, namely, that adaptation to current environments determines organic form. They stressed instead the importance of history. In this paper, we elaborate upon their concerns by appealing to other writings in which those issues are treated in greater detail. Gould and Lewontin’s combined emphasis on history was three-fold. First, evolution by natural selection does not start from scratch, but always refashions preexisting forms. Second, preexisting forms are refashioned (...) by the selection of whatever mutational variations happen to arise: the historical order of mutations needs to be taken into account. Third, the order of environments and selection pressures also needs to be taken into account. (shrink)

This paper considers definitions of classical dynamical chaos that focus primarily on notions of predictability and computability, sometimes called algorithmic complexity definitions of chaos. I argue that accounts of this type are seriously flawed. They focus on a likely consequence of chaos, namely, randomness in behavior which gets characterized in terms of the unpredictability or uncomputability of final given initial states. In doing so, however, they can overlook the definitive feature of dynamical chaos--the fact that the underlying motion generating the (...) behavior exhibits extreme trajectory instability. I formulate a simple criterion of adequacy for any definition of chaos and show how such accounts fail to satisfy it. (shrink)

Stephen Jay Gould argued that replaying the ‘tape of life’ would result in radically different evolutionary outcomes. Recently, biologists and philosophers of science have paid increasing attention to the theoretical importance of convergent evolution—the independent origination of similar biological forms and functions—which many interpret as evidence against Gould’s thesis. In this paper, we examine the evidentiary relevance of convergent evolution for the radical contingency debate. We show that under the right conditions, episodes of convergent evolution can constitute valid natural experiments (...) that support inferences regarding the deep counterfactual stability of macroevolutionary outcomes. However, we argue that proponents of convergence have problematically lumped causally heterogeneous phenomena into a single evidentiary basket, in effect treating all convergent events as if they are of equivalent theoretical import. As a result, the ‘critique from convergent evolution’ fails to engage with key claims of the radical contingency thesis. To remedy this, we develop ways to break down the heterogeneous set of convergent events based on the nature of the generalizations they support. Adopting this more nuanced approach to convergent evolution allows us to differentiate iterated evolutionary outcomes that are probably common among alternative evolutionary histories and subject to law-like generalizations, from those that do little to undermine and may even support, the Gouldian view of life. (shrink)

Maxwell's deduction of the probability distribution over the velocity of gas molecules—one of the most important passages in physics (Truesdell)—presents a riddle: a physical discovery of the first importance was made in a single inferential leap without any apparent recourse to empirical evidence. -/- Tychomancy proposes that Maxwell's derivation was not made a priori; rather, he inferred his distribution from non-probabilistic facts about the dynamics of intermolecular collisions. Further, the inference is of the same sort as everyday reasoning about the (...) physical probabilities attached to such canonical chance setups as tossed coins or rolled dice. The structure of this reasoning is investigated and some simple rules for inferring physical probabilities from symmetries and other causally relevant properties of physical systems are proposed. -/- Not only physics but evolutionary biology and population ecology, the science of measurement error, and climate modeling have benefited enormously from the same kind of reasoning, the book goes on to argue. Inferences from dynamics to probability are so obvious to us, however, that their methodological importance has been largely overlooked. (shrink)

Reconstructing the Past seeks to clarify and help resolve the vexing methodological issues that arise when biologists try to answer such questions as whether human beings are more closely related to chimps than they are to gorillas. It explores the case for considering the philosophical idea of simplicity/parsimony as a useful principle for evaluating taxonomic theories of evolutionary relationships. For the past two decades, evolutionists have been vigorously debating the appropriate methods that should be used in systematics, the field that (...) aims at reconstructing phylogenetic relationships among species. This debate over phylogenetic inference, Elliott Sober observes, raises broader questions of hypothesis testing and theory evaluation that run head on into long standing issues concerning simplicity/parsimony in the philosophy of science. Sober treats the problem of phylogenetic inference as a detailed case study in which the philosophical idea of simplicity/parsimony can be tested as a principle of theory evaluation. Bringing together philosophy and biology, as well as statistics, Sober builds a general framework for understanding the circumstances in which parsimony makes sense as a tool of phylogenetic inference. Along the way he provides a detailed critique of parsimony in the biological literature, exploring the strengths and limitations of both statistical and nonstatistical cladistic arguments. (shrink)

What Is Biodiversity? is a theoretical and conceptual exploration of the biological world and how diversity is valued. Maclaurin and Sterelny explore not only the origins of the concept of biodiversity, but also how that concept has been shaped by ecology and more recently by conservation biology. They explain the different types of biodiversity important in evolutionary theory, developmental biology, ecology, morphology and taxonomy and conclude that biological heritage is rich in not just one biodiversity but many. Maclaurin and Sterelny (...) also explore the case for the conservation of these biodiversities using option value theory, a tool borrowed from economics. (shrink)

In the wake of the paleobiological revolution of the 1970s and 1980s, paleontologists continue to investigate far-reaching questions about how evolution works. Many of those questions have a philosophical dimension. How is macroevolution related to evolutionary changes within populations? Is evolutionary history contingent? How much can we know about the causes of evolutionary trends? How do paleontologists read the patterns in the fossil record to learn about the underlying evolutionary processes? Derek Turner explores these and other questions, introducing the reader (...) to exciting recent work in the philosophy of paleontology and to theoretical issues including punctuated equilibria and species selection. He also critically examines some of the major accomplishments and arguments of paleontologists of the last 40 years. (shrink)

The paper focuses on the Epistemic Challenge for mind-independent accounts of modality. The challenge can be formulated as an inconsistency problem among three premises and, therefore, any strategy to meet the challenge will require the negation of (at least) one of its premises. The aim of the paper is not to offer a positive solution to the challenge, but rather to argue for the claim that to follow a hybrid strategy is probably the best way to meet it. With some (...) qualifications, reasons are given as to why empiricism should be the way to meet the challenge as far as de re modality is concerned, whereas rationalism might be the correct way of addressing it for the case of de dicto modality. (shrink)