•  456
    Signals that make a Difference
    with Paul E. Griffiths and Arnaud Pocheville
    British Journal for the Philosophy of Science. 2017.
    Recent work by Brian Skyrms offers a very general way to think about how information flows and evolves in biological networks — from the way monkeys in a troop communicate, to the way cells in a body coordinate their actions. A central feature of his account is a way to formally measure the quantity of information contained in the signals in these networks. In this paper, we argue there is a tension between how Skyrms talks of signalling networks and his formal measure of information. Although S…Read more
  •  256
    We provide an account of mechanistic representation and explanation that has several advantages over previous proposals. In our view, explaining mechanistically is not simply giving an explanation of a mechanism. Rather, an explanation is mechanistic because of particular relations that hold between a mechanical representation, or model, and the target of explanation. Under this interpretation, mechanistic explanation is possible even when the explanatory target is not a mechanism. We argue th…Read more
  •  177
    This review of Wimsatt’s book Re-engineering Philosophy for Limited Beings focuses on analysing his use of robustness, a central theme in the book. I outline a family of three distinct conceptions of robustness that appear in the book, and look at the different roles they play. I briefly examine what underwrites robustness, and suggest that further work is needed to clarify both the structure of robustness and the relation between it various conceptions
  •  167
    Lineage Explanations: Explaining How Biological Mechanisms Change
    British Journal for the Philosophy of Science 60 (1): 51-78. 2009.
    This paper describes a pattern of explanation prevalent in the biological sciences that I call a ‘lineage explanation’. The aim of these explanations is to make plausible certain trajectories of change through phenotypic space. They do this by laying out a series of stages, where each stage shows how some mechanism worked, and the differences between each adjacent stage demonstrates how one mechanism, through minor modifications, could be changed into another. These explanations are important, f…Read more
  •  149
    The notion of a genetic program has been widely criticized by both biologists and philosophers. But the debate has revolved around a narrow conception of what programs are and how they work, and many criticisms are linked to this same conception. To remedy this, I outline a modern and more apt idea of a program that possesses many of the features critics thought missing from programs. Moving away from over-simplistic conceptions of programs opens the way to a more fruitful interplay of ideas bet…Read more
  •  142
    Measuring Causal Specificity
    with Paul E. Griffiths, Arnaud Pocheville, Karola Stotz, Hyunju Kim, and Rob Knight
    Philosophy of Science 82 (4): 529-555. 2015.
    Several authors have argued that causes differ in the degree to which they are ‘specific’ to their effects. Woodward has used this idea to enrich his influential interventionist theory of causal explanation. Here we propose a way to measure causal specificity using tools from information theory. We show that the specificity of a causal variable is not well-defined without a probability distribution over the states of that variable. We demonstrate the tractability and interest of our proposed mea…Read more
  •  123
    Cooperation and its Evolution (edited book)
    MIT Press. 2013.
    This collection reports on the latest research on an increasingly pivotal issue for evolutionary biology: cooperation. The chapters are written from a variety of disciplinary perspectives and utilize research tools that range from empirical survey to conceptual modeling, reflecting the rich diversity of work in the field. They explore a wide taxonomic range, concentrating on bacteria, social insects, and, especially, humans. Part I (“Agents and Environments”) investigates the connections of soci…Read more
  •  118
    Mechanistic models of population-level phenomena
    Biology and Philosophy 26 (5): 737-756. 2011.
    This paper is about mechanisms and models, and how they interact. In part, it is a response to recent discussion in philosophy of biology regarding whether natural selection is a mechanism. We suggest that this debate is indicative of a more general problem that occurs when scientists produce mechanistic models of populations and their behaviour. We can make sense of claims that there are mechanisms that drive population-level phenomena such as macroeconomics, natural selection, ecology, and epi…Read more
  •  101
    The other cooperation problem: Generating benefit
    Biology and Philosophy 23 (2): 179-203. 2008.
    Understanding how cooperation evolves is central to explaining some core features of our biological world. Many important evolutionary events, such as the arrival of multicellularity or the origins of eusociality, are cooperative ventures between formerly solitary individuals. Explanations of the evolution of cooperation have primarily involved showing how cooperation can be maintained in the face of free-riding individuals whose success gradually undermines cooperation. In this paper I argue th…Read more
  •  90
    Like Laland et al., I think Mayr’s distinction is problematic, but I identify a further problem with it. I argue that Mayr’s distinction is a false dichotomy, and obscures an important question about evolutionary change. I show how this question, once revealed, sheds light on some debates in evo-devo that Laland et al.’s analysis cannot, and suggest that it provides a different view about how future integration between biological disciplines might proceed
  •  62
    Engineering and evolvability
    Biology and Philosophy 29 (3): 293-313. 2014.
    Comparing engineering to evolution typically involves adaptationist thinking, where well-designed artifacts are likened to well-adapted organisms, and the process of evolution is likened to the process of design. A quite different comparison is made when biologists focus on evolvability instead of adaptationism. Here, the idea is that complex integrated systems, whether evolved or engineered, share universal principles that affect the way they change over time. This shift from adaptationism to e…Read more
  •  61
    The Major Transitions in Evolution Revisited (edited book)
    MIT Press. 2011.
    Drawing on recent advances in evolutionary biology, prominent scholars return to the question posed in a pathbreaking book: how evolution itself evolved.
  •  53
    Assessing the fitness landscape revolution
    Biology and Philosophy 23 (5): 639-657. 2008.
    According to Pigliucci and Kaplan, there is a revolution underway in how we understand fitness landscapes. Recent models suggest that a perennial problem in these landscapes—how to get from one peak across a fitness valley to another peak—is, in fact, non-existent. In this paper I assess the structure and the extent of Pigliucci and Kaplan’s proposed revolution and argue for two points. First, I provide an alternative interpretation of what underwrites this revolution, motivated by some recent w…Read more
  •  52
    Causal specificity and the instructive–permissive distinction
    Biology and Philosophy 32 (4): 481-505. 2017.
    I use some recent formal work on measuring causation to explore a suggestion by James Woodward: that the notion of causal specificity can clarify the distinction in biology between permissive and instructive causes. This distinction arises when a complex developmental process, such as the formation of an entire body part, can be triggered by a simple switch, such as the presence of particular protein. In such cases, the protein is said to merely induce or "permit" the developmental process, whil…Read more
  •  48
    The Creation and Reuse of Information in Gene Regulatory Networks
    Philosophy of Science 81 (5): 879-890. 2014.
    Recent work on the evolution of signaling systems provides a novel way of thinking about genetic information, where information is passed between genes in a regulatory network. I use examples from evolutionary developmental biology to show how information can be created in these networks and how it can be reused to produce rapid phenotypic change
  •  42
    Engineering and Biology: Counsel for a Continued Relationship
    with Arnon Levy, Mark L. Siegal, Orkun S. Soyer, and Andreas Wagner
    Biological Theory 10 (1): 50-59. 2015.
    Biologists frequently draw on ideas and terminology from engineering. Evolutionary systems biology—with its circuits, switches, and signal processing—is no exception. In parallel with the frequent links drawn between biology and engineering, there is ongoing criticism against this cross-fertilization, using the argument that over-simplistic metaphors from engineering are likely to mislead us as engineering is fundamentally different from biology. In this article, we clarify and reconfigure the l…Read more
  •  35
    Signals That Make a Difference
    with Arnaud Pocheville and Paul Griffiths
    British Journal for the Philosophy of Science 71 (1): 233-258. 2020.
    Recent work by Brian Skyrms offers a very general way to think about how information flows and evolves in biological networks—from the way monkeys in a troop communicate to the way cells in a body coordinate their actions. A central feature of his account is a way to formally measure the quantity of information contained in the signals in these networks. In this article, we argue there is a tension between how Skyrms talks of signalling networks and his formal measure of information. Although Sk…Read more
  •  9
    Further clarification on permissive and instructive causes
    Biology and Philosophy 34 (5): 50. 2019.
    I respond to recent criticism of my analysis of the permissive-instructive distinction and outline problems with the alternative analysis on offer. Amongst other problems, I argue that the use of formal measures is unclear and unmotivated, that the distinction is conflated with others that are not equivalent, and that no good reasons are provided for thinking the alternative model or formal measure tracks what biologists are interested in. I also clarify my own analysis where it has been misunde…Read more
  •  4
    Further clarification on permissive and instructive causes
    Biology and Philosophy 34 (5): 1-11. 2019.
    I respond to recent criticism of my analysis of the permissive-instructive distinction and outline problems with the alternative analysis on offer. Amongst other problems, I argue that the use of formal measures is unclear and unmotivated, that the distinction is conflated with others that are not equivalent, and that no good reasons are provided for thinking the alternative model or formal measure tracks what biologists are interested in. I also clarify my own analysis where it has been misunde…Read more