Published by Oliver M Lean
Synthese
Bio-ontologies are digital frameworks for handling biological and biomedical data. They consist o... more Bio-ontologies are digital frameworks for handling biological and biomedical data. They consist of theoretical entities and relations with explicitly defined logical structures and precise definitions, whose purpose is to provide a shared language for representing information to be distributed and integrated across diverse scientific contexts. It is tempting to view bio-ontologies as clear and formal expressions of a scientific community's ontological commitments about their domain of inquiry, and to view their integration as tantamount to the metaphysical unification of science that some philosophers have envisaged. However, I argue that the local, practical, social and technological factors that influence their design prevent us from straightforwardly reading metaphysical conclusions from them. I discuss these complications and suggest how they can be overcome, revealing more general lessons for the development of a well-founded scientific metaphysics.
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Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 2019
Jacques Monod (1971) argued that certain molecular processes rely critically on the property of ... more Jacques Monod (1971) argued that certain molecular processes rely critically on the property of chemical arbitrariness, which he claimed allows those processes to "transcend the laws of chemistry". It seems natural, as some philosophers have done, to interpret this in modal terms: a biological relationship is chemically arbitrary if it is possible, within the constraints of chemical "law", for that relationship to have been otherwise than it is. But while modality is certainly important for understanding chemical arbitrariness, understanding its biological role also requires an account of the concrete causal-functional features that distinguish arbitrary from non-arbitrary phenomena. In this paper I elaborate on this under-emphasised aspect by offering a general account of these features: arbitrary relations are instantiated by mechanisms that involve molecular adapters , which causally couple two properties or processes which would otherwise be uncorrelated. More specifically, adapters work by acting as intermediate rather than cooperating causes.
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Philosophy of Science, 2020
Binding specificity is a centrally important concept in molecular biology, yet it has received l... more Binding specificity is a centrally important concept in molecular biology, yet it has received little philosophical attention. Here I aim to remedy this by analyzing binding specificity as a causal property. I focus on the concept's role in drug design, where it is highly prized and hence directly studied: From a causal perspective, understanding why binding specificity is a valuable property of drugs contributes to an understanding of causal selection ーof how and why scientists distinguish between causes, not just causes from non-causes. In particular, the specificity of drugs is precisely what underwrites their value as experimental interventions on biological processes.
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Shannon information is commonly assumed to be the wrong way in which to conceive of information i... more Shannon information is commonly assumed to be the wrong way in which to conceive of information in most biological contexts. Since the theory deals only in correlations between systems, the argument goes, it can apply to any and all causal interactions that affect a biological outcome. Since informational language is generally confined to only certain kinds of biological process, such as gene expression and hormone signalling, Shannon information is thought to be unable to account for this restriction. It is often concluded that a richer, teleosemantic sense of information is needed. I argue against this view, and show that a coherent and sufficiently restrictive theory of biological information can be constructed with Shannon information at its core. This can be done by paying due attention some crucial distinctions: between information quantity and its fitness value, and between carrying information and having the function of doing so. From this I construct an account of how informational functions arise, and show that the “subject matter” of these functions can easily be seen as the natural information dealt with by Shannon’s theory.
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Thesis Chapters by Oliver M Lean
This thesis addresses the active controversy regarding the nature and role of informational conce... more This thesis addresses the active controversy regarding the nature and role of informational concepts as applied to the biological sciences { in particular, the relationship between statistical or correlational information on one hand and meaningful, semantic, intentional information on the other. It first develops a set of basic conceptual
tools that can be applied to any, or at least most, putative cases of information processing in biological systems. This framework shows that, contrary to popular belief, we can make sense of biological information in the former, statistical sense, without it trivially applying to any and all physical processes that take place in living things.
I then demonstrate the utility of this framework by applying its tools to specfic information-related controversies: the concept of innateness, and information versus influence in animal communication. These chapters demonstrate that these issues can be clarified with the tools previously developed. I also discuss the notion of primitive content - the simplest form of biological phenomenon that can reasonably be said to be contentful. This issue serves as a biological basis for future research
regarding the ongoing philosophical problem of relating the physical to the mental.
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Drafts by Oliver M Lean
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Papers by Oliver M Lean
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Synthese, 2021
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Philosophy of Science, 2020
Binding specificity is a centrally important concept in molecular biology, yet it has received li... more Binding specificity is a centrally important concept in molecular biology, yet it has received little philosophical attention. Here I aim to remedy this by analyzing binding specificity as a causal property. I focus on the concept’s role in drug design, where it is highly prized and hence directly studied. From a causal perspective, understanding why binding specificity is a valuable property of drugs contributes to an understanding of causal selection—of how and why scientists distinguish between causes, not just causes from noncauses. In particular, the specificity of drugs is precisely what underwrites their value as experimental interventions on biological processes.
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A talk relating our work in digital history and philosophy of science to the broader landscape of... more A talk relating our work in digital history and philosophy of science to the broader landscape of experimental/empirical philosophy.
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The British Journal for the Philosophy of Science
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Philosophers of science regularly use scientific publications in their research. To make their an... more Philosophers of science regularly use scientific publications in their research. To make their analyses of the literature more thorough, some have begun to use computational methods from the digital humanities (DH). Yet this creates a tension: it’s become a truism in science studies that the contents of scientific publications do not accurately reflect the complex realities of scientific investigation. In this paper, we outline existing views on how scientific publications fit into the broader picture of science as a system of practices, and find that none of these views exclude articles as valuable sources for philosophical inquiry. Far from ignoring the gap between texts and practice, proper use of DH tools requires, and can even contribute to, our understanding of that gap and its implications.
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Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences
Jacques Monod (1971) argued that certain molecular processes rely critically on the property of ... more Jacques Monod (1971) argued that certain molecular processes rely critically on the property of chemical arbitrariness, which he claimed allows those processes to "transcend the laws of chemistry". It seems natural, as some philosophers have done, to interpret this in modal terms: a biological relationship is chemically arbitrary if it is possible, within the constraints of chemical "law", for that relationship to have been otherwise than it is. But while modality is certainly important for understanding chemical arbitrariness, understanding its biological role also requires an account of the concrete causal-functional features that distinguish arbitrary from non-arbitrary phenomena. In this paper I elaborate on this under-emphasised aspect by offering a general account of these features: arbitrary relations are instantiated by mechanisms that involve molecular adapters , which causally couple two properties or processes which would otherwise be uncorrelated. More specifically, adapters work by acting as intermediate rather than cooperating causes.
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Biology & Philosophy, 2014
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Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences
Jacques Monod (1971) argued that certain molecular processes rely critically on the property of ... more Jacques Monod (1971) argued that certain molecular processes rely critically on the property of chemical arbitrariness, which he claimed allows those processes to "transcend the laws of chemistry". It seems natural, as some philosophers have done, to interpret this in modal terms: a biological relationship is chemically arbitrary if it is possible, within the constraints of chemical "law", for that relationship to have been otherwise than it is. But while modality is certainly important for understanding chemical arbitrariness, understanding its biological role also requires an account of the concrete causal-functional features that distinguish arbitrary from non-arbitrary phenomena. In this paper I elaborate on this under-emphasised aspect by offering a general account of these features: arbitrary relations are instantiated by mechanisms that involve molecular adapters , which causally couple two properties or processes which would otherwise be uncorrelated. More specifically, adapters work by acting as intermediate rather than cooperating causes.
Bookmarks Related papers MentionsView impact
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Published by Oliver M Lean
Thesis Chapters by Oliver M Lean
tools that can be applied to any, or at least most, putative cases of information processing in biological systems. This framework shows that, contrary to popular belief, we can make sense of biological information in the former, statistical sense, without it trivially applying to any and all physical processes that take place in living things.
I then demonstrate the utility of this framework by applying its tools to specfic information-related controversies: the concept of innateness, and information versus influence in animal communication. These chapters demonstrate that these issues can be clarified with the tools previously developed. I also discuss the notion of primitive content - the simplest form of biological phenomenon that can reasonably be said to be contentful. This issue serves as a biological basis for future research
regarding the ongoing philosophical problem of relating the physical to the mental.
Drafts by Oliver M Lean
Papers by Oliver M Lean
tools that can be applied to any, or at least most, putative cases of information processing in biological systems. This framework shows that, contrary to popular belief, we can make sense of biological information in the former, statistical sense, without it trivially applying to any and all physical processes that take place in living things.
I then demonstrate the utility of this framework by applying its tools to specfic information-related controversies: the concept of innateness, and information versus influence in animal communication. These chapters demonstrate that these issues can be clarified with the tools previously developed. I also discuss the notion of primitive content - the simplest form of biological phenomenon that can reasonably be said to be contentful. This issue serves as a biological basis for future research
regarding the ongoing philosophical problem of relating the physical to the mental.