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Papers by Alexander Powell

Genomics, society and policy, Dec 1, 2011

The ability to stave off, if only for a time, the seemingly inevitable eventual decay to thermody... more The ability to stave off, if only for a time, the seemingly inevitable eventual decay to thermodynamic equilibrium is one of the chief distinguishing characteristics of life. That it is achieved in large part through the exploitation of ambient thermal energy is generally under-appreciated, however. The ATP that powers the cell, meanwhile, is still often described as the bearer of high-energy bonds, when even if that were true it is in any case a quite different factor that underlies its motive capacity. This article aims to act as a corrective with respect to both of those points, whilst also providing a broad-brush perspective on causality in the living cell. It is proposed that the living cell may be regarded as the exemplification of a particularly distinctive kind of machine, here termed Schrödinger Machine.

The ability to stave off, if only for a time, the seemingly inevitable eventual decay to thermody... more The ability to stave off, if only for a time, the seemingly inevitable eventual decay to thermodynamic equilibrium is one of the chief distinguishing characteristics of life. That it is achieved in large part through the exploitation of ambient thermal energy is generally under-appreciated, however. The ATP that powers the cell, meanwhile, is still often described as the bearer of high-energy bonds, when even if that were true it is in any case a quite different factor that underlies its motive capacity. This article aims to act as a corrective with respect to both of those points, whilst also providing a broad-brush perspective on causality in the living cell. It is proposed that the living cell may be regarded as the exemplification of a particularly distinctive kind of machine, here termed Schrödinger Machine.

In recent years the topic of mechanistic explanation has attracted considerable philosophical int... more In recent years the topic of mechanistic explanation has attracted considerable philosophical interest. Works by Glennan (1996, 2002) and by Machamer, Darden and Craver (2000) in particular have spawned a proliferating mechanism literature that makes contact with debates about many of the subjects of greatest concern to philosophers of science and philosophers of biology. These subjects include (besides explanation) causation, reduction, and function, as well as laws, theories and models. A specifically biological debate centres on whether evolution is to be understood in mechanistic terms (Skipper and Millstein 2005).

Life Sciences, Society and Policy, 2011

A previously unpublished synthesis of ideas about protein structure and folding is presented. Inc... more A previously unpublished synthesis of ideas about protein structure and folding is presented. Incorporating a number of theoretical speculations and proposals for research, it sheds light on what researchers knew at a specific point in time and how they were thinking about a fundamental but recalcitrant biological problem. Additional context and insight come from graphical representations of the occurrence over time of key terms in the literature relating to protein structure and its wider scientific context.

Talk given at ESRC Genomics Network Conference, London, October 2007

The concept of emergence, which came to renewed prominence with the rise of the complexity scienc... more The concept of emergence, which came to renewed prominence with the rise of the complexity sciences, has proved surprisingly resistant to analysis. After summarizing some of the characteristics associated with phenomena typically described as emergent I contrast the apparent ease with which we make sense of human behaviour with the difficulties we encounter in relation to emergent phenomena. What distinguishes and unites such phenomena, I suggest, is not primarily a matter of their objective ontological nature. Rather, we regard such phenomena as emergent because we lack cognitive schemas capable of modelling their causal structure.

Slides from 2015 setting out the significance of thermal energy-driven molecular dynamics as a ce... more Slides from 2015 setting out the significance of thermal energy-driven molecular dynamics as a central causal player in living systems, along with ATP as a metabolic driver. Subsequent related preprint available at https://osf.io/8ms6u/.

Work to automate the identification of related articles in corpora of academic research content i... more Work to automate the identification of related articles in corpora of academic research content is described. Pairs of related articles are recognised on the basis of the phrases they contain, using a similarity measure that emphasizes the importance of phrase overlap. Phrases are weighted according to their significance, evaluated in terms of statistical under- or over-representation relative to corpus-level frequency, and the significance scores of n-grams with higher n values are boosted. The measure proves broadly effective at identifying meaningfully related pairs of content items and may provide a useful basis for the development of ‘see also’-type functionality.

Talk given at Egenis, University of Exeter, May 2007

Talk given at Egenis, University of Exeter, May 2009

OSF Preprints

The ability to stave off, if only for a time, the seemingly inevitable eventual decay to thermody... more The ability to stave off, if only for a time, the seemingly inevitable eventual decay to thermodynamic equilibrium is one of the chief distinguishing characteristics of life. That it is achieved in large part through the exploitation of ambient thermal energy is generally under-appreciated, however. The ATP that powers the cell, meanwhile, is still often described as the bearer of high-energy bonds, when even if that were true it is in any case a quite different factor that underlies its motive capacity. This article aims to act as a corrective with respect to both of those points, whilst also providing a broad-brush perspective on causality in the living cell. It is proposed that the living cell may be regarded as the exemplification of a particularly distinctive kind of machine, here termed Schrödinger Machine.

PsyArXiv

The concept of emergence, which came to renewed prominence with the rise of the complexity scienc... more The concept of emergence, which came to renewed prominence with the rise of the complexity sciences, has proved surprisingly resistant to analysis. After summarizing some of the characteristics associated with phenomena typically described as emergent I contrast the apparent ease with which we make sense of human behaviour with the difficulties we encounter in relation to emergent phenomena. What distinguishes and unites such phenomena, I suggest, is not primarily a matter of their objective ontological nature. Rather, we regard such phenomena as emergent because we lack cognitive schemas capable of modelling their causal structure.

Abstract: In this thesis I examine a number of topics that bear on explanation and understanding ... more Abstract: In this thesis I examine a number of topics that bear on explanation and understanding in molecular and cell biology, in order to shed new light on explanatory practice in those areas and to find novel angles from which to approach relevant philosophical debates. The topics I look at include mechanism, emergence, cellular complexity, and the informational role of the genome. I develop a perspective that stresses the intimacy of the relations between ontology and epistemology. Whether a phenomenon ...

Genomics, society and policy, Dec 1, 2011

The ability to stave off, if only for a time, the seemingly inevitable eventual decay to thermody... more The ability to stave off, if only for a time, the seemingly inevitable eventual decay to thermodynamic equilibrium is one of the chief distinguishing characteristics of life. That it is achieved in large part through the exploitation of ambient thermal energy is generally under-appreciated, however. The ATP that powers the cell, meanwhile, is still often described as the bearer of high-energy bonds, when even if that were true it is in any case a quite different factor that underlies its motive capacity. This article aims to act as a corrective with respect to both of those points, whilst also providing a broad-brush perspective on causality in the living cell. It is proposed that the living cell may be regarded as the exemplification of a particularly distinctive kind of machine, here termed Schrödinger Machine.

The ability to stave off, if only for a time, the seemingly inevitable eventual decay to thermody... more The ability to stave off, if only for a time, the seemingly inevitable eventual decay to thermodynamic equilibrium is one of the chief distinguishing characteristics of life. That it is achieved in large part through the exploitation of ambient thermal energy is generally under-appreciated, however. The ATP that powers the cell, meanwhile, is still often described as the bearer of high-energy bonds, when even if that were true it is in any case a quite different factor that underlies its motive capacity. This article aims to act as a corrective with respect to both of those points, whilst also providing a broad-brush perspective on causality in the living cell. It is proposed that the living cell may be regarded as the exemplification of a particularly distinctive kind of machine, here termed Schrödinger Machine.

In recent years the topic of mechanistic explanation has attracted considerable philosophical int... more In recent years the topic of mechanistic explanation has attracted considerable philosophical interest. Works by Glennan (1996, 2002) and by Machamer, Darden and Craver (2000) in particular have spawned a proliferating mechanism literature that makes contact with debates about many of the subjects of greatest concern to philosophers of science and philosophers of biology. These subjects include (besides explanation) causation, reduction, and function, as well as laws, theories and models. A specifically biological debate centres on whether evolution is to be understood in mechanistic terms (Skipper and Millstein 2005).

Life Sciences, Society and Policy, 2011

A previously unpublished synthesis of ideas about protein structure and folding is presented. Inc... more A previously unpublished synthesis of ideas about protein structure and folding is presented. Incorporating a number of theoretical speculations and proposals for research, it sheds light on what researchers knew at a specific point in time and how they were thinking about a fundamental but recalcitrant biological problem. Additional context and insight come from graphical representations of the occurrence over time of key terms in the literature relating to protein structure and its wider scientific context.

Talk given at ESRC Genomics Network Conference, London, October 2007

The concept of emergence, which came to renewed prominence with the rise of the complexity scienc... more The concept of emergence, which came to renewed prominence with the rise of the complexity sciences, has proved surprisingly resistant to analysis. After summarizing some of the characteristics associated with phenomena typically described as emergent I contrast the apparent ease with which we make sense of human behaviour with the difficulties we encounter in relation to emergent phenomena. What distinguishes and unites such phenomena, I suggest, is not primarily a matter of their objective ontological nature. Rather, we regard such phenomena as emergent because we lack cognitive schemas capable of modelling their causal structure.

Slides from 2015 setting out the significance of thermal energy-driven molecular dynamics as a ce... more Slides from 2015 setting out the significance of thermal energy-driven molecular dynamics as a central causal player in living systems, along with ATP as a metabolic driver. Subsequent related preprint available at https://osf.io/8ms6u/.

Work to automate the identification of related articles in corpora of academic research content i... more Work to automate the identification of related articles in corpora of academic research content is described. Pairs of related articles are recognised on the basis of the phrases they contain, using a similarity measure that emphasizes the importance of phrase overlap. Phrases are weighted according to their significance, evaluated in terms of statistical under- or over-representation relative to corpus-level frequency, and the significance scores of n-grams with higher n values are boosted. The measure proves broadly effective at identifying meaningfully related pairs of content items and may provide a useful basis for the development of ‘see also’-type functionality.

Talk given at Egenis, University of Exeter, May 2007

Talk given at Egenis, University of Exeter, May 2009

OSF Preprints

The ability to stave off, if only for a time, the seemingly inevitable eventual decay to thermody... more The ability to stave off, if only for a time, the seemingly inevitable eventual decay to thermodynamic equilibrium is one of the chief distinguishing characteristics of life. That it is achieved in large part through the exploitation of ambient thermal energy is generally under-appreciated, however. The ATP that powers the cell, meanwhile, is still often described as the bearer of high-energy bonds, when even if that were true it is in any case a quite different factor that underlies its motive capacity. This article aims to act as a corrective with respect to both of those points, whilst also providing a broad-brush perspective on causality in the living cell. It is proposed that the living cell may be regarded as the exemplification of a particularly distinctive kind of machine, here termed Schrödinger Machine.

PsyArXiv

The concept of emergence, which came to renewed prominence with the rise of the complexity scienc... more The concept of emergence, which came to renewed prominence with the rise of the complexity sciences, has proved surprisingly resistant to analysis. After summarizing some of the characteristics associated with phenomena typically described as emergent I contrast the apparent ease with which we make sense of human behaviour with the difficulties we encounter in relation to emergent phenomena. What distinguishes and unites such phenomena, I suggest, is not primarily a matter of their objective ontological nature. Rather, we regard such phenomena as emergent because we lack cognitive schemas capable of modelling their causal structure.

Abstract: In this thesis I examine a number of topics that bear on explanation and understanding ... more Abstract: In this thesis I examine a number of topics that bear on explanation and understanding in molecular and cell biology, in order to shed new light on explanatory practice in those areas and to find novel angles from which to approach relevant philosophical debates. The topics I look at include mechanism, emergence, cellular complexity, and the informational role of the genome. I develop a perspective that stresses the intimacy of the relations between ontology and epistemology. Whether a phenomenon ...

Life Sciences, Society & Policy (formerly Genomics, Society & Policy), 2011