Molecules, Cells and Minds
Aspects of Bioscientific Explanation
Submitted by Alexander Powell, to the University of Exeter as a thesis for the degree of Doctor
of Philosophy in Philosophy, December 2009.
This thesis is available for Library use on the understanding that it is copyright material and that
no quotation from the thesis may be published without proper acknowledgement.
I certify that all material which is not my own work has been identified and that no material has
previously been submitted and approved for the award of a degree by this or any other
University.
Alexander Powell
..................................................................
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Acknowledgements
The work described in this thesis in part builds on earlier experience, and I should like first to
acknowledge several long-standing debts. One is to Hilary Muirhead, who was notably generous
with her time when I was undertaking my final year biochemistry project at Bristol. At Oxford I
benefited greatly from (even if I could have done rather more to deserve) the support of Janos
Hajdu and Chris Dobson, while Andrew Martin and Dan Raleigh were munificent with their
time and expertise.
As for the research reported here, a key enabling condition was John Dupré’s willingness to take
me on as a research student. I am extremely grateful to him for that, and for the patient and
subtle way in which he facilitated my discovery of the limitations of various of my philosophical
thoughts and assumptions. Warm thanks go to Cheryl Sutton for performing administrative
magic in order to make things feasible. Sabina Leonelli organized the viva with characteristic
brio, and I am grateful to her for much besides her inspiring intellectual breadth and generosity.
Maureen O’Malley provided encouragement and vital critical opinion on several chapter drafts,
as well as on my various other productions over the past four years, for which a big thank you.
Jane Calvert and Staffan Mueller-Wille did much to make my time at Egenis rewarding. I am
especially grateful to Jane for several enjoyable collaborations and for her moral support at
various times, while Steve Hughes was an assiduous mentor and a reassuring presence.
Beyond that the debts start to proliferate to such a degree that it becomes tempting to resort to
catch-all expressions of gratitude. For their company and conversation, however, I cannot resist
singling out Daniele Carrieri, Jonathan Davies (who was good enough to read a late draft of the
entire thesis), Mattia Gallotti, Katie Kendig (who steered me away from several philosophical tar
pits), Maren Klotz, Michiru Nagatsu and Sally Wasmuth. The kindnesses of my fellow 2005-ers
Kate Getliffe and Jean Harrington have been legion, and frankly they deserve medals for putting
up with my puns and musings. Doctoral life would have been much the worse without them.
Special thanks also go to Pierre-Olivier Méthot. In addition to making many pertinent
suggestions regarding several chapters, his general soundness and joie de vivre helped to make
the write-up stage considerably less burdensome than it otherwise would have been. Exploring
obscure corners of Devon with him and the Bootlegs was a highlight of 2009. Another
important stimulus has been the splendid hospitality of Tom Gaertner and Nadine Schaefer.
When on occasion I felt delighted enough by philosophical reflection the excellence of their
company and their cuisine were very reliable restoratives.
Implicit in this thesis is the idea that words can only get one so far. When it comes to family,
where the debts are deepest, they become especially inadequate. (Although it is straightforwardly
the case that Jo Anson did wonders for the bibliography.) Suffice it to say that without the
steadfast support and encouragement of Jo, Mike, and my parents Pam and Chris none of this
would have been even vaguely possible. This thesis is therefore dedicated to them and to Sarah,
with love and thanks.
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Molecules, Cells and Minds: Aspects of Bioscientific Explanation
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 looks mechanistic, or
complex, or indeed emergent, is largely an epistemic matter, yet has an objective basis in
features of the world.
After reviewing several concepts of mechanism I consider the influential recent account of
Machamer, Darden and Craver (MDC). That account makes interesting proposals
concerning the relationship between mechanistic explanation and intelligibility, which are
consistent with the results of the investigation I undertake into the science surrounding
protein folding. In relation to a number of other issues pertaining to biological systems I
conclude that the MDC account is insufficiently nuanced, however, leading me to outline
an alternative approach to mechanism. This emphasizes the importance of structure—
function relations and addresses issues raised by reflection on the nature of cellular
complexity. These include the distinction between structure and process and the different
possible bases on which system organization may be maintained.
The account I give of emergence construes the phenomenon in terms of psychological
deficit: phenomena are emergent when we lack the capacity to trace through and model
their causal structures using our cognitive schemas. I conclude by developing these ideas
into a preliminary and partial account of explanation and understanding. This aspires to
cover the significant fraction of work in molecular and cell biology that correlates
biological structures, processes and functions by visualizing phenomena and making them
imaginable.
(298 words)
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List of Contents
List of Figures ......................................................................................................................... 6
Author’s declaration ................................................................................................................ 7
1.
The logical empiricist legacy............................................... Error! Bookmark not defined.
Introduction ............................................................................................................. Error! Bookmark not defined.
The received view and aftermath ......................................................................... Error! Bookmark not defined.
Reduction .................................................................................................................................. Error! Bookmark not defined.
Explanation .............................................................................................................................. Error! Bookmark not defined.
Causation................................................................................................................................... Error! Bookmark not defined.
Explanation and understanding ........................................................................... Error! Bookmark not defined.
Explanation and understanding in biology ........................................................................ Error! Bookmark not defined.
Outline summary .................................................................................................... Error! Bookmark not defined.
2.
Concepts of mechanism ...................................................... Error! Bookmark not defined.
Introduction ............................................................................................................. Error! Bookmark not defined.
A material conception of mechanism: machines .............................................. Error! Bookmark not defined.
First thoughts about structures and functions................................................... Error! Bookmark not defined.
A causal conception of mechanism ..................................................................... Error! Bookmark not defined.
The neo-mechanistic perspective ......................................................................... Error! Bookmark not defined.
Varieties of molecular mechanism ....................................................................... Error! Bookmark not defined.
Conclusions.............................................................................................................. Error! Bookmark not defined.
3.
Protein folding and mechanism schemas ........................... Error! Bookmark not defined.
Introduction ............................................................................................................. Error! Bookmark not defined.
Protein folding......................................................................................................... Error! Bookmark not defined.
The ‘new view’ ......................................................................................................................... Error! Bookmark not defined.
Modelling and simulation ...................................................................................... Error! Bookmark not defined.
Simulation, models and laws ................................................................................. Error! Bookmark not defined.
Entropy and the stochastic exploration of state space ..................................... Error! Bookmark not defined.
Mechanism schematicity and abstraction ........................................................... Error! Bookmark not defined.
Conclusions.............................................................................................................. Error! Bookmark not defined.
4.
Complexity and cellular causality - I ................................... Error! Bookmark not defined.
Introduction ............................................................................................................. Error! Bookmark not defined.
Structures, processes and material flux ............................................................... Error! Bookmark not defined.
Capturing complexity ............................................................................................. Error! Bookmark not defined.
Emergence and metabolic reaction networks .................................................... Error! Bookmark not defined.
Metabolic circularity and system autonomy ....................................................... Error! Bookmark not defined.
M,R systems ............................................................................................................................. Error! Bookmark not defined.
Autopoiesis ............................................................................................................................... Error! Bookmark not defined.
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5.
Complexity and cellular causality - II ................................. Error! Bookmark not defined.
The diversity of causal factors .............................................................................. Error! Bookmark not defined.
Molecular machines ................................................................................................................ Error! Bookmark not defined.
Self-assembly ............................................................................................................................ Error! Bookmark not defined.
Competitive assembly/disassembly ..................................................................................... Error! Bookmark not defined.
Templating structures ............................................................................................................. Error! Bookmark not defined.
Fluidity ....................................................................................................................................... Error! Bookmark not defined.
Logic and structure ................................................................................................. Error! Bookmark not defined.
Hyperstructures ....................................................................................................................... Error! Bookmark not defined.
Statically versus dynamically maintained organization ..................................... Error! Bookmark not defined.
An expanded view of mechanism ........................................................................ Error! Bookmark not defined.
Conclusions.............................................................................................................. Error! Bookmark not defined.
6.
Emergence and cognition ................................................... Error! Bookmark not defined.
Introduction ............................................................................................................. Error! Bookmark not defined.
Facets of emergence ............................................................................................... Error! Bookmark not defined.
Reducibility, deducibility and predictability........................................................................ Error! Bookmark not defined.
Downward causation and levels ........................................................................................... Error! Bookmark not defined.
Agents, environments and parallel processes .................................................................... Error! Bookmark not defined.
Patterns and surprise .............................................................................................................. Error! Bookmark not defined.
Divergent and convergent processes................................................................................... Error! Bookmark not defined.
Causal comprehension and imaginative simulation .......................................... Error! Bookmark not defined.
Imagination and scientific thought ...................................................................... Error! Bookmark not defined.
Cognition and material systems ............................................................................................ Error! Bookmark not defined.
Simulation and causal schemas ............................................................................. Error! Bookmark not defined.
Emergence, simulation and epistemic prostheses............................................................. Error! Bookmark not defined.
Ontological emergence .......................................................................................... Error! Bookmark not defined.
7.
Functional attributions and the causal status of the genomeError! Bookmark not defined.
Introduction ............................................................................................................. Error! Bookmark not defined.
Functions in biology ............................................................................................... Error! Bookmark not defined.
The determining genome ...................................................................................... Error! Bookmark not defined.
Information talk ...................................................................................................... Error! Bookmark not defined.
Informational structures and informational roles ............................................. Error! Bookmark not defined.
Networks................................................................................................................................... Error! Bookmark not defined.
Genomes across generations................................................................................................. Error! Bookmark not defined.
Conclusions.............................................................................................................. Error! Bookmark not defined.
8.
Mind in biology ................................................................... Error! Bookmark not defined.
Mechanism, complexity and emergence ............................................................. Error! Bookmark not defined.
Explanation and understanding in biology ........................................................ Error! Bookmark not defined.
Mind in biology ....................................................................................................... Error! Bookmark not defined.
Bibliography ................................................................................ Error! Bookmark not defined.
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List of Figures
p.36
Figure 1 – Mechanical clock
p.83
Figure 2 – Tracking particles
p.120
Figure 3 – Ontic/epistemic mechanistic framework
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Author’s declaration
Four sentences in Chapter 1, dealing with the Oppenheim-Putnam view of the ontological
stratification and unity of science (page 13), are taken from Powell and Dupré 2009 (listed
in the Bibliography).
Chapter 6 is based on the talk on ‘Emergence, imaginability, and causal schemas’ I
delivered at the meeting of the International Society for the History, Philosophy, and
Social Studies of Biology held at Exeter University in July 2007. Several passages of that
chapter also appear in Powell and Dupré 2009.
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