Contemporary Debates in Philosophy of Biology (Contemporary Debates in Philosophy)

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Contemporary
Debates in
Philosophy of Biology
Edited by

Francisco J. Ayala and Robert Arp

A John Wiley & Sons, Ltd., Publication

Contemporary Debates in Philosophy of Biology

Contemporary Debates in Philosophy
In teaching and research, philosophy makes progress through argumentation and
debate. Contemporary Debates in Philosophy provides a forum for students and
their teachers to follow and participate in the debates that animate philosophy
today in the western world. Each volume presents pairs of opposing viewpoints
on contested themes and topics in the central subfields of philosophy. Each
volume is edited and introduced by an expert in the field, and also includes an
index, bibliography, and suggestions for further reading. The opposing essays,
commissioned especially for the volumes in the series, are thorough but accessible
presentations of opposing points of view.
1. Contemporary Debates in Philosophy of Religion edited by Michael L. Peterson
and Raymond J. Vanarragon
2. Contemporary Debates in Philosophy of Science edited by Christopher
Hitchcock
3. Contemporary Debates in Epistemology edited by Matthias Steup and Ernest
Sosa
4. Contemporary Debates in Applied Ethics edited by Andrew I. Cohen and
Christopher Heath Wellman
5. Contemporary Debates in Aesthetics and the Philosophy of Art edited by
Matthew Kieran
6. Contemporary Debates in Moral Theory edited by James Dreier
7. Contemporary Debates in Cognitive Science edited by Robert Stainton
8. Contemporary Debates in Philosophy of Mind edited by Brian McLaughlin
and Jonathan Cohen
9. Contemporary Debates in Social Philosophy edited by Laurence Thomas
10. Contemporary Debates in Metaphysics edited by Theodore Sider, John
Hawthorne, and Dean W. Zimmerman
11. Contemporary Debates in Political Philosophy edited by Thomas Christiano
and John Christman
12. Contemporary Debates in Philosophy of Biology edited by Francisco J. Ayala
and Robert Arp
Forthcoming Contemporary Debates title:
Contemporary Debates in Philosophy of Language edited by Ernest Lepore

Contemporary
Debates in
Philosophy of Biology
Edited by

Francisco J. Ayala and Robert Arp

A John Wiley & Sons, Ltd., Publication

This edition first published 2010
© 2010 Blackwell Publishing Ltd
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Library of Congress Cataloging-in-Publication Data
Contemporary debates in philosophy of biology / edited by Francisco J. Ayala and Robert Arp.
p. cm. — (Contemporary debates in philosophy)
Includes bibliographical references and index.
ISBN 978-1-4051-5998-2 (hardcover : alk. paper) — ISBN 978-1-4051-5999-9 (pbk. : alk. paper)
1. Biology—Philosophy. 2. Evolution (Biology)—Philosophy. I. Ayala, Francisco Jos?, 1934–
II. Arp, Robert.
QH331.C8465 2010
570.1—dc22
2009032169
A catalogue record for this book is available from the British Library.
Set in 10/12.5pt Rotis Serif by Graphicraft Limited, Hong Kong
Printed in Singapore
01 2010

Contents

Notes on Contributors

ix

General Introduction
References and Further Reading

1
7

PART I IS IT POSSIBLE TO REDUCE BIOLOGICAL
EXPLANATIONS TO EXPLANATIONS IN
CHEMISTRY AND/OR PHYSICS?

13

Introduction
References and Further Reading

13
15

1 It Is Possible to Reduce Biological Explanations to Explanations
in Chemistry and/or Physics Evelyn Fox Keller

19

2 It Is Not Possible to Reduce Biological Explanations to Explanations in
Chemistry and/or Physics John Dupré

32

PART II HAVE TRAITS EVOLVED TO FUNCTION THE WAY
THEY DO BECAUSE OF A PAST ADVANTAGE?

49

Introduction
References and Further Reading

49
51

3 Traits Have Evolved to Function the Way They Do Because of
a Past Advantage Mark Perlman

53

4 Traits Have Not Evolved to Function the Way They Do Because of
a Past Advantage Robert Cummins and Martin Roth

72

PART III ARE SPECIES REAL?

87

Introduction
References and Further Reading

87
88

5 Species Are Real Biological Entities

Michael F. Claridge

6 Species Are Not Uniquely Real Biological Entities

Brent D. Mishler

91
110

PART IV DOES SELECTION OPERATE PRIMARILY
ON GENES?

123

Introduction
References and Further Reading

123
125

7 Selection Does Operate Primarily on Genes: In Defense of the Gene
as the Unit of Selection Carmen Sapienza

127

8 Selection Does Not Operate Primarily on Genes

Richard M. Burian

141

PART V ARE MICROEVOLUTION AND MACROEVOLUTION
GOVERNED BY THE SAME PROCESSES?

165

Introduction
References and Further Reading

165
166

9 Microevolution and Macroevolution Are Governed by the
Same Processes Michael R. Dietrich

169

10 Microevolution and Macroevolution Are Not Governed by the
Same Processes Douglas H. Erwin

180

PART VI DOES EVOLUTIONARY DEVELOPMENTAL
BIOLOGY OFFER A SIGNIFICANT CHALLENGE
TO THE NEO-DARWINIAN PARADIGM?

195

Introduction
References and Further Reading

195
197

11 Evolutionary Developmental Biology Offers a Significant
Challenge to the Neo-Darwinian Paradigm Manfred D. Laubichler

199

12 Evolutionary Developmental Biology Does Not Offer a Significant
Challenge to the Neo-Darwinian Paradigm Alessandro Minelli

213

PART VII WERE THE BASIC COMPONENTS OF
THE HUMAN MIND SOLIDIFIED DURING
THE PLEISTOCENE EPOCH?

227

Introduction
References and Further Reading

227
228

13 The Basic Components of the Human Mind Were Solidified During
the Pleistocene Epoch Valerie G. Starratt and Todd K. Shackelford

231

vi

Contents

14 The Basic Components of the Human Mind Were Not Solidified
During the Pleistocene Epoch Stephen M. Downes

243

PART VIII DOES MEMETICS PROVIDE A USEFUL WAY
OF UNDERSTANDING CULTURAL EVOLUTION?

253

Introduction
References and Further Reading

253
254

15 Memetics Does Provide a Useful Way of Understanding
Cultural Evolution Susan Blackmore

255

16 Memetics Does Not Provide a Useful Way of Understanding Cultural
Evolution: A Developmental Perspective William C. Wimsatt

273

PART IX CAN THE BIOLOGICAL SCIENCES ACT AS A
GROUND FOR ETHICS?

293

Introduction
References and Further Reading

293
295

17 The Biological Sciences Can Act as a Ground for Ethics
Michael Ruse

297

18 What the Biological Sciences Can and Cannot Contribute to
Ethics Francisco J. Ayala

316

PART X IS THERE A PLACE FOR INTELLIGENT DESIGN
IN THE PHILOSOPHY OF BIOLOGY?

337

Introduction
References and Further Reading

337
340

19 There Is a Place for Intelligent Design in the Philosophy of Biology:
Intelligent Design in (Philosophy of) Biology: Some Legitimate Roles
Del Ratzsch

343

20 There Is No Place for Intelligent Design in the Philosophy of Biology:
Intelligent Design Is Not Science Francisco J. Ayala

364

Index

391

Contents

vii

Notes on Contributors

Robert Arp has specializations in philosophy of biology and ontology in the informatics sense of the term. With Alex Rosenberg, he is co-editor of Philosophy of Biology:
An Anthology (Wiley-Blackwell, 2009), with George Terzis, he is co-editor of Information
and Living Systems: Philosophical and Scientific Perspectives (forthcoming), and his
latest book dealing with issues in evolutionary psychology is titled Scenario Visualization: An Evolutionary Account of Creative Problem Solving (2008). Currently, he works
for The Analysis Group (Falls Church, VA) as an ontologist and is completing a book
with Barry Smith and Andrew Spear that deals with the construction of ontologies.
Francisco J. Ayala is University Professor and Donald Bren Professor of Biological
Sciences at the University of California, Irvine. He has published over 900 articles
and is author or editor of 31 books. He is a member of the U.S. National Academy
of Sciences and the American Philosophical Society, and received the 2001 U.S. National
Medal of Science. The New York Times named Ayala the “Renaissance Man of
Evolutionary Biology.”
Susan Blackmore is a freelance writer and lecturer, previously Reader in Psychology
at the University of the West of England, Bristol. Her research on consciousness, memes,
and anomalous experiences has been published in over 60 academic papers, as well
as book chapters, reviews, and popular articles. She writes a regular blog for The
Guardian, and often appears on radio and television. Her books include The Meme
Machine (translated into 13 other languages, 2000), Consciousness: An Introduction
(2005), and Conversations on Consciousness (2007). She has been practicing Zen for
20 years, and has recently published Ten Zen Questions (One World Press, 2009).
Richard M. Burian, Ph.D. University of Pittsburgh, is Professor Emeritus of
Philosophy and Science Studies at Virginia Tech. He is a historian and philosopher
of biology, with research focusing on history and philosophy of genetics, exploratory
experimentation in biology, interactions among developmental biology, evolutionary
Notes on Contributors

ix

biology, and genetics, and philosophical accounts of conceptual change in science.
He was one of the co-founders of the International Society for History, Philosophy,
and Social Studies of Biology, of which he was President, 1999–2001.
Michael F. Claridge is Emeritus Professor of Entomology at Cardiff University. After
graduating M.A. and D.Phil. in zoology and entomology at Oxford in 1959, he has
since worked continuously from a base in Wales. He has served as Presidents of the
Linnean Society of London (1988–1991), the Systematics Association (1991–1994),
and the Royal Entomological Society (2000–2002). He has published in areas such
as insect systematics, ecology, behavior, and evolutionary biology and has always
had a particular interest in the nature of species and species concepts.
Robert Cummins is Professor and Chair of the Department of Philosophy at the University
of Illinois, Urbana-Champaign. He is the author of The Nature of Psychological
Explanation, Meaning and Mental Representation (1989) and Representations, Targets
and Attitudes (1996), as well as articles in the philosophy of mind, science, and
biology and the history of early modern philosophy. His current research focuses
on representation as well as the interaction development, learning, and selection that
pertain to informing the mind.
Michael R. Dietrich is a historian and philosopher of biology in the Department of
Biological Sciences at Dartmouth College. His work ranges from historical and conceptual issues in molecular evolution to the gendered division of labor in Drosophila
genetics. He is currently completing a biography of Richard Goldschmidt.
Stephen M. Downes is Professor of Philosophy at the University of Utah. His main
areas of specialization are philosophy of science and philosophy of biology. He has
recently published on evolutionary psychology, the levels of selection debates, and
modeling in science.
John Dupré is Professor of Philosophy of Science, and Director of the ESRC Centre
for Genomics in Society (Egenis) at the University of Exeter. He has held posts at
Oxford, Stanford, and London, and in 2006 was the Spinoza Professor of Philosophy
at the University of Amsterdam. He has published widely in the philosophy of
biology. His most recent book, co-authored with the sociologist Barry Barnes, is Genomes
and What to Make of Them (2008).
Douglas H. Erwin is a Senior Scientist and Curator of Paleozoic Invertebrates in the
Department of Paleobiology, National Museum of Natural History, Smithsonian
Institution and Professor at the Santa Fe Institute. He has a Ph.D. in Geology from
UC Santa Barbara, and his research concerns major evolutionary innovations, the
end-Permian mass extinction, and related issues.
Evelyn Fox Keller is Professor Emerita of History and Philosophy of Science at MIT.
With a Ph.D. in theoretical physics from Harvard University, she is the author of
publications extending from technical contributions to physics and biology to
historical and philosophical analyses of scientific practices. She is the recipient of
x

Notes on Contributors

many awards and honorary degrees, a member of the American Philosophical
Society, the American Academy of Arts and Sciences, a MacArthur Fellow, and, most
recently, holder of the Chaire Blaise Pascal in Paris. Her most recent book is The
Mirage of a Space between Nature and Nurture (2009).
Manfred D. Laubichler is Professor of Theoretical Biology and History of Biology
and Affiliated Professor of Philosophy at the School of Life Sciences and Centers for
Biology and Society and Social Dynamics and Complexity at Arizona State
University. He is the co-editor of From Embryology to Evo-Devo (2007), Modeling
Biology (2007), Der Hochsitz des Wissens (2006), Form and Function in Developmental
Evolution (2009), and an associate editor of Endothelial Biomedicine (2007). He is
also an associate editor of the Journal of Experimental Zoology, Part B Molecular
and Developmental Evolution and of Biological Theory.
Alessandro Minelli is a Professor of Zoology at the University of Padova. His research
interests include animal phylogeny, the principles of systematics, and especially evodevo, with a focus on the evolution of modular body parts. He is the author of Biological
Systematics (1993), The Development of Animal Form (2003), Perspectives in Animal
Phylogeny and Evolution (2009), and Forms of Becoming (2009).
Brent D. Mishler is Director of the University and Jepson Herbaria at University of
California-Berkeley, as well as Professor in the Department of Integrative Biology,
where he teaches phylogenetic systematics and plant diversity. He received his Ph.D.
from Harvard University in 1984, and then was on the faculty at Duke University
before moving to UC Berkeley in 1993. His research interests are in the systematics,
evolution, and ecology of bryophytes, especially the diverse moss genus Tortula, as
well as in the phylogeny of green plants and the theory of systematics. He applies
methods ranging from microscopy through growth experiments, DNA sequencing, and
genomics.
Mark Perlman is Professor of Philosophy at Western Oregon University. He received
his Ph.D. from the University of Arizona in 1994, working with Robert Cummins.
He is the author of Conceptual Flux: Mental Representation, Misrepresentation, and
Concept Change (2000), and is co-editor, with André Ariew and Robert Cummins, of
Functions: New Essays in Philosophy of Psychology and Biology (2002), as well as other
papers on functions, philosophy of law, conceptual role semantics, and philosophy
of music. He is also a musician, both orchestral conductor and string bassist.
Del Ratzsch (Ph.D., University of Massachusetts-Amherst) is Professor and Chair of
the Philosophy Department of Calvin College in Grand Rapids, Michigan. His primary
areas of research are philosophy of science, and interactions between science and
religion. His published work in those areas includes Nature, Design and Science (2001)
and Philosophy of Science: The Natural Sciences in Christian Perspective (1986).
Martin Roth is an Assistant Professor of Philosophy at Drake University. A Ph.D.
in philosophy from UC-Davis, he has published in the areas of philosophy of mind,
cognitive science, and epistemology.
Notes on Contributors

xi

Michael Ruse is Lucyle T. Werkmeister Professor of Philosophy at Florida State University
and Director of the Program in the History and Philosophy of Science. He is the
author of many books, most recently Charles Darwin (Wiley-Blackwell, 2008), a work
which looks at Darwin’s importance for philosophy, and he is the co-editor of the
Cambridge Companion to the Origin of Species (2008).
Carmen Sapienza is Professor of Pathology and Laboratory Medicine at the Fels Institute
for Cancer Research at Temple University. His laboratory was among the first to
discover DNA methylation differences between maternally and paternally inherited
genes. The Sapienza laboratory is studying natural variation in epigenetic marking,
the selective forces at play, and whether environmental factors have an effect on the
stability of epigenetic marks, leading to disease.
Todd K. Shackelford received his Ph.D. in psychology from the University of Texas
at Austin in 1997. He is Professor of Psychology at Florida Atlantic University,
and chair of the Evolutionary Psychology Area. His current research interests include
conflict between the sexes, particularly with regard to sexual behavior (see
www.ToddKShackelford.com).
Valerie G. Starratt received her Ph.D. in psychology from Florida Atlantic University
in 2008 while working with Todd Shackelford. Currently, she is a visiting Assistant
Professor of Psychology at Nova Southeastern University. Her research interests include
intimate relationships and human sexuality from an evolutionary psychological
perspective.
William C. Wimsatt, Peter B. Ritzma Professor, teaches philosophy, history of
science, and evolutionary biology at the University of Chicago. He studied engineering
physics and philosophy at Cornell, and then went from philosophy at Pitt in 1969
to a post-doc with Richard Lewontin at Chicago. He has written on functional
organization, reductionism, and reductionistic research strategies, levels of organization and mechanistic explanation, units of selection, heuristics, emergence, modeling,
robustness, satisficing, generative entrenchment, and methods and problems in
studying complex systems. His book Re-Engineering Philosophy for Limited Beings
(2007) integrates many of these themes. He currently works on issues surrounding
cultural evolution and on the role of generative entrenchment in evolutionary
processes.

xii

Notes on Contributors

General Introduction

Who Is This Book For?
This book features current research by scholars doing work in the central areas of
philosophy of biology. Further, the papers are presented in a debate style with yes
and no responses—often qualified—to basic questions posed in this continually developing sub-discipline of philosophy. This being the case, this book is ideal as (1) a
stimulus for students in philosophy of biology and biology classrooms, as well as (2)
a reference work for scholars who are working in this exciting field.

What Is the Philosophy of Biology?
The word “philosophy” comes from two Greek words: philos, meaning “love,” and
sophos, meaning “wisdom.” Love here means something like an intense desire for
something, while wisdom is arguably a kind of knowledge gained from experience,
whether this be practical experience (gained from living life with all of its ups and
downs) or theoretical experience (gained from understanding, evaluating, critiquing,
and synthesizing ideas, positions, and concepts). Ever the theoretician, the philosopher
has always been the person who not only desires to look deeper into some claim, idea,
argument, event, or state of affairs by questioning assumptions and challenging status
quo thinking, but also attempts to broadly explain and systematize aspects of reality
(also see Craig, 2002; Pojman, 2007). In Bertrand Russell’s (1912/1999) words, which
are appropriate given the nature of this book: “Philosophy, like all other studies, aims
primarily at knowledge. The knowledge it aims at is the kind of knowledge which
gives unity and system to the body of the sciences, and the kind which results from
a critical examination of the grounds of our convictions, prejudices, and beliefs” (p. 9).
The word “biology” comes from two Greek words as well: bios, meaning “life,”
and logos, meaning “word,” “rational account,” or “science.” Thus, biology is the kind
or type of science that studies life, which most of us already know. Whereas biology

can be characterized as a set of sub-disciplines (the biological or life sciences) under
science, the concern of which includes the description, classification, analysis, explanation, prediction, and ultimately control of living things (Audesirk, Audesirk, & Byers,
2008; Campbell & Reece, 2007), philosophy of biology can be characterized as a
sub-discipline of philosophy—complete with topical subject-matter to be discussed
momentarily—the concern of which is the meta-leveled attempt on the part of
philosophers, biologists, and other thinkers to understand, evaluate, and critique the
methods, foundations, history, and logical structure of biology in relation to other
sciences, disciplines, and life endeavors so as to better clarify the nature and
purpose of biological science and its practices (see Hull & Ruse, 2007; Rosenberg &
Arp, 2009; Rosenberg & McShea, 2007; Ruse, 2008; Sarkar & Plutynski, 2008).

The Classification of Biology and Philosophy
of Biology
Concerning the classification of biology within the general discipline of science, it
is usually envisioned as a natural, empirical, pure science, as we illustrate in Figure 0.1
(also see Sadava, Heller, Orians, Purvis, & Hillis, 2008; Silberberg, 2008; Tippens, 2007).
We are aware that what is represented in the figure is a partial taxonomy, and that
there may be other ways to classify the sciences.

science
pure science
(goal is not practical application,
per se)
formal science
e.g., logic, mathematics

applied science
e.g., engineering, medicine, agriculture,
aeronautics

empirical science

natural science

social science
e.g., sociology, ceonomics,
anthropology

physical science
e.g., physics, chemistry
behavioral science
e.g., psychology
biology (life science)
e.g., genetics, molecular biology, botany, zoology,
ecology, cell biology, etc.
Figure 0.1: A basic classification of biology as a science

2

General Introduction

philosophy
metaphysics

epistemology

ethics

political philosophy

logic

philosophy
of science
philosophy
of physics

philosophy
of chemistry

philosophy
of medicine

philosophy
of biology

Figure 0.2: Philosophy of biology classified

Concerning the classification of philosophy of biology within the general discipline
of philosophy, it is usually envisioned as a sub-discipline of philosophy of science,
along with others like philosophy of physics, philosophy of chemistry, and philosophy
of medicine. Because it concerns not only what kinds of things exist (metaphysical parts,
processes, principles) as well as how we can know these things (epistemological
perceptions, models, beliefs, justifications), the classification of philosophy of science
itself can be considered a hybrid under metaphysics and epistemology; although, of
course, this is debatable (Godfrey-Smith, 2003; Newton-Smith, 2001). Figure 0.2
represents a partial taxonomic classification of philosophy of biology, and we are
aware that there are many other philosophical disciplines and sub-disciplines not shown,
as well as that it is possible to classify the discipline of philosophy by historical timeperiods or major movements (Copleston, 1994; Jones, 1997; Solomon, 2005).

The Relationship between the Biologist and
the Philosopher
There are many biologists who think philosophically, and there are many philosophers
who think like biologists, and this has always been the case in Western history since
these two disciplines began coexisting with one another. In fact, researchers in these
two disciplines have been able to assist one another in advancing ideas, putting issues
to rest once and for all, and overthrowing faulty paradigms, as well as furthering
technological comforts, establishing moral codes, and alleviating pain and disease
(National Research Council, 1996, 2000; Watson & Arp, 2008).
A universally known example of this relationship between biology and philosophy
is Charles Darwin (1809–1882), the field biologist and scientific naturalist, thinking
like a philosopher of biology by mounting his self-proclaimed “one long argument”
for natural selection in his famous work titled On the Origin of Species by Means of
Natural Selection, or the Preservation of Favoured Races in the Struggle for Life
(1859/1999). In line with our descriptions of philosophy and philosophy of biology
put forward above, Darwin definitely challenged status quo thinking with natural
selection and offered a meta-level analysis, explanation, and systematization of the
biosphere. Darwin’s contemporaries even referred to him as a philosopher (Schad,
General Introduction

3

2004, p. 9). There is a famous paper by Theodosius Dobzhansky (1900–1975) titled
“Nothing in Biology Makes Sense Except in the Light of Evolution” (1973) and it is
obvious that, were it not for Darwin’s philosophy of biology-like thinking and
theorizing concerning natural selection and evolution, the biological sciences would
be foundationless today.
Just as many biological conundrums have been aided by philosophical thinking,
so, too, many philosophical problems have been either solved or enlightened with
the help of the biological sciences. Let us focus on one example. In philosophy of
mind, substance dualism is the belief that a person is made up of two fundamental
things—a material or physical body and an immaterial or non-physical mind/soul/
spirit—that can exist apart from one another. Those who believe in the immortality
(or reincarnation) of the soul are substance dualists because they think that the death
of the body does not mean the death of the soul (for example, Catechism of the Catholic
Church, 1994; also Baker & Morris, 1996). The soul lives on as a separate substantial
thing after the death of the body, which is another, distinct, separate substantial thing.
A lot of people on the planet are substance dualists of one sort or another, probably
because of their religious upbringing (Morgan & Laungani, 2005). Think of the
cartoons where a character gets killed and the body stays flat on the ground while
the soul/mind/spirit/immaterial substantial part leaves the body and ascends into a
heavenly world—this is straight-forward mind–body substance dualism.
Contemporary discussions of religious and non-religious forms of substance
dualism in Western history usually trace their roots back to the famous Modern philosopher, René Descartes (1596–1650) (Descartes, 1998; see also Baker & Morris, 1996),
but forms of substance dualism can be found in the history of Western philosophy
in the twentieth century and back through Aquinas (1225–1274) to Augustine
(354–430), Plotinus (ca. 204–270), Aristotle (384–322 BCE), and Plato (ca. 428–348
BCE) (Foster, 1991; Aquinas, 1949; Augustine, 1991; Plotinus, 1992; Aristotle, 1995;
Plato, 1997). In fact, the cartoon character rendition of the soul leaving the body is
very close to what people actually believed in most Western societies throughout the
history of Western civilization. The histories of Eastern and Middle Eastern philosophy
are also peppered with beliefs in various forms of substance dualism (Abramson &
Kilpatrick, 1995; Hook, 1963; Knapp, 1992).
Now, here is where neurobiology has made important contributions to the philosophy of mind, and our thinking concerning substance dualism. First, it seems that
the mind is, at best, an emergent or supervenient property that is the result of brain
states; it may not be reducible to brain states, but it is certainly dependent upon
brain state processes (Baars & Newman, 2001; Bisiach, 1999; Gold & Roskies, 2008;
Hardcastle, 2007; Kim, 2000, 1999, 1995). If there is any doubt about this, one need
only peruse any textbook or journal devoted to the human brain’s workings and read
about the effects of brain damage upon the psychology of a person (see Bear, Connors,
& Paradiso, 2006; Kandel, Schwartz, & Jessell, 2000). For example, without the normal
functioning of the prefrontal cortex, individuals are not able to make plans, nor are
they able to carry out the behavior necessary to fulfill those plans (Fuster, 1997;
Passingham, 1993). Also, as Finke (1980) demonstrated many years ago, damage to
the prefrontal cortex causes a person to be unable to store short-term memories. Further,
damage to the limbic system can cause certain autisms and other emotional dysfunctions (Bauman & Kemper, 1994).
4

General Introduction

Given the influence and preponderance of neurobiological data, and the fact that
no one has ever witnessed a soul leaving a body or existing in some other “state”—
both indicating the fact that, no brain, no mind—many philosophers and other thinkers
who still think that there is something special about the mind and mental capacities
have opted for forms of property dualism in place of substance dualism. According
to property dualism, a person is one substance that is made up of two wholly distinct features, characteristics, or properties: an immaterial mental property (the mind
and mental states) and a material bodily property (the brain and neurobiological states).
On this view, the mind and brain are distinct properties of some one person,
similar to the way roundness and blackness are distinct properties found in the one
period at the end of this sentence. Just as we can distinguish the property of roundness from the property of blackness in some one period, so, too, we can distinguish
an immaterial mental property from a material bodily property in some one person.
However, just as the roundness and blackness of that particular period can exist only
while that particular period exists, so, too, according to property dualists, the mental and
bodily properties of a person can exist only while that person is alive. So when we
delete the period, the properties of roundness and blackness in that particular period
cease to exist along with the period. Likewise, when a person dies, both that person’s
body and mind cease to exist (no brain, no mind). Such a view of mind in relation
to body seems to be consistent with neurobiological and other scientific data, and is
appealing to those who do not believe in the immortality or reincarnation of the soul.
There is another possibility, namely, that the mind and mental states are completely
illusory notions and all that really takes place when one thinks, decides, calculates,
feels, believes, and the like, consists solely of neurobiological parts, processes, and
principles. Thus, there is neither mental substance nor mental property, just brain
and various brain functions. Given the influence and success of neurobiology—as well
as the influence and success of physics, cognitive science, and artificial intelligence—
many famous living philosophers, such as Paul Churchland (1989), Daniel Dennett
(1990), and Jerry Fodor (2001), hold to this materialistic or physicalistic view of
mind/brain. There are other positions concerning the nature and existence of mind
that have come about as a result of the interaction of philosophy with the various
life and behavioral sciences (see Heil, 1998; Lowe, 2000).
There are countless other ways in which the biologist and the philosopher have
been helpful to one another, and this will become all the more evident to the reader
after having gone through this book. Also, the reader is encouraged to investigate
the material in the philosophy of biology, philosophy of science, and the history of
biology and science that is referenced at the end of this introduction. It is through
the fruitful interactions of the biologist and the philosopher that the subject-matter
of philosophy of biology has come to be the way that it is in its present state today.

The Subject-Matter of Philosophy of Biology
Every body of knowledge—science, discipline, study, domain—has a subject-matter and
specific questions that give a limit, form, and function to that body. So, for example,
biology studies parts, processes, and principles associated with living things primarily
as its subject-matter, and not stamp-collecting, business ethics, or World War II.
General Introduction

5

Philosophy of Biology
• reductionism and the biological sciences
• biological function and teleology
• species and classification problems
• units and levels of selection
• microevolution vs. macroevolution
• evolutionary developmental biology
• evolutionary psychology
• memetics and cultural evolution
• sociobiology and ethics
• design and creationism
• Darwinism and evolution's influence in biology
• chance and its influence in biology
• the concept of fitness and the tautology problem
• adaptationism
Figure 0.3: Topics that comprise much of the subject-matter of philosophy of biology

Philosophy of biology, too, has a subject-matter and specific questions which it
has developed near the end of the twentieth century, and we have included material
in this book that reflects much of the current discipline. Figure 0.3 offers some of
the central topics that comprise the subject-matter of philosophy of biology (there
are others). We have included most of these topics in this book, and describe and
explain the basics of the topics in the introductions to each section, complete with
further reading material.
There are other topics that, depending upon whom you talk to, can be considered
either central or peripheral to philosophy of biology. For example, the philosopher
of biology and the ethicist converge (along with other thinkers) in bioethics, a subdiscipline of ethics or moral philosophy that deals with issues such as abortion,
personhood, contraception, euthanasia, advance directives, informed consent, human
and animal experimentation, cloning, prenatal screening, gene therapy, and others
(Beauchamp & Childress, 2001; Kuhse & Singer, 2001). The philosopher of biology,
the epistemologist, the neurobiologist, and other thinkers converge in evolutionary
epistemology, a sub-discipline of epistemology that investigates (among other things)
the extent to which human perception, cognition, and theorizing are reliable because
of natural selection and other evolutionary factors (Harms, 2004; Radnitzky &
Bartley, 1993). Philosophers of biology, metaphysical ontologists, biologists, practitioners of medicine, bioinformaticians, and others converge in the burgeoning field
of biomedical ontology, an area concerned with building domain and formal ontologies
(here, understood as standardized, structured, taxonomic classification systems) so as
to assist biomedical researchers in classifying, categorizing, and coding their data
and information so that it may become optimally interoperable, re-usable, and
shareable with the assistance of computational systems and the World Wide Web
(Arp, 2007; Arp, Romagnoli, Chhem, & Overton, 2008; Smith, 2003, 2004).
Several of the topics in philosophy of biology exist because of Charles Darwin’s
ideas concerning evolutionary biology, many of which can be found in the The Origin
6

General Introduction

of Species. Also, every topic in philosophy of biology touches upon Darwin’s principles
in some way, and vice versa. In the Introduction to the Origin, Darwin (1859/1999) notes:
In considering the Origin of Species, it is quite conceivable that a naturalist, reflecting
on the mutual affinities of organic beings, on their embryological relations, their
geographical distribution, geological succession, and other such facts, might come to
the conclusion that each species had not been independently created, but had
descended, like varieties, from other species. Nevertheless, such a conclusion, even if
well founded, would be unsatisfactory, until it could be shown how the innumerable
species inhabiting this world have been modified so as to acquire that perfection of
structure and co-adaptation which most justly excites our admiration. . . . It is, therefore, of the highest importance to gain a clear insight into the means [italics added] of
modification and coadaptation. (pp. 4–5)

Chapters 3 and 4 of the Origin describe Darwin’s principle of natural selection, his
means or explanatory mechanism for the modification and coadaptation of species.
Based upon observations of the biosphere, thinkers in the past had hypothesized that
evolution took place, but it was Darwin who explained how evolution occurred with
the principle of natural selection, complete with several arguments, numerous pieces
of evidence, and other principles that provided a coherent picture of the so-called
“Tree of Life” (also see Ayala, 1985; Gould, 2002; Stebbins & Ayala, 1987; Strickberger,
2000; Mayr, 2001). We encourage you to read all of the Origin, as this is a classic
and foundational piece of writing for anyone doing research in biology or philosophy
of biology.
The reader can consult various other resources in philosophy of biology to get a
sense of the scope and breadth of this discipline (e.g., Grene & Depew, 2004;
Rosenberg & Arp, 2009; Rosenberg & McShea, 2007; Sarkar & Plutynski, 2008; Garvey,
2007; Hull & Ruse, 1998, 2007; Sober, 2000; Sterelny & Griffiths, 1999). The philosophy of biology has a long, varied, and complex history that would take several
lifetimes to ingest completely. Besides references to research in the philosophy of
biology, we have also included further reading material related to philosophy of
science and the history of biology and science below. We hope that students and
scholars of philosophy of biology alike will benefit from the material in this book.

References and Further Reading
Abramson, G., & Kilpatrick, H. (Eds.). (1995). Religious perspectives in modern Muslim and
Jewish literatures. London: Routledge.
Aquinas, T. (1949). The soul: A translation of St. Thomas Aquinas’ De Anima (J. Patrick, Trans.).
New York: B. Herder Book Company.
Aristotle. (1995). On the Soul. In J. Barnes (Ed.), The complete works of Aristotle. Princeton:
Princeton University Press.
Arp, R. (2007). Philosophical ontology, domain ontology, and formal ontology. The Reasoner,
1, 12.
Arp, R., Romagnoli, C., Chhem, R., & Overton, J. (2008). Radiological and biomedical knowledge integration: The ontological way. In R. Chhem, K. Hibbert, & T. Van Deven (Eds.), Radiology
education (pp. 87–104). Berlin: Springer-Verlag.

General Introduction

7

Audesirk, T., Audesirk, G., & Byers, B. (2008). Biology: Life on earth. Upper Saddle River, NJ:
Prentice Hall, Inc.
Augustine. (1991). St. Augustine’s Confessions (H. Chadwick, Trans.). Oxford: Oxford
University Press.
Ayala, F. (1985). The theory of evolution: Recent successes and challenges. In E. McMullin
(Ed.), Evolution and Creation (pp. 59–90). Notre Dame, IN: University of Notre Dame Press.
Baars, B., & Newman, J. (Eds.). (2001). Essential sources in the scientific study of consciousness. Cambridge, MA: MIT Press.
Baker, G., & Morris, K. (1996). Descartes’ dualism. London: Routledge.
Bauman, M., & Kemper, T. (Eds.). (1994). The neurobiology of autism. Baltimore: Johns Hopkins
University Press.
Bear, M., Connors, B., & Paradiso, M. (2006). Neuroscience: Exploring the brain. New York:
Lippincott Williams & Wilkins.
Beauchamp, T., & Childress, J. (2001). Principles of biomedical ethics. Oxford: Oxford
University Press.
Bisiach, E. (1999). Understanding consciousness: Clues from unilateral neglect and related
disorders. In N. Block, O. Flanagan, & G. Güzeldere (Eds.), The nature of consciousness
(pp. 237–276). Cambridge, MA: MIT Press.
Campbell, N., & Reece, M. (2007). Biology. Menlo Park, CA: Benjamin-Cummings.
Catechism of the Catholic Church. (1994). New York: Doubleday Books.
Churchland, P. (1989). A neurocomputational prespective. Cambridge, MA: MIT Press.
Copleston, F. (1994). A history of Western philosophy: Volumes I–IX. New York: Image Books.
Craig, E. (2002). Philosophy: A very short introduction. Oxford: Oxford University Press.
Darwin, C. (1859/1999). The origin of species by natural selection: Or, the preservation of favoured
races in the struggle for life. New York: Bantam Books.
Dennett, D. (1990). Consciousness explained. New York: Penguin.
Descartes, R. (1998). Meditations on first philosophy, and Discourse on method (D. Cress, Trans.).
Indianapolis, IN: Hackett Publishing Company.
Dobzhansky, T. (1973). Nothing in biology makes sense except in the light of evolution. American
Biology Teacher, 35, 125–129.
Finke, R. (1980). Levels of equivalence in imagery and perception. Psychological Review, 87,
113–132.
Fodor, J. (2001). Materialism. In D. Rosenthal (Ed.), Materialism and the mind–body problem
(pp. 128–149). Indianapolis, IN: Hackett Publishing Company.
Foster, J. (1991). The immaterial self: A defence of the Cartesian dualist conception of the
mind. London: Routledge.
Fuster, J. (1997). The prefrontal cortex: Anatomy, physiology, and neuropsychology of the frontal
lobe. New York: Lippincott-Raven.
Garvey, B. (2007). Philosophy of biology. Montreal: McGill-Queen’s University Press.
Godfrey-Smith, P. (2003). Theory and reality: An introduction to the philosophy of science.
Chicago: University of Chicago Press.
Gold, I., & Roskies, A. (2008). Philosophy of neuroscience. In M. Ruse (Ed.), The Oxford handbook of philosophy of biology (pp. 349–380). Oxford: Oxford University Press.
Gould, S. (2002). The structure of evolutionary theory. Cambridge, MA: Harvard University Press.
Grene, M., & Depew, D. (2004). The philosophy of biology: An episodic history. Cambridge,
UK: Cambridge University Press.
Hardcastle, V. (2007). Neurobiology. In D. Hull & M. Ruse (Eds.), The Cambridge companion
to the philosophy of biology (pp. 275– 290). Cambridge, UK: Cambridge University Press.
Harms, W. (2004). Information and meaning in evolutionary processes. Cambridge, UK:
Cambridge University Press.
Heil, J. (1998). Philosophy of mind: A contemporary introduction. London: Routledge.

8

General Introduction

Hook, S. (1963). Middle Eastern mythology: From the Assyrians to the Hebrews. London: Penguin
Books.
Hull, D., & Ruse, M. (Eds.). (1998). The philosophy of biology. Oxford, UK: Oxford University
Press.
Hull, D., & Ruse, M. (Eds.). (2007). The Cambridge companion to the philosophy of biology.
Cambridge, UK: Cambridge University Press.
Jones, W. (1997). A history of Western philosophy: Volumes I–V. Belmont, CA: Wadsworth
Publishing.
Kandel, E., Schwartz, J., & Jessell, T. (Eds.). (2000). Principles of neural science. New York:
McGraw-Hill.
Kim, J. (1995). Emergent properties. In T. Honderich (Ed.), The Oxford companion to philosophy
(pp. 220–241). Oxford, UK: Oxford University Press.
Kim, J. (1999). Making sense of emergence. Philosophical Studies, 95, 3–36.
Kim, J. (2000). Mind in a physical world: An essay on the mind–body problem and mental
causation. Cambridge, MA: MIT Press.
Knapp, S. (1992). The universal path to enlightenment: The Eastern answers to the mysteries
of life. New York: World Relief Press.
Kuhse, H., & Singer, P. (Eds.). (2001). A companion to bioethics. Oxford, UK: Blackwell.
Lowe, E. (2000). Causal closure principles and emergentism. Philosophy, 75, 571–585.
Mayr, E. (2001). What evolution is. New York: Basic Books.
Morgan, J., & Laungani, P. (Eds.). (2005). Death and bereavement around the world. Amityville,
NY: Baywood Publishing Company.
National Research Council. (1996). National science education standards. Washington, DC: National
Academies Press.
National Research Council. (2000). Inquiry and national science education standards: A guide
for teaching and learning. Washington, DC: National Academies Press.
Newton-Smith, W. (Ed.). (2001). A companion to the philosophy of science. Oxford, UK: Blackwell.
Passingham, R. (1993). The frontal lobes and voluntary action. Oxford, UK: Oxford University
Press.
Plato. (1997). The Republic and Phaedo. In J. Cooper (Ed.), The complete works of Plato.
Indianapolis, IN: Hackett Publishing Company.
Plotinus. (1992). The Enneads (S. MacKenna, Trans.). Burdett, NY: Larson Publications.
Pojman, L. (Ed.). (2007). Introduction to philosophy: Classical and contemporary readings. Oxford,
UK: Oxford University Press.
Radnitzcky, G., & Bartley, W. (Eds.). (1993). Evolutionary epistemology, rationality, and the
sociology of knowledge. LaSalle, IL: Open Court Publishers.
Rosenberg, A., & Arp, R. (2009). Philosophy of biology: An anthology. Malden, MA:
Wiley-Blackwell.
Rosenberg, A., & McShea, D. (2007). Philosophy of biology: A contemporary introduction. London:
Routledge.
Ruse, M. (Ed.). (2008). The Oxford handbook of philosophy of biology. Oxford, UK: Oxford University
Press.
Russell, B. (1912/1999). The problems of philosophy. In J. Perry & M. Bratman (Eds.),
Introduction to philosophy: Classical and contemporary readings (pp. 9–12). Oxford, UK:
Oxford University Press.
Sadava, D., Heller, H., Orians, G., Purvis, W., & Hillis, D. (2008). Life: the science of biology.
Sunderland, MA: Sinauer Associates.
Sarkar, S., & Plutynski, A. (Eds.). (2008). A companion to the philosophy of biology. Malden,
MA: Wiley-Blackwell.
Schad, J. (2004). Queer fish: Christian unreason from Darwin to Derrida. Eastbourne, UK: East
Sussex Press.

General Introduction

9

Silberberg, M. (2008). Chemistry: The molecular nature of matter and change. New York: McGrawHill Publishers.
Smith, B. (2003). Ontology. In L. Floridi (Ed.), Blackwell guide to the philosophy of computing
and information (pp. 155–166). Malden, MA: Blackwell.
Smith, B. (2004). The logic of biological classification and the foundations of biomedical
ontology. In D. Westerstahl (Ed.), Logic, methodology, and philosophy of science (pp. 1–16).
Amsterdam: Elsevier.
Sober, E. (2000). Philosophy of biology. Boulder, CO: Westview Press.
Solomon, R. (2005). The big questions: A short introduction to philosophy. Belmont, CA:
Wadsworth Publishing.
Stebbins, G., & Ayala, F. (1987). The evolution of Darwinism. Scientific American, 253, 54–64.
Sterelny, K., & Griffiths, P. (1999). Sex and death: An introduction to philosophy of biology.
Chicago: University of Chicago Press.
Strickberger, M. (2000). Evolution. Sudbury, MA: Jones and Bartlett.
Tippens, P. (2007). Physics. New York: McGraw-Hill Publishers.
Watson, J., & Arp, R. (2008). Checks and balances: The welcomed tension between philosophy
and science. The Quarterly Review of Biology, 83, 1–12.

Further Reading in Philosophy of Science
Ayala, F. (1994). On the scientific method, its practice and pitfalls. History and Philosophy of
the Life Sciences, 16, 205–240.
Balashov, Y. (Ed.). (2002). Philosophy of science: Contemporary readings. London: Routledge.
Boyd, R., Gasper, R., & Trout, J. (Eds.). (1991). The philosophy of science. Cambridge, MA: MIT
Press.
Curd, M., & Cover, J. (Eds.). (1998). Philosophy of science: The central issues. New York: W.W.
Norton.
Godfrey-Smith, P. (2003). Theory and reality: An introduction to the philosophy of science.
Chicago: University of Chicago Press.
Hempel, C. (1965). Aspects of scientific explanation. New York: Free Press.
Hodge, J., & Radick, G. (Eds.). (2003). The Cambridge companion to Darwin. Cambridge, UK:
Cambridge University Press.
Hung, E. (1998). The nature of science: Problems and perspectives. Belmont, CA: Wadsworth
Publishing.
Klemke, E., Hollinger, R., & Rudge, D. (Eds.). (1998). Introductory readings in the philosophy
of science. New York: Prometheus.
Kuhn, T. (1962). The structure of scientific revolutions. Chicago: University of Chicago Press.
Kuipers, T. (Ed.). (2007). General philosophy of science: Focal issues. London: Elsevier.
Ladyman, J. (2002). Understanding philosophy of science. London: Routledge.
Losee, J. (2001). A historical introduction to the philosophy of science. Oxford, UK: Oxford
University Press.
Machamer, P., & Silberstein, M. (Eds.). (2002). The Blackwell guide to the philosophy of
science. Malden, MA: Blackwell Publishers.
Nagel, E. (1961). The structure of science. New York: Harcourt, Brace and World.
Newton-Smith, W. (Ed.). (2001). A companion to the philosophy of science. Oxford, UK: Blackwell.
Okasha, S. (2002). Philosophy of science: A very short introduction. Oxford, UK: Oxford University
Press.
Papineau, D. (Ed.). (1996). The philosophy of science. Oxford, UK: Oxford University Press.
Popper, K. (1959). The logic of scientific discovery. London: Hutchinson.
Rosenberg, A. (2005). Philosophy of science: A contemporary introduction. London: Routledge.

10

General Introduction

Rosenberg, A. (2008). Philosophy of social science. Boulder, CO: Westview Press.
Salmon, M., Earman, J., Glymour, C., Lennox, J., Schaffner, K., Salmon, W., et al. (1999). An
introduction to the philosophy of science. Indianapolis, IN: Hackett Publishing Company.
Schick, T. (Ed.). (1999). Readings in the philosophy of science: From positivism to postmodernism. New York: McGraw-Hill.
Solomon, J., & Hunt, A. (1992). What is science? Hatfield, UK: Association for Science Education.

Further Reading in the History of Science and Biology
Bowler, P. (2003). Evolution: The history of an idea. Berkeley: University of California Press.
Cormack, L., & Ede, A. (2004). A history of science in society: From philosophy to utility. New
York: Broadview Press.
Ede, A., & Cormack, L. (2007). A history of science in society: A reader. New York: Broadview
Press.
Gaukroger, S. (2007). The emergence of a scientific culture: Science and the shaping of modernity, 1210–1685. New York: Oxford University Press.
Grant, E. (1996). The foundations of modern science in the Middle Ages: Their religious,
institutional and intellectual contexts. Cambridge, UK: Cambridge University Press.
Grant, E. (2007). A history of natural philosophy: From the ancient world to the nineteenth
century. Cambridge, UK: Cambridge University Press.
Gregory, F. (2007). Natural science in Western history, Volumes 1 & 2. Boston: Houghton
Mifflin.
Grene, M., & Depew, D. (2004). The philosophy of biology: An episodic history. Cambridge,
UK: Cambridge University Press.
Gribbin, J. (2003). Science: A history. New York: Penguin Books.
Gribbin, J. (2004). The scientists: A history of science told through the lives of its greatest
inventors. New York: Random House.
Hull, D. (2008). The history of the philosophy of biology. In M. Ruse (Ed.), The Oxford handbook
of philosophy of biology (pp. 11–33). Oxford, UK: Oxford University Press.
Larson, E. (2004). Evolution: The remarkable history of a scientific theory. New York: Random
House.
Laudan, L. (1982). Commentary: Science at the bar—causes for concern. Science, Technology
& Human Values, 7, 16–19. (See Ruse’s response: Ruse, 1982.)
Lindberg, D. (2008). The beginnings of Western science: The European scientific tradition in
philosophical, religious, and institutional context, prehistory to AD 1450. Chicago:
University of Chicago Press.
Lindberg, D., & Numbers, R. (Eds.). (2002–2009). The Cambridge history of science, Vols. 3–7.
Cambridge, UK: Cambridge University Press.
Magner, L. (2002). A history of the life sciences. New York: Marcel Dekker.
McClellan, J., & Dorn, H. (1999). Science and technology in world history: An introduction.
Baltimore: Johns Hopkins University Press.
Moore, J. (1999). Science as a way of knowing: The foundations of modern biology. Cambridge,
MA: Harvard University Press.
Morange, M. (2000). A history of molecular biology (M. Cobb, Trans.). Cambridge, MA: Harvard
University Press.
Ruse, M. (1982). Response to the commentary: Pro judis. Science, Technology & Human Values,
7, 19–23. (See Laudan’s criticisms: Laudan, 1982.)

General Introduction

11

PART I

IS IT POSSIBLE TO
REDUCE BIOLOGICAL
EXPLANATIONS TO
EXPLANATIONS IN
CHEMISTRY AND/OR
PHYSICS?

Introduction

Humans seek both unity and simplicity when classifying and explaining reality, and
this is especially true in the sciences. This way, we can understand, control, and—in
the words of the famous Modern philosopher, René Descartes (1596–1650)—“thus
render ourselves, as it were, masters and possessors of nature” and other aspects of
reality (Descartes, 1637/1998, p. 35). Consider the law of gravity, the kinetic theory
of gas, or the principle of natural selection and how they form unified, simple,
powerful bases for our explanations of many of the events that occur in the
universe. This being the case, there is a tendency for researchers to reduce diverse
and complex parts, processes, and principles to their most basic constituents, or
“lowest common denominator” (as Evelyn Fox Keller calls it in the first paper included
in this part), if this is possible.
Now reductionism is a complicated term that has many meanings, distinctions,
and uses, and one can look at the material in the further reading section at the end

of this introduction for further insights and clarifications. It is arguable that wholes
can be reduced to parts, higher levels can be reduced to lower ones, the complex
can be reduced to the simple, the older theory can be reduced to the newer one—
and there are other forms of reduction. For our purposes here, following the
excellent work of Michael Silberstein (2002), we can distinguish (broadly) between
a metaphysical form of reductionism and an epistemological form of reductionism,
bearing in mind that there are multiple versions and subversions of each form.
Metaphysics concerns what exists in reality. According to metaphysical reductionists,
there are really no entities, properties, or substances that arise out of more fundamental chemical or physical ones since, once the more fundamental ones have been
described, that is all there is to the reality of an entity, property, or substance. Thus,
for example, when people speak about water, they may take it to be a substance in its
own right. However, according to the metaphysical reductionist, water just is hydrogen
and oxygen—nothing new emerges when two hydrogen molecules combine with one
oxygen molecule. The same goes for biological phenomena as, for example, a cell
just is the basic chemico-physical parts, process, and principles of which it is composed. In the first paper of this part, Evelyn Fox Keller seems to be expressing this
position when she claims: “I am committed to the position that all biological
phenomena, including evolution, require nothing more than the workings of physics
and chemistry.”
Conversely, according to a metaphysical non-reductionist, there is something about
water—for example, its liquidity or liquid property—that emerges from (or supervenes
on) the hydrogen and oxygen molecules, making it such that this liquidity exists on
a separate metaphysical plane from the molecules on which it depends. In the case
of the cell, this emergence or supervenience is true even more so, since a cell is a
complexly organized hierarchical system of interactions. After all, reasons the
metaphysical anti-reductionist, liquidity and the cellular system itself appear to be
something distinct from hydrogen, oxygen, and DNA molecules, chemical bonds, and
other chemico-physical parts, processes, and principles.
In many researchers’ minds, the possible reduction of biological phenomena to
chemical and physical phenomena became all the more probable starting with James
Watson and Francis Crick’s elucidation of the molecular structure of DNA that occurred
in a Nature paper from 1953. In that paper (1953a) and a quick follow-up paper
(1953b), Watson and Crick got scientists and philosophers of science to think about
what parts, processes, and principles were really at work in heritability. Could
Mendelian genetics be reduced to molecular genetics in the same way that heat was
reduced to kinetic motion or lightning to electrical discharge? Given that chemistry
and physics were making incredible strides at revealing the real workings of other
parts of the universe—and, thereby, reducing things to chemical phenomena, then
physical phenomena—it would only seem to make sense that living things could be
revealed as chemical and/or physical phenomena too. Thus, the possibility of biology
being reduced to chemistry and/or physics became solidified as a topic in philosophy
of biology with papers such as J.J.C. Smart’s “Can Biology Be an Exact Science?”
(1959), Kenneth Schaffner’s “Approaches to Reduction” (1967), Francisco Ayala’s
“Biology as an Autonomous Science” (1968; also see Ayala & Dobzhansky, 1974),
Alexander Rosenberg’s “The Supervenience of Biological Concepts” (1978), Philip
Kitcher’s “1953 and All That: A Tale of Two Sciences” (1984), Ernst Mayr’s “The
14

Is It Possible to Reduce Biological Explanations?

Autonomy of Biology: The Position of Biology among the Sciences” (1996), and Elliot
Sober’s “The Multiple Realizability Argument against Reductionism” (1999), among
others.
Whereas metaphysics concerns what exist in reality, epistemology is concerned
with how we can know, describe, model, and explain reality, as well as our
justification for doing so. According to a standard epistemological form of
reductionism—often called theoretical reduction—it is possible to replace one theory
A by another more explanatorily powerful theory B; thus, in effect, intertheoretically
reducing A to B. For example, the phlogiston theory of combustion (which stated that
an undetected substance called phlogiston was released during combustion) was replaced
by the oxygen theory of combustion, while the caloric theory of heat (which stated
that a fluid substance called caloric was responsible for a thing’s temperature) was
replaced by the kinetic theory of heat. In Kitcher’s above-mentioned “1953 and All
That,” he responds to the typical epistemological reductionist’s claim that classical
genetics can now be intertheoretically reduced to—and, hence, replaced by—molecular
biology, especially now that we know “what’s really going on” with heredity at the
molecular level. By using the general line of reasoning that the biological sciences
are subfields corresponding to multiple levels of complex organization in nature, Kitcher
(1984) wants to show that, “despite the immense value of the molecular biology that
Watson and Crick launched in 1953, molecular studies cannot cannibalize the rest
of biology” (p. 373).
In his paper included in this part, John Dupré mounts a primarily epistemological
argument for non-reductionism in biology—and would likely agree with Kitcher—since
he argues that “properties of constituents cannot themselves be fully understood
without a characterization of the larger system of which they are part” and, hence,
the “notion that complex systems, such as those found in biology, can be fully understood from a sufficiently detailed knowledge of their constituents, is mistaken.” In
her paper included in this part, it would seem that Evelyn Fox Keller is advocating
a kind of promissory note that chemistry and physics will be able to explain
biology completely. She offers two examples—(1) bacterial chemotaxis and (2) regulating the levels of oxygen and CO2 in the termite nest—that she believes “provide
evidence of partial successes in the effort to ‘reduce biological explanations to
explanations in chemistry and/or physics.’”
Whatever the case may be, the best strategy for researchers in biology is probably
to pursue a general form of methodological reduction until parts, processes, or
principles in reality are encountered that cannot be reduced. If such non-reducibility
is encountered in the metaphysical or epistemological senses, then, following Keller,
it may be that what is required is “fundamental transformations in the conventional
approaches of both physics and chemistry.”

References and Further Reading
Arp, R. (2007). Homeostatic organization, emergence, and reduction in biological phenomena.
Philosophia Naturalis, 44, 238–270.
Arp, R. (2008). Life and the homeostatic organization view of biological phenomena. Cosmos
and History: The Journal of Natural and Social Philosophy, 4(1), 1–21.

Introduction

15

Ayala, F. (1968). Biology as an autonomous science. American Scientist, 56, 207–221.
Ayala, F., & Dobzhansky, T. (Eds.). (1974). Studies in the philosophy of biology: Reductionism
and related problems. New York: Macmillan.
Bechtel, W. (2006). Discovering cell mechanisms: The creation of modern cell biology.
Cambridge, UK: Cambridge University Press.
Beurton, P., Falk, R., & Rheinberger, H. (Eds.). (2000). The concept of the gene in development
and evolution: Historical and epistemological perspectives. Cambridge, UK: Cambridge
University Press.
Craver, C., & Darden, L. (Eds.). (2005). Studies in history and philosophy of biological and
biomedical sciences [Special issue]. Mechanisms in Biology, 31(2).
Darden, L. (2006). Reasoning in biological discoveries: Essays on mechanisms, interfield relations, and anomaly resolution. Cambridge, UK: Cambridge University Press.
Delehanty, M. (2005). Emergent properties and the context objection to reduction. Biology and
Philosophy, 20, 715–734.
Descartes, R. (1637/1998). Discourse on method, and Meditations on first philosophy (D. Cress,
Trans.). Indianapolis, IN: Hackett Publishing.
Griffiths, P. (2002). Molecular and developmental biology. In P. Machamer & M. Silberstein
(Eds.), The Blackwell guide to the philosophy of science (pp. 252–271). Malden, MA: Blackwell
Publishers.
Hoyningen-Huene, P., & Wuketits, F. (Eds.). (1989). Reductionism and systems theory in the
life sciences. Dordrecht: Kluwer.
Keller, E. (2002). The century of the gene. Cambridge, MA: Harvard University Press.
Kimbrough, S. (1978). On the reduction of genetics to molecular biology. Philosophy of Science,
46, 389–406.
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Introduction

17

C HAPTE R
O
N
E

It Is Possible to Reduce
Biological Explanations to
Explanations in Chemistry
and/or Physics
Evelyn Fox Keller

Despite all the dramatic successes we have witnessed in recent years in unraveling the
physics and chemistry behind biological phenomena, we still have a very long way to
go. The most fundamental question of what is the difference between living and nonliving matter remains unanswered. Unlike most physical and chemical systems, living
systems must—at the very least—be endowed with function, a concept that to this day
remains indispensable to biology, yet is effectively missing from the vocabulary of physics
and chemistry. Accordingly, we need an account of the evolution of function out of
simple physical and chemical dynamics which we do not as yet have. Nevertheless,
I retain a guarded optimism: we are, I believe, moving closer to answering this basic
question. Yet doing so, I argue, requires fundamental transformations in the conventional approaches of both physics and chemistry.

1 Introduction
My task in this paper is to respond to the question “Is it possible to reduce biological
explanations to explanations in chemistry and/or physics?” Forced to choose
between only two alternatives—yes or no—I opt for the positive response. But I could
as easily have gone the other way. Indeed, I suggest that the question is not wellposed. To the extent that a negative response would imply that I believe there is
something beyond physical and chemical processes involved in the formation of
living beings, I am obliged to respond affirmatively. I am an unambivalent materialist and do not harbor any such belief. But if by that proposition one means that
biological explanations can be reduced to the theories of matter currently available

in physics and chemistry, then my response is no. And not, as Niels Bohr
(1932/1958) once argued, because the study of biology can be expected to bring the
discovery of new laws. But rather, paraphrasing the arguments put forth by Nancy
Cartwright (1983), because laws of physics, by definition, have been developed with
reference to a narrow range of possible physical and chemical phenomena; and, one
might add, necessarily so. For that is the way with laws: they are developed to describe
(or explain) the lowest common denominator of physical and chemical processes, or
that which is said to underlie the manifest variety of these processes.
How is that lowest common denominator identified? In the actual practice of the
physical and chemical sciences, this has generally been translated (and for good pragmatic reasons) into the assumption that that common denominator is coextensive
with the simple. Thus, for example, highly oversimplified models, conspicuous for
their lack of realism, are often justified by the tacit expectation that, despite their
lack of realism (perhaps even by virtue of their simplicity), they contain the features
of greatest importance (see Keller, 2002, Ch. 3). In this fashion, a tradition has
developed in which concepts of underlying, basic, fundamental, and simple are all
expected to cluster together.
Such an expectation has worked astonishingly well in physics; not so, however,
in biology. As has often been observed, biology simply does not conform to these
expectations. Whatever the meaning of fundamental in biology, it clearly cannot be
equated with simple, nor is it at all obvious that it is common to all biological
entities. For example, DNA might be argued as fundamental to biological systems,
but DNA is an enormously complex molecule. Even in the early days, when molecular biologists believed that its primary function was to code for proteins, no one would
have thought of DNA as simple. Today, biologists have learned that this molecule
has a repertoire of capacities far richer than had originally been thought, with new
dimensions emerging every day. Also, they have learned that DNA is not universal:
some organisms make do with RNA, and some entities (e.g., prions) manage to
sustain themselves and reproduce without either DNA or RNA. Furthermore, not only
does biology not admit of a clustering of fundamental, common denominator, and
simple, but also a number of philosophers (starting with Jack Smart in 1963) have
concluded from this fact that biology, therefore, does not have laws of its own, at
least not in the sense that physics is said to have laws. As Ernst Mayr (1982) famously
put it, the only universal law in biology is that “All biological laws have exceptions”
(p. 38; also see Beatty, 1995; Mitchell, 2000; Smart, 1963).
Which is not to say that biology is not a science (although Smart seems to have
thought it was to say exactly that), but rather that it is a science in which the search
for “laws” has not, at least so far, played much of a role. True, one finds the term
used to describe many important biological discoveries: Mendel’s laws of segregation, power laws (referring to the distribution of nodes in biological networks), and
even the central dogma is sometimes referred to as a law. But crucially, these ought
properly be called generalities, not laws. They apply over a broad range of conditions;
but there is neither anything necessary about them (as things could have been
otherwise), nor need they be free of exceptions. Furthermore, where they do apply,
they may or may not be either fundamental or simple. They are simply empirical
statements about what generally seems to be the case. As such, they may (at least
in some cases) serve as explanations of what follows, but to the extent that they
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come with no account of how such generalizations emerge from the vicissitudes of
the evolutionary pathways that gave rise to such properties, the generalities themselves remain unexplained.
Where, then, is the role of physics and chemistry in the construction of biological
explanations? As a materialist, I am committed to the position that all biological
phenomena, including evolution, require nothing more than the workings of physics
and chemistry. But this position requires neither a belief in the adequacy of our
current understanding of physics and chemistry, nor any expectation that biology
will lead us to the discovery of new laws. New phenomena, to be sure, but regarding
the question of new laws, I concur with Jean-Baptiste Lamarck (1809/1984): “Nature
has no need for special laws” (p. 132). I believe that analysis of the specific physical
and chemical phenomenology involved in biological processes should, in principle,
suffice for an understanding of what endows biological systems with the properties
of life. I say “in principle” because there is no telling whether or not the complexity
of these systems might, in practice, exceed our analytic capacities. But in any case,
the more important question is, “What kinds of analysis, in fact, are required?”

2 Systems Biology
Efforts to develop explanations of biological phenomena based on the physical and
chemical properties of highly idealized biological systems were not infrequently made
over the course of the twentieth century, but they failed to persuade working biologists
of the value of such analyses (see Keller, 2002). Eric Ponder (Director of the Cold Spring
Harbor Institute from 1936 to 1941) summed up the sentiments of an entire community
when, in his response to such early efforts by Nicolas Rashevsky (1934), he argued:
[I]t is futile to conjure up in the imagination a system of differential equations for the
purpose of accounting for facts which are not only very complex, but largely unknown.
. . . It is said that if one asks the right question of Nature, she will always give you an
answer, but if your question is not sufficiently specific, you can scarcely expect her to
waste her time on you . . . what we require at the present time is more measurement and
less theory. (cited in Wilson, 1934, p. 201)

Rashevsky, it must be said, was only proceeding as mathematical physicists generally did—indeed, given the analytical technologies available at the time, he had little
choice but to begin with a highly idealized (and hence, simplified) model. Similarly,
biologists’ disdain for such models, and their demand for more measurement, was
also based on the realities of their discipline; in particular, on the recognition of both
the complexity of biological systems and their rootedness in evolution.
In any case, among biologists it was the demand for more data that prevailed
throughout most of the twentieth century. But at the century’s end, the dramatic
successes of the reductionist program of molecular biology and, perhaps especially,
the development of new technologies (e.g., for nucleotide sequencing, molecular labeling, and visual tracking) led to an avalanche of data that threatened to overwhelm
the ability of experimental biologists to make sense of their findings using their
traditional modes of analysis. In the physical and mathematical sciences, conditions
It Is Possible to Reduce Biological Explanations

21

were also changing, primarily due to the development of powerful high-speed computers and, together, these quite different developments created the conditions for
a new rapprochement between mathematical and biological science. Support for
interdisciplinary collaborations skyrocketed and, in the early years of the twenty first
century, new institutes, programs, and departments under the name of systems biology
have proliferated like wildfire.
Far from being a unified endeavor, systems biology encompasses a great variety
of mathematical, computational, and physical approaches to biological problems, and
there is substantial disagreement among researchers as to how far computational
analysis will enable one to proceed by working from the bottom up (i.e., from what
is known about the relevant molecular elements and their interactions), and to what
extent it is necessary to work downwards from known systemic properties to the
identification of the relevant actors. Nonetheless, virtually all are agreed on the importance of grounding analysis in the data that have become available, and on the need
to develop analytic techniques that would enable one to move beyond a list of parts
(e.g., genes, proteins, etc.). There is also widespread agreement on the extent to which
the analysis of systems with a large number of components yields (emergent) properties that could not have been predicted from the behavior of the components themselves. Of particular importance is the recognition of such key biological properties
as robustness, evolvability, and quorum sensing as properties that emerge only on
the systems level. Indeed, in less than a decade, work in systems biology has reconfigured
the frontier of biological inquiry, bringing issues to the fore that had previously gone
virtually unnoticed.
Thus far, the main strength of such analyses has come not from the application
of simple, highly idealized models, but from close attention to the kinds of experimental data that recent biological research has provided. Through imaginative
deployment of theoretical and computational techniques from the physical, mathematical, and computer sciences, from the application of methods and insights from
the engineering sciences, and from the use of sophisticated technologies developed
in experimental physics to obtain the kinds of micro-molecular data that analysis of
the physical underpinnings of molecular processes requires, we are beginning to acquire
the kinds of understanding that would permit the formulation of biological explanations in terms of physical and chemical processes. But it is becoming clear that these
accounts need not resemble the kinds of explanations in physics and chemistry to which
we are accustomed.
Among the most obvious differences are: (1) the large number and dense interactivity of parts; (2) the hierarchical (and multi-scale) organization of biological
systems; (3) the dependence of the identity of parts, and the interactions among them,
on higher-order effects; and (4) the robustness and adaptability of biological structures.
It is commonplace to observe that biological systems are vastly more complex than
physical systems (they might be said to be maximalist, in contrast with the minimalism of physical systems), and the question has recently surfaced as to why these
systems are so complex. As Arthur Lander (2004) puts it, “What purpose does all this
complexity serve?” (p. 713). Kunihiko Kaneko (2006) raises a similar question,
observing that: “For the purpose of simply responding to the external environment, a
simpler reaction consisting of a single level would be sufficient.” Kaneko’s answer, once
again, points us to evolution. He writes that “the great diversity or complexity we
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observe is a result of the history of organisms that experienced a great variety of
circumstances. . . . The past experiences have come to be embedded in the structure and
function of organisms” (p. 9), and that seems correct.

3 Function: A Minimalist Conception
But there are clearly qualitative, as well as quantitative, differences between biological and physical systems, and perhaps foremost among these is that biological systems
are endowed with function, a concept effectively missing from the vocabulary of physics
and chemistry yet, to this day, indispensable to biology. To avoid confusion, let me
make clear from the start that my use of the term “function” departs from the convention that has developed in recent years among philosophers of science, whereby
function is defined in terms of natural selection. Proper function—as first argued by
Ruth Millikan (1984), and now widely asserted—should be understood solely in the
context of natural selection: the function of X is that “which caused the genotype,
of which X is the phenotypic expression to be selected by natural selection”
(Neander, 1998, p. 319). This is not how I am using the term. Indeed, both logically
and historically, the notion of function with which I am concerned must precede the
onset of natural selection, at least as that term is usually construed.
Natural selection—at least since the neo-Darwinian synthesis and, probably, ever
since Darwin—has been conventionally understood as requiring the prior existence
of stable, autonomous, and self-reproducing entities. Minimally, it presupposes the
existence of single celled organisms, or, simply, of stable, autonomous, cells capable
of dividing. But these first cells contained, of necessity, numerous sub-cellular entities
(or modules), endowing the primitive cell with the functions that would be minimally
required for the cell to sustain itself and reproduce. In other words, even if the first
cells lacked many features of the modern cell, they had to have had primitive
mechanisms to support metabolism, cell division, etc., and there needed to have come
into being primitive embodiments of function that would work keep the cell going
and to protect it from insult.
To further clarify what I mean by function, let me turn to Michael Ruse’s (2003)
argument against the use of the term for inanimate systems and, more specifically,
against the sufficiency of circular causality for an understanding of biological
function. Ruse offers the familiar example of the cyclical process by which rain falls
on mountains, is carried by rivers to the sea, evaporated by the sun, whereby it forms
new rain clouds which, in turn, discharge their content as rain. The river is there
because it produces or conveys water to form new rain clouds. The rain clouds are
a result of the river’s being there. But Ruse argues that we would not want to say
the function of the river is to produce rain clouds, and he is right. What is missing,
he claims, is the means by which “things are judged useful.”
I will not follow Ruse in his deployment of such worrisomely adaptationist and
intentional notions as value and desire. Instead, I want to salvage his observation by
re-describing what he calls judgment as a measurement of some parameter, or, if you
like, as an evaluation performed by a mechanical sensor that, when exceeding some
pre-set limit, is fed back into a controller which is able to restore the proper range
of parameter. In other words, reverting to another philosophical tradition, I use the
It Is Possible to Reduce Biological Explanations

23

term function in the sense of a simple feedback mechanism. Like a thermostat. As
William Wimsatt (2002) puts it, “To say that an entity is functional is to say that
its presence contributes to the self-regulation of some entity of which it is a part”
(p. 177). Once such a mechanism is added to the rain–cloud–river cycle (say, a mechanism that triggers a change in evaporation rates when the water level falls too low),
we can, in this sense of the term, quite legitimately speak of function and say, for
example, that the function of such a mechanism is to maintain the water level within
a certain range of parameters. Furthermore, I argue, we can similarly refer to the
many different cellular mechanisms (proof-reading and repair, chaperones, cell-cycle
regulation) that maintain various aspects of cellular dynamics.
To make my minimalist conception of function more precise, I want to focus on
those effects that contribute to the stability of such properties that are essential to
the system’s continuance: its water level, or perhaps its physical integrity. Stability,
here, means little more than constancy, the fixity of some property of either the internal or external milieu, but it is important to note that maintaining a property within
a certain range does not necessarily contribute to the survival of the overall system.
For example, maintaining the water level within certain bounds does contribute to
the stability of the rain–cloud–river cycle, whereas maintaining a constant temperature of the system need not have anything to do with the stability of the system
as such. In order to distinguish the stability or constancy of a particular aspect of
the system from the stability of the system as a whole, I will use the term persistence
for the latter. The crucial point is that, when the stability of a property does contribute to the persistence of the overall system, a kind of selection—i.e., selection of
the most stable (or most persistent)—will operate automatically. Here, if you will, is
selection without reproduction. Like natural selection, it is entirely agnostic with
respect to the forces that threaten the stability of a system; it cares only about
persistence.
Indeed, if we think of reproduction as just one strategy for ensuring persistence—
as Frederick Bouchard (2004), Rosenberg and Kaplan (2005), and others have
advocated—we can think of natural selection as a subset of this more general category
of selection for persistence. And just as in the case of natural selection, the more
general selection process that kicks in with variable stability/persistence provides us
with an explanation of why the arrangement of device-cum-system is likely to be
common. It might also provide us with an explanation of progressive refinements of
organization leading to increases in stability. It will not, however, contribute to our
understanding of how such an arrangement of parts—an arrangement in which one
part exerts an effect that enhances the stability of the larger system in which it is
embedded—first came to be.
Put in these terms, the obvious question is how such a mechanism might arise. It
is striking that, for all the promise of recent attempts to treat biological systems as
instances of the kinds of non-linear dynamical systems encountered in statistical physics,
and for all the power of non-linear dynamics to generate emergent patterns, biological function—as I am using the term—seems not to be on the horizon. Apparently,
the emergence of function requires rather more than just non-linear interactions, and
the question is what that more consists of.
Addressing just this question, Walter Fontana and Leo Buss (1996) have concluded that “the traditional theory of ‘dynamical systems’ is not equipped for dealing
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with constructive processes. Indeed, the very notion of ‘construction’ requires a description that involves the structure of objects. Yet, it was precisely the elimination of
objects from the formalism that make dynamical systems approaches so tremendously
successful” (p. 59). They argue that the main problem is that, although conventional
dynamical systems theory is “well-suited to treat changes in the magnitudes of quantitative properties of fixed object species,” it is still “ill-suited to address interactions
that change the objects themselves” (p. 63). And this, of course, is precisely what
characterizes the objects of biological systems, which are necessarily subject to change
by the internal dynamics of the system, and not only by external insult. As they put
it: “Mutation is to construction like perturbation is to dynamics” (p. 63). Fontana
and Buss call their own very interesting effort to expand the traditional theory to
include objects, their internal properties, their construction, and their dynamics,
constructive dynamical systems.

4 Kant and As-If Purpose
Of course, function is not the only property that distinguishes living from non-living
systems (or, as a Nature (2005) editorial put it, that distinguishes a live cat from a
dead one), but it lies at the heart of that question of just what kind of science a
science of life might be. Certainly, it lay at the heart of Immanuel Kant’s (1724–1804)
concern about the prospects for a science of life. “Organisms,” he wrote in the
second Part of the Critique of Judgment (1790/1993), are the beings that “first afford
objective reality to the conception of an end that is an end of nature and not a
practical end. They supply natural science with the basis for a teleology . . . that would
otherwise be absolutely unjustifiable to introduce into that science seeing that we
are quite unable to perceive a priori the possibility of such a kind of causality”
(pp. 558, 66). For Kant, it was precisely here that the fundamental difficulty for a
scientific approach to life is to be found: in the fact that organisms are systems that
behave as if having a purpose, goals, ends (or functions) of their own. (It is true that
the term Kant actually used was not function, but rather Naturzwecke, translated as
“an end of nature” or “natural purpose,” but I would argue that all of these terms
are equally effective in capturing what was essential to his concerns.)
Kant did not believe that organisms really were teleological, but rather that we
have no way of understanding them other than by thinking of them as teleological.
Perhaps he should have written, “They supply natural science with the basis of an
as-if teleology”—something totally missing from natural science as he knew it
(which basically meant Newtonian mechanics). Indeed, this was the reason that he
famously (or infamously) concluded that “there will never be a Newton for a blade
of grass.” The kind of organization instantiated by organisms cannot be obtained
either from Newton’s laws themselves, or from any other set of laws of that kind.
As he wrote, it is “contrary to reason that crude matter on its own should have
structured itself originally in terms of mechanical laws, that life could have sprung
from the nature of what is lifeless, and that matter could have molded itself on
its own into the form of a self-preserving purposiveness” (Kant, 1987, p. 311).
Accordingly, if biology is to be a science, it would clearly have to be a different kind
of science.
It Is Possible to Reduce Biological Explanations

25

As Kant saw it, the difference between the life and the physical sciences lay precisely in the peculiar part–whole organization of living beings, or, as he suggested
(in what was, in fact, the first use of the term), in their “self-organization”:
In such a natural product as this every part is thought as owing its presence to the
agency of all the remaining parts, and also as existing for the sake of the others and
of the whole, that is as an instrument, or organ . . . the part must be an organ producing
the other parts, each, consequently, reciprocally producing the others. . . . Only under these
conditions and upon these terms can such a product be an organized and self-organized
being, and, as such, be called a physical end. (Kant, 1987, p. 557)

An organism, in short, is “an organized natural product is one in which every part
is reciprocally both end and means. In such a product nothing is in vain, without
an end, or to be ascribed to a blind mechanism of nature” (p. 558). In fact, Kant
does not exclude the possibility that such products are intrinsically mechanical, but
only the possibility that we can ever fully explain them in terms of blind mechanism, given the limits to our powers of judgment. Which is not to say that we should
not try, but only that we must accept our own cognitive limits. As Alix Cohen (2007)
explains:
It is reasonable, even praiseworthy, to try to explain natural products in terms of
natural mechanism as long as there is some probability of success. Indeed, if we give
up this attempt, we must not do so on the ground that it is intrinsically impossible to
find the purposiveness of nature by following this route, but only on the ground that
it is impossible for us as human beings. (p. 115)

Indeed, Kant’s argument is that it is precisely because of our limitations that we must
use the concept of teleology in our investigations of biological systems.
This work Critique of Judgment, written in 1790, might well be regarded as the
first philosophical treatise on systems biology, even though that term never appears
as such. Nor does it appear in any of the many research efforts that Kant’s discussion inspired over the next half-century, especially in Germany. What these efforts
shared was a commitment to finding a way of integrating teleology and mechanism
in the analysis of biological systems, qualifying in Tim Lenoir’s (1982) view as a
research tradition that he dubbed “teleo-mechanist.” But whatever the successes of
this tradition, their unifying goal soon fell out of favor, effectively drowned out by
the increasing polarization between mechanistic science and a purposeful divine
architect, on the one hand, and by Darwin’s great success, on the other. Indeed, even
Kant’s essay on teleological judgment, the second part of his Critique, fell into neglect.
But with the rise of systems biology over the last few years, it is hard not to hark
back to this earlier tradition, and, more specifically, to the concerns of Kant’s inquiry.

5 Cybernetics and Bernard Machines
The chief difference between then and now, between Kant’s despair of ever being
able to provide a mechanistic account of natural ends, and the optimism of our own
time, came out of the development of mechanisms that promised a self-directed
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functioning, in the middle of the twentieth century. “Out of the wickedness of war,”
as Warren Weaver (1948, p. 540) wrote shortly after the end of World War II, emerged
not only a new machine, but also a new vision of a science of the inanimate: a
science based on principles of feedback and circular causality, and aimed at the mechanical implementation of exactly the kind of purposive behavior that so worried
Kant. I am referring to the birth of cybernetics, a science that would repudiate the
very distinction between organism and machine on which Kant’s concept of selforganization was predicated.
Certainly, the early vision associated with cybernetics promised far more than it
delivered, conspicuously failing to fill the gap between self-piloting aircraft and
living organisms. Nevertheless, since then, appreciation of the central role of feedback in the design (or organization) of functional units has never flagged and, in
recent years, this concept has come to play a more prominent role in the analysis
of regulatory systems in biology. It seems to me that contemporary methods of
analysis of feedback in cybernetics just might be able to fill that critical gap, providing a mechanistic (i.e., physical and chemical) account of, at least, some cases of
biological function.
Scott Turner (2007), borrowing from his colleague Cosma Shalizi, has recently
introduced a felicitous term into the literature that I believe will serve well for the
minimalist conception of function I proposed above. Turner is interested in “agents
(or organs) of homeostasis” and, referring to the famous physiologist most associated
with homeostasis, Claude Bernard (1813–1878), he calls these agents Bernard
machines. Bernard machines are devices for creating (and maintaining) a fixed milieu
either inside the organism or immediately surrounding it; they are the mainstay of
physiology, or, rather, they are embodiments of physiology.
In terms of my earlier discussion of function, a Bernard machine is exactly what
is required to turn the rain–cloud–river cycle into a system with function; a Bernard
machine is the mechanism that introduces function into such a system. Such devices
are ubiquitous in biological systems, yet extremely complex from an evolutionary
point of view (even when considered simple from an engineering perspective).
Furthermore, and clearly attesting to the power of contemporary systems biology
(especially of those efforts that proceed, simultaneously, from the bottom up and the
top down), there are now a number of examples in which a naturalist account of
such mechanisms is either available or close to available. I have chosen two cases
to illustrate.
My first case is bacterial chemotaxis, the ability of bacteria to sense and move
toward an attractant (e.g., a nutrient), or away from a repellent (e.g., a toxin). Over
the last few years, biologists have unraveled virtually the entire structure of this
system—indeed, bacterial chemotaxis might be said to be a poster child of systems
biology. The machinery that has evolved to make chemotaxis possible, itself, is built
out of relatively sophisticated, and pre-existing, structures, the main components of
which are the flagella (the motor system) and the chemical receptors (the sensors).
The paradigmatic example is E. coli, where each bacterium has several flagella,
capable of rotating clockwise and counter-clockwise. Given the helical structure of
the individual flagellum, counter-clockwise motion has the effect of aligning them
into a single rotating bundle, leading to motion in a straight line; conversely, clockwise rotation disrupts the bundle, causing the bacterium to tumble in place. The net
It Is Possible to Reduce Biological Explanations

27

effect is a random motion of alternating straight swims and tumbles. But the
addition of a simple feedback between the receptors and flagella that regulates the
direction of rotation according to chemical concentration leads, straightforwardly, to
directional motion.
The actual system of feedback that E. coli employs is at least one step up from
the simplest possible. In particular, it employs a mechanism allowing temporal comparison of concentrations, linked to the motor system in such a way that the time
between tumbles is reduced if the bacterium is going in the “right” direction, thereby
leading to a more direct chemotactic response than would otherwise have been
possible. Over the course of evolution, still further feedback loops have been added,
resulting in an extraordinarily robust and efficient device for maintaining a favorable environment for the modern bacterium—an environment free of toxins in the
case of negative chemotaxis, or rich in nutrients in the case of positive chemotaxis.
This is a Bernard machine par excellence, but it is one that regulates the
environment of the bacterium by moving the organism until its local environment
is improved, rather than by directly changing that environment (as, for example, a
thermostat would). It works by means of a hierarchy of feedback loops between the sensory and motor system that are now well-understood, and that have been effectively
modeled in terms of the chemical and physical processes involved. How such a machine
came to be built, however, is another question, and that process is not well-understood.
Yet it can safely be said that it, too, depended on a kind of feedback; more specifically,
on feedback between variations in chemical processes, changes in the physical,
material environment these variations lead to, and shifts in the selective pressure
operating on the chemical innovations caused by the changed physical environment.
Here, function is built, as it were, by a kind of evolutionary transduction of the
interactions between chemical reactions and the physical dynamics of the spatialtemporal-material medium in which these reactions occur.
My second example of a Bernard machine is one of Turner’s own examples: the
mound, built by a colony of termites that serves as a wind tunnel, regulating the
level of CO2 (and oxygen) in the termite nest. Here, the environment of the colony
is maintained at a more or less constant level of comfort, not by moving the
colony, but by the work of individual termites in constructing a physical device that
regulates the flow of wind, and that, by so doing, works to stabilize the temperature
and concentration of gases in the nest. Unlike the machinery of chemotaxis, this
mechanism is not part of the body of the individual organism, but rather part of the
organism’s environment. Equivalently, it might be said to be a component (indeed,
a necessary component) of the extended body of the colony. Without it, the colony
could not survive.
Here is the problem the termites face: A typical colony begins with a single
queen and king, housed under the surface of the soil, with impressive reproductive
powers. In a short time, the colony reaches a population of approximately a million
termites, with the respiratory requirement roughly that of a rabbit (Turner tells
us that when you add in the respiratory needs of the accompanying fungi, the
respiratory need of the colony approximates that of a goat). Yet, throughout this
explosive growth in population, the atmosphere of the nest—viz., the temperature,
concentrations of O2 and CO2—remains quite stable. The question is, “How is this
accomplished?”
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Turner answers the question as follows. The behavioral repertoire of the individual
termite includes two actions: picking up grains of soil and gluing them down. Which
action is performed depends on CO2 level, with a high probability of picking up the
grain of soil when the level of CO2 is high concentration, and of gluing it down at
low concentrations. In other words, just as with the bacteria undergoing chemotaxis,
each termite is equipped with a sensor that is coupled to its behavior. The link between
the levels of CO2 recorded by the sensor, and the activity of the termite, guides the
construction of a mound in which the rate of air circulation is effectively matched
to the metabolic needs of the colony. The mound, one would have to say, has a
function, namely, to maintain the atmosphere of the nest at comfortable levels. We
might call this an atmospherostat, built not by intentional agents, but by mindless
termites who know only how to pick up and deposit grains of dirt at rates that depend
on the concentration of CO2. But this simple sensor–behavior link in the individual
termite, no more complex than that found in the bacterium, leads, on the level of
the colony, to an ongoing and apparently purposive rearrangement of the soil between
the nest and the open. Indeed, the net result is the construction and continual reconstruction of a mound that, at any given moment, operates as a well-designed wind
tunnel adapted to the respiratory needs of the colony.
Once again, the presence of feedback loops is of key importance. The physical
structure of the mound determines (feeds back on) the flow of air through the mound
(the air, of course, includes CO2), the distribution of CO2 determines (feeds back on)
the activity of the termites in their subsequent building activities, and the activity
of the termi