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The Philosophy of Evolutionary Theory
E L L IO T T S OBE R
University of Wisconsin–Madison
www.cambridge.org
Information on this title: www.cambridge.org/9781009376051
DOI: 10.1017/9781009376037
© Elliott Sober 2024
This publication is in copyright. Subject to statutory exception and to the provisions
of relevant collective licensing agreements, no reproduction of any part may take
place without the written permission of Cambridge University Press & Assessment.
First published 2024
A catalogue record for this publication is available from the British Library
A Cataloging-in-Publication data record for this book is available from the Library of Congress
ISBN 978-1-009-37605-1 Hardback
ISBN 978-1-009-37601-3 Paperback
Cambridge University Press & Assessment has no responsibility for the persistence
or accuracy of URLs for external or third-party internet websites referred to in this
publication and does not guarantee that any content on such websites is, or will
remain, accurate or appropriate.
1 A Darwinian Introduction 1
1.1 Common Ancestry 1
1.2 Species 3
1.3 Evolution 3
1.4 Divergence and Opportunism 5
1.5 Selection – Natural, Artificial, Sexual, and Bi-leveled 6
1.6 Heredity 9
1.7 Gradualism 12
1.8 Mutation 13
1.9 Was Darwin “Illogical”? 14
3 Units of Selection 39
3.1 Darwin on Altruism and Group Selection 39
3.2 Simpson’s Paradox 42
vii
4 Common Ancestry 77
4.1 Darwin on Common Ancestry 77
4.2 What Is Ancestry? 79
4.3 The Law of Likelihood 81
4.4 When Common Ancestry Has the Higher Likelihood 88
4.5 Matches Sometimes Provide Evidence Against a Common Cause 93
4.6 Matches and Strength of Evidence 94
4.7 Hypothetico-Deductivism 98
4.8 Mismatches 99
4.9 Correlations to the Rescue? 101
4.10 Concluding Comments 108
5 Drift 110
5.1 The Extinction of Family Names 111
5.2 Strict Neutrality 114
5.3 The Molecular Clock 117
5.4 Null Hypotheses 119
5.5 Alternatives to the Strictly Neutral Theory 125
5.6 When Drift and Selection Both Affect a Trait’s Evolution 127
5.7 Drift as Cause and Process 131
5.8 Selection, Drift, and Domination 134
6 Mutation 141
6.1 Darwin and Asa Gray 141
6.2 Two Experiments 144
6.3 The Evolution of Mutation Rates 149
6.4 Darwin’s Gradualism 152
6.5 Fisher’s Geometric Argument 155
8 Adaptationism 206
8.1 Darwin’s Formulation 206
8.2 What Is Adaptationism? 210
8.3 How Genetics Can Get in the Way 213
8.4 Ancestral Influence (aka “Phylogenetic Inertia”) 217
8.5 Optimality Models 221
8.6 The Chronological-Order Test of Adaptation Hypotheses 225
8.7 Testability and Research Programs 227
References 258
Index 281
xiii
• What is fitness?
• What is a unit of selection?
• What is drift?
• What is random mutation?
• What is evolutionary gradualism?
• What is adaptation?
• What is phylogenetic inertia?
• What is a species?
• What is race?
• operationalism
• reductionism
• conventionalism
• null hypotheses and default reasoning
• instrumentalism versus realism
• Duhem’s thesis
• hypothetico-deductivism
• the underdetermination of theory by evidence
• essentialism
• falsifiability
• the principle of parsimony
• the principle of the common cause
• interpretations of probability
• what it means for one cause of an event to be more powerful than another
• determinism versus indeterminism
• the knowability of the past
Philosophy of biology is a subject in its own right but it should not be iso-
lated from the rest of philosophy of science.
Probability is a thread running through this book and it has two strands.
First, there is the probabilistic character of evolutionary theory itself,
which I discuss in several contexts – the definition of fitness, the bearing
of Simpson’s paradox on the evolution of altruism, the neutral theory of
molecular evolution, the concept of random mutation, and Markov mod-
els of evolution. Second, there is the use of probability to make inferences
about various propositions in evolutionary biology. Bayesianism is an
influential epistemology in philosophy of science, but it is not the one I
favor. I am more inclined to reach into a grab-bag that contains the Law
of Likelihood and the Akaike information criterion. As a result, I address
topics in the philosophy of probability and statistics. Instead of starting the
book by describing all the probability tools I want to use, I introduce them
gradually, as needed, in different chapters. If you want to begin with a brief
probability primer, I suggest you look at the ABCs in Sober (2015, pp. 64–84)
or Sober (2018, pp. 7–23).
I feel obliged to issue a content warning: In a few places in this book,
I discuss ideas that grew out of sexist, classist, or racist assumptions.
Understanding something of that history helps one understand ideas in
biology that are neither sexist nor classist nor racist. Airbrushing history
would remove painful reminders, but I think the reminders are valuable in
spite of the pain.
I have placed bold-faced questions and exercises in footnotes. I hope
they will be thought-provoking.
Madison, Wisconsin
July, 2023
I started work on the book you see before you with the idea of revising my
book Philosophy of Biology (published in 1993 by Westview Press and now in
print with Taylor & Francis), but along the way, numerous changes – both
major and minor – accumulated. I came to think that the result is a new
book, not a revision of an old one, though this raises thorny questions
about identity through time that I hope experts on the Ship of Theseus
can resolve. I am grateful to Taylor & Francis for allowing me to reprint
excerpts and illustrations from that ancestral volume.
I thank the following people for helping me think through ideas: David
Baum, Matthew Barker, John Beatty, Dylan Beshoner, Brianna Bixler, Michael
Buckner, Eddy Keming Chen, Rachel Cherian, Phnuyal Abiral Chitrakar,
Hayley Clatterbuck, Nathan Cofnas, Marisa Considine, Andrew Cuda, Katie
Deaven, Michael Dietrich, Ford Doolittle, Marc Ereshefsky, Marcus Feldman,
Joe Felsenstein, Branden Fitelson, Malcolm Forster, Hunter Gentry, Clark
Glymour, Aaron Guerrero, Paula Gottlieb, Hank Greely, Daniel Hausman,
Masami Hasegawa, Jonathan Hodge, Hanti Lin, Kate Lohnes, Josephine
Lovejoy, Jun Li, Masahiro Matsuou, Matthew J. Maxwell, Kiel McElroy, James
Messina, Alexander Michael, Roberta Millstein, Yusaku Ohkubo, Samir
Okasha, Steven Orzack, Diane Paul, Bret Payseur, Erik Peterson, Abiral
Chitrakar Phnuyal, Aaron Peace Ragsdale, Sean Rice, Alex Rosenberg,
Casey Rufener, Alex Sardjev, Larry Shapiro, Nathaniel Sharp, Maxim Shpak,
Alan Sidelle, Quayshawn Spencer, Mike Steel, Robert Streiffer, Naoyuki
Takahata, Joel Velasco, Donald Waller, David Sloan Wilson, Polly Winsor,
Rasmus Winther, James Woodward, and Shimin Zhao.
Finally, I am grateful to Hilary Gaskin, my editor at Cambridge University
Press, and her assistant, Abi Sears, for their help, and to the William F.
Vilas Trust of the University of Wisconsin–Madison for financial support.
xviii
Figure 1.1 is the only illustration that Darwin included in his 1859 book On
the Origin of Species by Means of Natural Selection, or the Preservation of Favoured
Races in the Struggle for Life. He used it to represent some of the main ele-
ments of his theory. The figure depicts a phylogenetic tree in which objects
at the top of the page exist now, and as you go down the page you’re going
back in time, tracing items at the top to their recent and more remote
ancestors. You can think of the objects at the top as current species, though
Darwin’s picture also applies to single organisms alive today. There are fif-
teen objects at the top of the figure, but they descend from only three of
the objects (A, F, and I) at the bottom. If you trace those three back in time,
they will eventually coalesce into a single common ancestor. Modern biol-
ogy agrees with Darwin, in that the standard view now is:
This thesis does not mean that life evolved from non-living materials only
once. Universal common ancestry is compatible with numerous start-ups.
There also is no requirement that only one of those start-ups managed to have
descendants that are alive today. To see why, compare Darwin’s Figure 1.1
1
Darwin’s theorizing evolved in his lifetime, on which see Ruse (1979) and Ospovat
(1981). In this book, I use the term “Darwin’s theory” to refer to what appeared in the
first edition of the Origin and was further articulated in subsequent editions of that book
and in his subsequent writings.
1
The motion of the planes and apsides of the planetary orbits was
one of the first results of their mutual perturbation which was
observed. In 1706, La Hire and Maraldi compared Jupiter with the
Rudolphine Tables, and those of Bullialdus: it appeared that his
aphelion had advanced, and that his nodes had regressed. In 1728,
J. Cassini found that Saturn’s aphelion had in like manner travelled
forwards. In 1720, when Louville refused to allow in his solar tables
the motion of the aphelion of the earth, Fontenelle observed that this
was a misplaced scrupulousness, since the aphelion of Mercury
certainly advances. Yet this reluctance to admit change and
irregularity was not yet overcome. When astronomers had found an
approximate and apparent constancy and regularity, they were
willing to believe it absolute and exact. In the satellites of Jupiter, for
instance, they were unwilling to admit even the eccentricity of the
orbits; and still more, the variation of the nodes, inclinations, and
apsides. But all the fixedness of these was successively disproved.
Fontenelle in 1732, on the occasion of Maraldi’s discovery of the
change of inclination of the fourth satellite, expresses a suspicion
that all the elements might prove liable to change. “We see,” says
he, “the constancy of the inclination already shaken in the three first
satellites, and the eccentricity in the fourth. The immobility of the
nodes holds out so far, but there are strong indications that it will
share the same fate.”
The motions of the nodes and apsides of the satellites are a
necessary part of the Newtonian theory; and even the Cartesian
astronomers now required only data, in order to introduce these
changes into their Tables.
442 Attempts have been made, from the time of the solution of the
Problem of three bodies to the present, to give the greatest possible
accuracy to the Tables of the Sun, by considering the effect of the
various perturbations to which the earth is subject. Thus, in 1756,
Euler calculated the effect of the attractions of the planets on the
earth (the prize-question of the French Academy of Sciences), and
Clairaut soon after. Lacaille, making use of these results, and of his
own numerous observations, published Tables of the Sun. In 1786,
Delambre 88 undertook to verify and improve these tables, by
comparing them with 314 observations made by Maskelyne, at
Greenwich, in 1775 and 1784, and in some of the intermediate
years. He corrected most of the elements; but he could not remove
the uncertainty which occurred respecting the amount of the
inequality produced by the reaction of the moon. He admitted also, in
pursuance of Clairaut’s theory, a second term of this inequality
depending on the moon’s latitude; but irresolutely, and half disposed
to reject it on the authority of the observations. Succeeding
researches of mathematicians have shown, that this term is not
admissible as a result of mechanical principles. Delambre’s Tables,
thus improved, were exact to seven or eight seconds; 89 which was
thought, and truly, a very close coincidence for the time. But
astronomers were far from resting content with this. In 1806, the
French Board of Longitude published Delambre’s improved Solar
Tables; and in the Connaissance des Tems for 1816, Burckhardt
gave the results of a comparison of Delambre’s Tables with a great
number of Maskelyne’s observations;—far greater than the number
on which they were founded. 90 It appeared that the epoch, the
perigee, and the eccentricity, required sensible alterations, and that
the mass of Venus ought to be reduced about one-ninth, and that of
the Moon to be sensibly diminished. In 1827, Professor Airy 91
compared Delambre’s tables with 2000 Greenwich observations,
made with the new transit-instrument at Cambridge, and deduced
from this comparison the correction of the elements. These in
general agreed closely with Burckhardt’s, excepting that a diminution
of Mars appeared necessary. Some discordances, however, led
Professor Airy to suspect the existence of an inequality which had
escaped the sagacity of Laplace and Burckhardt. And, a few weeks
after this suspicion had been expressed, the same mathematician
announced to the Royal Society that he had 443 detected, in the
planetary theory such an inequality, hitherto unnoticed, arising from
the mutual attraction of Venus and the Earth. Its whole effect on the
earth’s longitude, would be to increase or diminish it by nearly three
seconds of space, and its period is about 240 years. “This term,” he
adds, “accounts completely for the difference of the secular motions
given by the comparison of the epochs of 1783 and 1821, and by
that of the epochs of 1801 and 1821.”
88 Voiron, Hist. p. 315.
Thus the secular inequalities of the celestial motions, like all the
others, confirm the law of universal gravitation. They are called
“secular,” because ages are requisite to unfold their existence, and
because they are not obviously periodical. They might, in some
measure, be considered as extensions of the Newtonian theory, for
though Newton’s law accounts for such facts, he did not, so far as
we know, foresee such a result of it. But on the other hand, they are
exactly of the same nature as those which he did foresee and
calculate. And when we call them secular in opposition to periodical,
it is not that there is any real difference, for they, too, have their
cycle; but it is that we have assumed our mean motion without
allowing for these long inequalities. And thus, as Laplace observes
on this very occasion, 92 the lot of this great discovery of gravitation
is no less than this, that every apparent exception becomes a proof,
every difficulty a new occasion of a triumph. And such, as he truly
adds, is the character of a true theory,—of a real representation of
nature.
92 Syst. du Monde, 8vo, ii. 37.
After this discovery, Olbers sought the sky for additional fragments
of his planet with extraordinary perseverance. He conceived that one
of two opposite constellations, the Virgin or the Whale, was the place
where its separation must have taken place; and where, therefore,
all the orbits of all the portions must pass. He resolved to survey,
three times a year, all the small stars in these two regions. This
undertaking, so curious in its nature, was successful. The 29th of
March, 1807, he discovered Vesta, which was soon found to be a
planet. And to show the manner in which Olbers pursued his labors,
we may state that he afterwards published a notification that he had
examined the 449 same parts of the heavens with such regularity,
that he was certain no new planet had passed that way between
1808 and 1816. Gauss and Burckhardt computed the orbit of Vesta;
and when Gauss compared one of his orbits with twenty-two
observations of M. Bouvard, he found the errors below seventeen
seconds of space in right ascension, and still less in declination.
But if this were so, the Comet must reappear in 1758 or 1759.
Halley predicted that it would do so; and the fulfilment of this
prediction was naturally looked forwards to, as an additional stamp
of the truths of the theory of gravitation. 451
But in all this, the Comet had been supposed to be affected only
by the attraction of the sun. The planets must disturb its motion as
they disturb each other. How would this disturbance affect the time
and circumstances of its reappearance? Halley had proposed, but
not attempted to solve, this question.