Brief introduction by webmaster JJ…


The domination of dinosaur palaeontology by skeletal-morphologically based cladistics is progressing beyond detailed beliefs concerning particular animals, to shape the very bases of ideas concerning the best practice of scientific thought.

At a time when molecular-based phylogenies of various kidneys are increasingly earning our qualified respect while famously clashing with those based on morphology, we really ought to be asking ourselves whether the latter is a worthy nulceus around which to reform our entire view of the universe. Sober's analysis of cladistics down a number of lines highlights the problems arising through the reversals and parallelisms that sap the process of its validity, particularly in the morphological domain. He is formidably proficient in a variety of disciplines I don't even know the name of, and far from having the "warm and fuzzy" style of thinking certain dino-palaeos so unappealingly accuse their dissenters of, Sober's writings are redolent of priest-chunkled marble trinkets on the slopes of Mount Fuji at dawn.

I've been asked to summarise the book. I can't. However I can provide here, at great risk to myself, its preface, which makes an admirable summary. It adopts the well-worn tradition of starting by quoting the Old Fakir, and what's more, it isn't the "Everything should be made as simple as possible, but no simpler" one, which I would have thought unbeatable for the topic, but then, when Sober quotes Einstein, who's going to quibble...



Preface to: "Reconstructing The Past: Parsimony, Evolution & Inference" by Elliott Sober. MIT 1988. Second printing 1991 ISBN 0-262-19273-X (hb) 0-262-69144-2 (pb)


...concepts which have proved useful for ordering things easily assume so great an authority over us, that we forget their terrestrial origin and accept them as unalterable facts. They then become labeled as "conceptual necessities", "a priori situations", etc. The road of scientific progress is frequently blocked for long periods by such errors. It is therefore not just an idle game to exercise our ability to analyse familiar concepts, and to demonstrate the conditions on which their justification and usefulness depend, and the way in which these developed, little by little, from the data of experience. In this way they are deprived of their excessive authority.
Albert Einstein


The philosophy of biology, as the name suggests, lies at the intersection of two sets of concerns. It is there that issues specific to biological inquiry make contact with broader questions in the philosophy of science. Much of biology, and much of philosophy as well, takes place outside of this intersection. When unencumbered by conceptual confusion and methodological difficulty, biology can take the form of a Kuhnian "normal science," in which well-understood techniques are brought to bear on well-defined problems. When cast at a very general level, questions in philosophy can be addressed without the need to focus on any particular-scientific theory or problem. The separate sciences may afford examples of explanation or confirmation, for instance, but the examples are often thought to exhibit general patterns that are not subject matter specific.

Until recently, this separation of Kuhnian normal science from perfectly general philosophical inquiry has been taken to describe most of what goes on in both science and its philosophy. But it has become increasingly evident that this picture is seriously incomplete. In addition to normal science, there is science at the frontiers, where techniques are developed but not immediately understood and where problems are new enough that their proper formulation is more a goal than a given. In addition to traditional philosophical problems focusing on science in general, there are the philosophical questions that grow out of the specifics of particular scientific theories and problems. This sort of philosophical question is of longest standing in the philosophy of physics; more recently, it has made itself felt in philosophy of psychology and philosophy of biology.

This book is located at the intersection of evolutionary theory and the philosophy of science. It concerns a biological problem that has occasioned a great deal of conceptual and methodological discussion within evolutionary theory itself. At the same time, it involves a set of philosophical problems about confirmation and theory evaluation that, having traditionally been approached at a level of great generality, would benefit from making contact with the details of specific scientific controversies. The problem of phylogenetic inference brings biological and philosophical questions together, so that it is sometimes difficult to say whether a given issue is of one sort rather than the other.

Evolutionists have vigorously debated the proper methods that should be used in reconstructing how species are related to each other. If the organisms we now observe are a consequence of descent with modification, then the resulting tree of life will be such that some species are closely related while others are related more distantly. We do not observe this branching process directly; it is not by direct inspection that we know that human beings and chirnps are more closely related to each other than either is to snakes. Rather, evolutionists seek to recover the relationships engendered by this branching process by examining its end product. We observe species and their characteristics; we begin with these similarities and differences and hope to use them as evidence supporting some hypotheses of relationship and disconfirrning others.

During the last twenty years or so, biologists have developed several different methods for inferring relatedness from facts of similarity and difference. These methods often disagree with each other. As a result, biologists hoping to address problems of phylogeny have been forced to address the prior issue of methodology.

Questions of method are often raised in science, and often they are routinely dispatched. But this has not happened in the present case. For some twenty years the debate has continued, with no resulting consensus. Why has this methodological problem proved so recalcitrant? One central reason is that it recapitulates a very difficult problem that has for sometime bedeviled philosophical thinking about theory choice in science. One of the methods of phylogenetic inference that has been widely employed is called parsimony. As will be explained in chapter 1, this method holds that a set of observations best supports that phylogenetic hypothesis that requires the fewest parallelisms and convergences. The question naturally arises as to what the use of this method assumes about the evolutionary process; does preferring parsimonious hypotheses presuppose that evolution proceeds parsirnoniously ?

In this way, a contemporary biological problem has made contact with a long-standing issue in the philosophy of science. Philosophers have often asserted that simplicity is one of the criteria that scientists use in evaluating competing explanations. But how could this policy be legitimate, unless science is likewise entitled to assume that nature is simple?

The reader will already see one central agenda of this book. We shall have a detailed look at the biological debate, with an eye to connecting it with philosophical discussions of parsimony and simplicity. Chapter 1 sets the biological problem; chapter 2 describes the way philosophers have typically discussed the general methodological issue.

We shall see that a proper understanding of parsimony cannot isolate that concept from broader questions of hypothesis testing and theory evaluation. Parsimony may be a virtue; but to understand why it is, we must see its connection with other methodological constraints. It is an unsatisfactory mixture of hand waving and numerology to insist without argument that less is better than more. Ockham may have been right, but we need to see just how and why.

In chapter 2, I trace the provenance of our current philosophical understanding of the idea of simplicity. This will involve a detailed look at Hume's ideas about induction. Hume's claim that induction presupposes that nature is uniform is an ancestor of the modern idea that scientific inference relies on a simplicity criterion. I shall argue that an appreciation of what is right and wrong in Hume's skepticism about induction helps bring into focus the status of parsimony and simplicity as methodological criteria.

This approach is broadened and deepened in chapter 3, where I switch from inductive inference to the problem of inferring causes from observing their effects. If two events are correlated, this may be due to their sharing a common cause, or the correlation may be a coincidence, if the two events are the result of quite separate causes. Hans Reichenbach defended and Wesley Salmon elaborated a principle governing such inference problems. The principle of the common cause, as they called it, operationalizes a very Ockhamite idea: postulating a single (common) cause is often more plausible than postulating two (separate) causes. In this third chapter, I develop two rationales for this principle. We shall see that each rationale provides assumptions that suffice to justify the principle, but, perhaps what is more important, we shall see that the principle cannot claim a universal validity.

So the results of chapters 2 and 3 are meant to induce a healthy skepticism about some familiar global methodological pronouncements. Are explanations that postulate fewer entities or processes to be preferred over ones that postulate more? Not always. Are common cause explanations always preferable to ones that invoke separate causes? Again, not always. Besides encouraging this sort of circumspection, these two chapters are meant to begin the task of developing tools that will allow us to say when a given inference principle makes sense and when it does not.

In chapters 4 and 5, we shift back to the details of the biological controversy. Biologists subscribing to the approach now called cladism have devoted considerable effort to disarming criticisms of parsimony and providing that notion with a powerful justification. In chapter 4, I explore the strengths and limitations of the nonstatistical arguments they have constructed. In chapter 5, I take up the statistical arguments that have been developed both for and against cladistic parsimony.

The verdicts in these two chapters are largely negative. Attempts to justify parsimony have not been successful, but neither have attempts to show that it is fatally flawed. The methodological problem of phylogenetic inference is still a very open one, although some progress has been made.

Chapter 4 largely concerns the effort by cladists to use Karl Popper's ideas on falsifiability and simplicity. My approach in this chapter is not to criticize Popper; nor is it to argue that cladists have misunderstood him. Rather, I shall argue that hypothetico-deductivism - the idea that hypotheses are tested by deducing observational predictions from them (in conjunction with auxiliary assumptions) - is not the logical form taken by the problem of phylogenetic inference. The chapter concludes with some untrendy, but hopefully sober, words on the theory/observation distinction.

Chapter 5, as I said, wades into the details of the statistical arguments.But there is material of broader philosophical interest to be found here as well. For example, I address the question of whether a reasonable method of inference must converge on the truth in the limit. Besides bearing on the phylogenetic inference problem, this issue also pertains to reliability theories of justification and to epistemological problems posed by Descartes' evil demon. At the same time, this chapter explores the problem of nuisance parameters in likelihood inference, carrying further an important theme first introduced in chapter 3.

The net result to this point is a general framework for thinking about the use of parsimony arguments in science and a detailed critique of discussions of parsimony (both for and against it) in the biological literature. In the last chapter, I attempt something more positive on the biological problem. By exploring a simple model of an evolutionary branching process, I try to contribute to an understanding of the circumstances in which parsimony makes sense as a tool of phylogenetic inference.

I am only too aware that the audience for this book is quite heterogeneous. This book brings together biology, philosophy, and some statistical ideas. A reader from any one of these disciplines will probably not be conversant with the ideas drawn from the other two. I have tried to build almost all the ideas I need from the ground up (one of the few exceptions is the assumption of a few simple facts about probability). I therefore must ask your indulgence when you come upon an idea that is right up your alley, and your patient attention when an idea is new.

Given the way academic disciplines have become compartmentalized, it is inconvenient that philosophers must look to biology and statistics to tell them something about methodological ideas they have long thought of as their special subject matter. It is likewise inconvenient that biological systematists should find themselves facing a recalcitrant methodological problem that requires foundational ideas from philosophy and statisticsfor its elucidation. But academic divisions are, to some significant degree, accidents of history; there is no guarantee that the problems that actually arise in inquiry can always be resolved by methods internal to a single approach. It is my belief that progress on the problem of phylogenetic inference requires the crossing of disciplinary boundaries. I hope that biologists will learn something about parsimony from this book and that philosophers will as well. No doubt, what the one group learns will be very different from what the other does.

Willi Hennig, the founding father of cladism, emphasized that theory and observation bear on each other by a process of "reciprocal illurnination." The working hypothesis of this book is that the diverse collection of ideas brought together here forms a unity because of the way they throw light on each other. So in justifying the inconvenient demands this sort of project sometimes places on the reader, I can only say that it was the logic of the problem that drove me to it. The patient and open-minded reader, I can only hope, will concur.