The causal structure of mechanisms

Recently, a number of philosophers of science have claimed that much explanation in the sciences, especially in the biomedical and social sciences, is mechanistic explanation. I argue the account of mechanistic explanation provided in this tradition has not been entirely satisfactory, as it has neglected to describe in complete detail the crucial causal structure of mechanistic explanation. I show how the interventionist approach to causation, especially within a structural equations framework, provides a simple and elegant account of the causal structure of mechanisms. This account explains the many useful insights of traditional accounts of mechanism, such as Carl Craver’s account in his book Explaining the Brain (2007), but also helps to correct the omissions of such accounts. One of these omissions is the failure to provide an explicit formulation of a modularity constraint that plays a significant role in mechanistic explanation. One virtue of the interventionist/structural equations framework is that it allows for a simple formulation of a modularity constraint on mechanistic explanation. I illustrate the role of this constraint in the last section of the paper, which describes the form that mechanistic explanation takes in the computational, information-processing paradigm of cognitive psychology.     

On the validity of Freud's dream interpretations

In this article I defend Freud's method of dream interpretation against those who criticize it as involving a fallacy-namely, the reverse causal fallacy-and those who criticize it as permitting many interpretations, indeed any that the interpreter wants to put on the dream. The first criticism misconstrues the logic of the interpretative process: it does not involve an unjustified reversal of causal relations, but rather a legitimate attempt at an inference to the best explanation. The judgement of whether or not a particular interpretation is the best explanation depends on the details of the case in question. I outline the kinds of probabilities involved in making the judgement. My account also helps to cash out the metaphors of the jigsaw and crossword puzzles that Freudians have used in response to the 'many interpretations' objection. However, in defending Freud's method of dream interpretation, I do not thereby defend his theory of dreams, which cannot be justified by his interpretations alone.     

Leaving the Magic Out: Knowledge and Effect in Different Places

In 2010, Porer Nombo and I launched a book about indigenous Papua New Guinean plant knowledge to a large audience at a university near to his village on the north coast of that country. Members of the audience commented that the book made a record of important practices. But they asked if those practices were dependent on secret magic to be effective? What gave us the right to include such secrets? Or, if there was in fact something fundamental missing from the book (magical formulae to activate the processes described), then what was the use of publishing the book? Thinking through their questions suggested the need to analyse what ‘knowledge’ is in different places, and why plants might be effective in some, but not others. In this paper I attempt an explanation that does not rely on a ‘social’ explanation of magic but instead suggest that what we call ‘magic’ are mechanisms whereby a gardener (or healer, or hunter) positions an action, or a thing in relation to other things. I liken the way myth works in these systems to the way intellectual property law provides a comparable ‘mythic’ structure that locates effect in the places that have developed ‘knowledge economies’ and I conclude by asking; if places embody their history and politics, and generate different understandings of effect, then what are the implications of calling Porer's practices with regard to plants, ‘knowledge’?     

Kant's concept of natural purpose and the reflecting power of judgement

This paper examines how in the 'Critique of teleological judgment' Kant characterized the concept of natural purpose in relation to and in distinction from the concepts of nature and the concept of purpose he had developed in his other critical writings. Kant maintained that neither the principles of mechanical science nor the pure concepts of the understanding through which we determine experience in general provide adequate conceptualizations of the unique capacities of organisms. He also held that although the concept of natural purpose was derived through reflection upon an analogy to human purposive activity in artistic production and moral action, it articulates a unique notion of intrinsic purposiveness. Kant restricted his critical reflections on organisms to phenomena that can be given to us in experience, criticizing speculations on their first origins or final purpose. But I argue that he held that the concept of natural purpose is a product of the reflecting power of judgment, rather than an empirical concept, and represents only the relation of things to our power of judgment. Yet it is necessary for the identification of organisms as organized and self-organizing, and as subject to unique norms and causal relations between parts and whole.     

Do we need theory to study disease? Lessons from cancer research and their implications for mental illness

This article applies general ideas from contemporary philosophy of science--chief among them that much good science proceeds without theories and laws--to the science of medicine. I claim that traditional philosophical debates over the nature of disease make demands on medicine that are mistaken. I demonstrate this philosophical error by applying the perspective of the philosophy of science to understanding the nature of disease in two concrete cases, cancer and depression. I first argue that cancer research produces various kinds of piecemeal causal explanation and does so without any well-developed theory of normal and malignant functioning, despite the rhetoric of some leading cancer researchers. I then defuse doubts about the scientific status of psychiatry, by demonstrating that it is not necessary to have a theory of normal functioning in order to understand and treat depression.     

Discussion: Reply to Hitchcock

Christopher Hitchcocks discussion of my use of screening-off in analyzing the causal process of natural selection raises some interesting issues to which I am pleased to reply. The bulk of his article is devoted to some fairly general points in the theory of explanation. In particular, he questions whether or not my point that phenotype screens off genotype from reproductive success (in cases of organismic selection) supports my claim that the explanation of differential reproductive success should be in terms of phenotypic differences, not genotypic differences. I will respond to this and show why the two supposed counter-examples to my position fail.     

Kant’s concept of natural purpose and the reflecting power of judgement

This paper examines how in the ‘Critique of teleological judgment’ Kant characterized the concept of natural purpose in relation to and in distinction from the concepts of nature and the concept of purpose he had developed in his other critical writings. Kant maintained that neither the principles of mechanical science nor the pure concepts of the understanding through which we determine experience in general provide adequate conceptualizations of the unique capacities of organisms. He also held that although the concept of natural purpose was derived through reflection upon an analogy to human purposive activity in artistic production and moral action, it articulates a unique notion of intrinsic purposiveness. Kant restricted his critical reflections on organisms to phenomena that can be given to us in experience, criticizing speculations on their first origins or final purpose. But I argue that he held that the concept of natural purpose is a product of the reflecting power of judgment, rather than an empirical concept, and represents only the relation of things to our power of judgment. Yet it is necessary for the identification of organisms as organized and self-organizing, and as subject to unique norms and causal relations between parts and whole.     

Michael Akam and the rise of evolutionary developmental biology

Michael Akam has been awarded the 2007 Kowalevsky medal for his many research accomplishments in the area of evolutionary developmental biology. We highlight three tributaries of Michael’s contribution to evolutionary developmental biology. First, he has made major contributions to our understanding of development of the fruit fly, Drosophila melanogaster. Second, he has maintained a consistent focus on several key problems in evolutionary developmental biology, including the evolving role of Hox genes in arthropods and, more recently, the evolution of segmentation mechanisms. Third, Michael has written a series of influential reviews that have integrated progress in developmental biology into an evolutionary perspective. Michael has also made a large impact on the field through his effective mentorship style, his selfless promotion of younger colleagues, and his leadership of the University Museum of Zoology at Cambridge and the European community of evolutionary developmental biologist.     

Mechanical explanation of nature and its limits in Kant's Critique of judgment

In this paper I discuss two questions. What does Kant understand by mechanical explanation in the Critique of judgment? And why does he think that mechanical explanation is the only type of the explanation of nature available to us? According to the interpretation proposed, mechanical explanations in the Critique of judgment refer to a particular species of empirical causal laws. Mechanical laws aim to explain nature by reference to the causal interaction between the forces of the parts of matter and the way in which they form into complex material wholes. Just like any other empirical causal law, however, mechanical laws can never be known with full certainty. The conception according to which we can explain all of nature by means of mechanical laws, it turns out, is based on what Kant calls 'regulative' or 'reflective' considerations about nature. Nothing in Kant's Critique of judgment suggests that these considerations can ever be justified by reference to how the natural world really is. I suggest that what, upon first consideration, appears to be a thoroughly mechanistic conception of nature in Kant is much more limited than one might have expected.     

Understanding pathology in the context of physiological mechanisms: the practicality of a broken-normal view

The topic of disease mechanisms is of clinical importance, as our understanding of such mechanisms plays an important role in how we approach devising treatments for disease. In this paper, I critique an argument made by Mauro Nervi, in which he asserts that pathology is often better viewed in the context of distinct theoretical mechanisms. I use this critique as a starting point to argue that viewing pathology as a broken-normal, malfunctioning mechanism is more therapeutically practical and more relevant to clinical drug design, than creating a theoretical separation of pathology from physiology.     

Explaining the freemartin: Tandler and Keller vs. Lillie and the question of priority

The correct explanation for the freemartin phenotype in the female twin of a female-male pair in cattle was first reported by Tandler and Keller (1911. Deutsche Tier?rzt Wochenschr 19:148-149). This same explanation for the freemartin was independently discovered by Lillie (1916. Science 43:611-613). Today both set of scientists are given credit for this discovery; it is the basis for much of the subsequent work on the developmental basis for sex differentiation in vertebrates. Even though Lillie published after Keller and Tandler, he gets credit for this discovery because: (1) Keller and Tandler published in a veterinary journal and as a consequence their work was not disseminated as broadly throughout the larger scientific community; this problem was compounded by the fact that their definitive 1916 paper was published under wartime conditions during World War I, and (2) Lillie was an influential scientist with a group of graduate students who could elaborate on and extend his work; they published a number of papers on the freemartin. At some point while Lillie was doing his initial work on the freemartin he may have become aware that Keller and Tandler were also working on the freemartin problem; this information may have shaped his decision on when to publish.     

Medicine in the age of " Ulysses ": James Joyce's portrait of life, medicine, and disease on a Dublin day a century ago

Over time, contemporary writing becomes part of the historical record. In medicine, it is an important learning tool, particularly for understanding the experience and context of disease and illness. Although a century has elapsed since the fictional events on a single day described in James Joyce's Ulysses, the work is still fresh with references and allusions to doctors, illnesses, and the human experience. Ulysses provides perspective on medical and social history and offers a biting commentary of continuing relevance to the doctor-patient relationship.     

Development and mechanistic explanation

Within modern philosophy of biology the topic of mechanistic explanation has become a central theme for critical discussion. The neo-mechanical philosophers have developed accounts that emphasize intervention and manipulation as the central epistemic tools that allow gaining epistemic access upon the mechanisms and have argued that the processes of inter-field integration across disciplines can be understood through the analysis of mechanisms spanning multiple levels. In this paper I revisit current proposals on mechanistic explanation in order to show some of their limitations when dealing with developmental mechanisms. I basically argue that (i) developmental mechanisms cannot be accommodated within a framework centered upon the mutual manipulation principle, (ii) the distinction between causal relations vs. constitutive relations cannot be easily demarcated within developmental biology and (iii) the notion of "part" underlying the neo-mechanical accounts on explanation is not suitable for developmental biology.     

Viability explanation

This article deals with a type of functional explanation, viability explanation, that has been overlooked in recent philosophy of science. Viability explanations relate traits of organisms and their environments in terms of what an individual needs to survive and reproduce. I show that viability explanations are neither causal nor historical and that, therefore, they should be accounted for as a distinct type of explanation.The investigations for this paper were supported by the Foundation for Philosophical Research (SWON), which is subsidized by the Netherlands Organization for Scientific Research (NWO). I am grateful to Theo Kuipers and Ton Derksen for their useful comments on early versions, to Josje Lodder for improving my logic, and to Jaap van Brakel for his help in structuring this article.     

From Darkness to Light

Not so long ago I happened to treat a Jewish eighth-grade gymnasium student brought to Petrograd from a province. It was fall and the following spring he was to take his qualifying examinations. The young man, who belonged to a prosperous family, had brilliant abilities and graduated from each class with excellent grades—what would you think his illness was? He suffered—in his own words—from the throes of creative writing. Days and nights he poured over a notebook with his compositions in search of the best form to express his thoughts. Only after applying incredible efforts could one tear him away from his note-books and send him to bed at five or six o'clock in the morning, and this happened on a daily basis. With each day his mental health grew worse. It was clear that the young man undermined his health by overstudying, and that he had reached the point where he needed to worry about his health, not his studies, because a serious mental illness was descending upon him. The young man was well liked by everyone in his high-school. The teachers considered him the best student, and having learned about his illness, they promised to petition to grant him the right to graduate from school without the final examination and with a certificate of excellent. But none of that helped. The young man could not relax, spending days and nights over his compositions and constantly tormenting himself with his "throes of creative writing."     

Unravelling causal components of the Ordovician Radiation: the Builth Inlier (central Wales) as a case study

Hypotheses about the causes of biodiversification during the Ordovician have been focused in three main areas: tectonic activity and nutrient supply, palaeogeography, and ecological escalation. There is as yet no consensus on mechanisms, and it is unclear whether it is better to study the patterns at local or regional scales. By applying ecological knowledge to the available palaeontological information, it can be shown that neither tectonic nor palaeogeographic effects could account for the permanence of the diversity rise, in the absence of elements of ecological escalation. However, it may be possible to identify trigger mechanisms resulting in enhanced speciation or reduced extinction. Areas of local diversity increase should be distinguished from speciation centres. An ongoing study of the Middle Ordovician Builth-Llandrindod Inlier of central Wales, conducted over 10 years, has identified elements of all three of the above categories of causal mechanisms affecting local diversity. This implies that the patterns of causal relationship and diversification are complex even at very local scales, and at this stage we should not anticipate a clear correlation of global diversity with any single factor. More data are needed from small-scale but intensive studies before we can generalize about the causal mechanisms of the Ordovician Radiation.     

International Cambrian Friendship北大核心CSCD

Professor Chang was a long-time friend and colleague.We began exchanging reprints in the 1950's and finally,in 1976 I was able to visit Nanjing and we met for the first time.Subsequently he came to the U.S.and I was able to show him some of our spectacular desert Cambrian exposures in the west.Later,he was a most gracious host as we toured much of eastern China,following an International Cambrian Symposium in Novosibirsk,dividing our time between Cambrian exposures and famous tourist sites.Our final personal meeting was in 2002 at his apartment following a Cambrian conference in Nanjing,where he was still pursuing research on Cambrian trilobites.He was the leader of his generation in Cambrian studies and his work provided important demonstrations of the significant differences between contemporaneous faunas in Laurentia and what was then eastern Gondwana.This work contributed significantly to our understanding of the biogeography of the Cambrian world,and is a lasting addition to global knowledge of the Cambrian of eastern Asia.     

Causation in the sciences: An inferentialist account

I present an alternative account of causation in the biomedical and social sciences according to which the meaning of causal claims is given by their inferential relations to other claims. Specifically, I will argue that causal claims are (typically) inferentially related to certain evidential claims as well as claims about explanation, prediction, intervention and responsibility. I explain in some detail what it means for a claim to be inferentially related to another and finally derive some implication of the proposed account for the epistemology, semantics and metaphysics of causation.     

D'Arcy Thompson and the theory of transformations

D'Arcy Thompson was a biologist, a mathematician and a classicist. His writing was great literature as well as great science. He is primarily known for a single book--On Growth and Form--and indeed for a single chapter within it, on his 'theory of transformations', which shows how the differences between the forms of related species can be represented geometrically. This theory cries out for causal explanation, which is something the great man eschewed. Perhaps the time is close when comparative developmental genetics will be able to provide such an explanation.