Mechanisms, History and Parts in Compositional Biology

Mechanisms, History and Parts in Compositional Biology Rasmus Grønfeldt Winther Instituto de Investigaciones Filosóficas, UNAM, Mexico City rgwinther@gmail.com

Outline 1. Law-Based vs. Part-Based Views of Science 2. Biological Practice 3. Philosophical Analysis of (most) Biology 4. Scientific Styles and Compositional Biology

Law-Based Views of Science (dominant)

Law-Based View Hempel Deductive-Nomological Model C 1, C 2,,C k Statements of antecedent conditions L 1, L 2,,L r General Laws E Description of the empirical phenomenon to be explained (Hempel and Oppenheim, 1948, 138)

Law-Based View van Fraassen Semantic View to present a scientific theory is, in the first instance, to present a family of models that is, mathematical structures offered for the representation of the theory's subject matter. (online ms.; 1970, 1980)

Law-Based View Friedman Explanation by unification [a] common pattern [of scientific explanations is that] they postulate a theoretical structure A = <A, R 1,, R n > with complex and interesting mathematical properties, and they construe some observational structure B = <B, R' 1,, R' n > as a substructure of A. (1983, 237)

Part-Based Views of Science (minority)

Part-Based View Cummins Explanation by analysis A major contention of this study is that psychological phenomena are typically not explained by subsuming them under causal laws, but by treating them as manifestations of capacities that are explained by analysis. The biologically significant capacities of an entire organism are explained by analyzing them into a number of 'systems' the circulatory system, the digestive system, the endocrine system each of which is defined by its characteristic capacities. (1983, 1, 29)

Part-Based View Haugeland Styles of explanation Besides mechanics, fields as diverse as optics, thermodynamics, and macro-economics commonly involve derivational-nomological explanations. Only the derivational-nomological style puts an explicit emphasis on equations of the sort that we usually associate with scientific laws. But I shall claim that only the systematic style is directly relevant to cognitive psychology. (1998(1978), 11, 14)

Two Camps of Scientists and Philosophers Law-Based on Part-Based: "Just engage in stamp collecting" "Obsessed with mechanistic detail" Part-Based on Law-Based: "Think mathematics can substitute for nature" "Don't understand the biology of the system"

Is Part-Based Science Really a Science? FOR AGAINST

Is Part-Based Science Really a Science? FOR AGAINST (Most) Biologists

Is Part-Based Science Really a Science? FOR AGAINST (Most) Biologists NSF

Is Part-Based Science Really a Science? FOR AGAINST (Most) Biologists NSF Nobel Prize Committee

Is Part-Based Science Really a Science? FOR AGAINST (Most) Biologists NSF Nobel Prize Committee General Public

Is Part-Based Science Really a Science? FOR AGAINST (Most) Biologists (Most) Philosophers of Science NSF Nobel Prize Committee General Public

Biological Practice

Physiology: Cellular Respiration http://library.thinkquest.org/c0045 35/respiration_overview.html

Developmental Biology

Systematics: the Panda's Thumb Gould 1980, 22

Systematics: the Panda's Thumb An engineer's best solution is debarred by history. The panda's true thumb is committed to another role, too specialized for a different function to become an opposable, manipulating digit. So the panda must use parts on hand and settle for an enlarged wrist bone and a somewhat clumsy, but quite workable, solution. (Gould 1980, 24)

Most biology is about parts and wholes!

Philosophical Analysis of (most) Biology

Explanation in Biology Physiology and Developmental Biology employ mechanistic explanation How are the parts of a complex system organized and how do they work (together)? Systematics uses historical explanation Which parts change over time to make new types of complex systems and for what reasons do the parts (and systems) change? The Argument: Part-Based Explanation is the general class

Mechanisms Glennan A mechanism for a behavior is a complex system that produces that behavior by the interaction of a number of parts, where the interactions between parts can be characterized by direct, invariant, change-relating generalizations. Parts Ontology: (2002, S344) Parts: "objects" that "have a relatively high degree of robustness or stability" Interaction: "an occasion on which a change in a property of one part brings about a change in a property of another part"

Mechanisms Machamer, Darden and Craver Mechanisms are entities and activities organized such that they are productive of regular changes from start or set-up to finish or termination conditions. Parts Ontology: (MDC 2000, 3) Entities: "the things that engage in activities" (emphasized by "substantivalists," such as Glennan) Activities: "the producers of change" (emphasized by "process ontologists")

Mechanistic Explanation is Part-Based Explanation G, MDC: What are the parts? Structural objects Counter-example: parts as processual (e.g., cellular respiration) What are the parts in general? Relations of parts? The Argument: There is a diversity of theoretical mechanistic identity conditions e.g., Mechanistic explanations can be reductionist or holist/emergentist

History Danto Narratives... are used to explain changes... It is the job of history to reveal to us these changes, to organize the past into temporal wholes, and to explain these changes at the same time as they tell what happened albeit with the aid of the sort of temporal perspective linguistically reflected in narrative sentences. (1985, 255)

History Roth Events simpliciter cannot be shown to exist; they are not known to be of nature's making rather than of ours. Events exist only by proxy. This is why one cannot presume that there are any ideal events for our erstwhile chronicler to chronicle; knowledge of events is restricted to happenings isolated under descriptions provided by interested parties. (1988, 9)

History Richards The varieties of narrative time shrink the proximity until the logical relation of post hoc ergo propter hoc is no longer a fallacy but virtually the very principle of narrative explanation. Narratives enmesh central events in causal networks that fix them with inevitability. (1992, 46-47)

Historical Explanation is Part-Based Explanation Historical explanations "explain changes" (Danto) of historical parts i.e., "central event in causal networks" (Richards) or "central subject" (Hull 1975) Narratives of historical explanation are temporallyframed generalizations What are the parts in general? Relations of parts? The Argument: There is a diversity of theoretical historical identity conditions e.g., The central event/subject (e.g., panda's thumb) is the pertinent part of the historical whole

Checkpoint The talk so far Most biology is about parts and wholes Many consider part-based biology a science A few philosophical accounts have been attempted, which I argue are fundamentally part-based Next What are the philosophical motivations for thinking of part-based biology as a science?

Scientific Styles

The Argument: Science and Styles What is Science? A constellation of activities guided by a Scientific Style What is a Scientific Style? A set of commitments regarding Abstraction Generalization Explanation Modeling Experimentation Theory Practice Systematic interrelation among aspects is key

Abstraction General Problems Abstraction as the organizing principle of a Scientific Style Constitutive of scientific research (sensu Kant) Process of abstraction in science How it works Enrichment and Subtractivist Views Friedman and Cartwright Partitioning Frames provide identity conditions of parts How it fails to work "Vicious Abstractionism" and "The Philosophic Fallacy" James and Dewey

Abstraction Boyd I argue that there are a number of scientifically important kinds (properties, relations, etc.) whose natural definitions are very much like the propertycluster definitions postulated by ordinary-language philosophers except that the unity of the properties in the defining cluster is mainly causal rather than conceptual. The natural definition of one of these homeostatic property cluster kinds is determined by the members of a cluster of often co-occurring properties and by the ("homeostatic") mechanisms that bring about their co-occurrence. (1991, 141)

Why Scientific Styles? Reconciles opposing intuitions regarding the study of science Rationalistic vs. sociological Normative vs. descriptive Science as theory vs. science as practice Holy Grail: A holistic philosophical account of scientific theory and practice

Conclusion: Two Scientific Styles in Biology Formal Biology Involves abstract mathematical laws/models formal modeling population genetics theoretical mathematical ecology Compositional Biology Focuses on an ontology of concrete parts and wholes wet-lab and museum physiology developmental biology systematics

Future Work Continue analyzing key philosophy of science issues (e.g., abstraction, explanation, modeling) in a partbased context Link the study of parts in philosophy of biology to formal mereology in general philosophy (e.g., Simons 1987, Casati&Varzi 1999, Burge, Fine) Investigate scientific practice within a part-based framework (e.g., high-throughput data-driven genomics and proteomics, "high-tech" methods in cell biology and medicine)

Bibliography Boyd, R. (1991). Realism, Anti-Foundationalism, and the Enthusiasm for Natural Kinds. Philosophical Studies, 61, 127-148. Casati, R & Varzi, A. (1999). Parts and Places. The Structures of Spatial Representation. (MIT Press) Cummins, R. (1983). The Nature of Psychological Explanation. (MIT Press) Danto, A. (1985). Narration and Knowledge. (Columbia University Press) Friedman, M. (1983). Foundations of Space-Time Theories. Relativistic Physics and Philosophy of Science. (Princeton University Press) Glennan, S. (2002). Rethinking Mechanistic Explanation. Philosophy of Science, 69, S342-S353 Gould, S.J. (1980). The Panda's Thumb. (In S.J. Gould (Ed.), The Panda's Thumb. Reflections in Natural History (pp. 19-26). New York: W. W. Norton & Co.) Haugeland, J. (1978). The Nature and Plausibility of Cognitivism. (In J. Haugeland (Ed.), 1998, Having Thought. Essays in the Metaphysics of Mind (pp. 9-45). Harvard University Press.) Hempel, CG, Oppenheim, P. (1948). Studies in the Logic of Explanation. Philosophy of Science, 15, 135-175. Hull, D.L. (1975). Central Subjects and Historical Narratives. History and Theory, 14, 253-74 Machamer, P., Darden, L. & Craver, C. (2000). Thinking About Mechanisms. Philosophy of Science, 67, 1-25 Richards, R. (1992). The Structure of Narrative Explanation in History and Biology. (In M.H. Nitecki & D.V. Nitecki, History and Evolution (pp. 19-53). SUNY Press.) Roth, P. (1988). Narrative Explanations: The Case of History. History and Theory, 27, 1-13 Simons, P. (1987). Parts. A Study in Ontology. (Oxford University Press) Van Fraassen, B. (1970). On the Extension of Beth's Semantics of Physical Theories. Philosophy of Science, 37, 325-39 ----- (1980). The Scientific Image. (Oxford University Press) ----- "Structure and Perspective: Philosophical Perplexity and Paradox" (online unpublished ms.)

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