Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on the articulation and development of mechanistic (...) models, identifying five constraints which guide the articulation of models in molecular systems biology. These constraints are not independent of one another, with the result that modeling becomes an iterative process. We illustrate the use of these constraints in the modeling of the mechanism for bistability in the lac operon. (shrink)
Multiple realization was once taken to be a challenge to reductionist visions, especially within cognitive science, and a foundation of the “antireductionist consensus.” More recently, multiple realization has come to be challenged on naturalistic grounds, as well as on more “metaphysical” grounds. Within cognitive science, one focal issue concerns the role of neural plasticity for addressing these issues. If reorganization maintains the same cognitive functions, that supports claims for multiple realization. I take up the reorganization involved in language dysfunctions to (...) deal with questions concerned with multiple realization and neural plasticity. Beginning with Broca’s case for localization and the nineteenth century discussion of “reorganization,” and returning to more recent evidence for neural plasticity, I argue that, in the end, there is substantial support for multiple realization in cognitive systems; I further argue that this is wholly consistent with a recognition of methodological pluralism in cognitive science. (shrink)
Multiple realization historically mandated the autonomy of psychology, and its principled irreducibility to neuroscience. Recently, multiple realization and its implications for the reducibility of psychology to neuroscience have been challenged. One challenge concerns the proper understanding of reduction. Another concerns whether multiple realization is as pervasive as is alleged. I focus on the latter question. I illustrate multiple realization with actual, rather than hypothetical, cases of multiple realization from within the biological sciences. Though they do support a degree of autonomy (...) for higher levels of explanation and organization, they do not have the dire consequences critics of multiple realization fear. †To contact the author, please write to: Department of Philosophy, University of Cincinnati, P.O. Box 210374, Cincinnati, OH 45221‐0374; e‐mail: email@example.com. (shrink)
I. Growing up zigzag: -- Art is my vocation -- Newport and the Jameses -- The father -- Harvard, 1861 -- Science and the Civil War -- Comparative anatomy and medical school -- The gulls at the mouth of the Amazon -- Tea squalls and a life according to nature -- We must be our own providence -- A dead and drifting life -- Minnie Temple -- William James, M.D. -- Treading water -- The end of youth -- II. The (...) action of consciousness: Hitting bottom -- Turning to physiology -- The Metaphysical Club and Chauncey Wright -- Charles Pierce -- Cambridge and Harvard, 1872 -- Teaching -- To Europe and back -- Emerson, Mill, and Blood -- From physiology to physiological psychology -- Days of rapture and heartbreak -- The trouble with Herbert Spencer -- The action of consciousness -- III. The principles of Psychology: Spaces -- The heart wants its chance -- The feeling of effort -- Hegel in Cambridge -- Death of a mother -- Goodbye, my sacred old father -- The wonderful stream of our consciousness -- Not a simple temperament -- What is an emotion? -- The literary remains of Henry James Sr. -- The death of Herman -- Mrs. Leonora Piper -- My only absolutely satisfying companion (Alice) -- Hypnotism and summers at Chocorua -- Instinct and will -- Santayana at Harvard -- The psychology of belief -- Reunion with Alice: the hidden self --. (shrink)
Evolutionary models can explain the dynamics of populations, how genetic, genotypic, or phenotypic frequencies change with time. Models incorporating chance, or drift, predict specific patterns of change. These are illustrated using classic work on blood types by Cavalli-Sforza and his collaborators in the Parma Valley of Italy, in which the theoretically predicted patterns are exhibited in human populations. These data and the models display properties of ensembles of populations. The explanatory problem needs to be understood in terms of how likely (...) an observed change, in either a population or an ensemble, would be under drift alone; this is fundamentally a matter of chance. Understood in this way, issues of drift and chance undercut most recent philosophical, but not biological, discussions of the role of "genetic drift.". (shrink)
We will show that there is a strong form of emergence in cell biology. Beginning with C.D. Broad's classic discussion of emergence, we distinguish two conditions sufficient for emergence. Emergence in biology must be compatible with the thought that all explanations of systemic properties are mechanistic explanations and with their sufficiency. Explanations of systemic properties are always in terms of the properties of the parts within the system. Nonetheless, systemic properties can still be emergent. If the properties of the components (...) within the system cannot be predicted, even in principle, from the behavior of the system's parts within simpler wholes then there also will be systemic properties which cannot be predicted, even in principle, on basis of the behavior of these parts. We show in an explicit case study drawn from molecular cell physiology that biochemical networks display this kind of emergence, even though they deploy only mechanistic explanations. This illustrates emergence and its place in nature. (shrink)
William Uttal's The new phrenology is a broad attack on localization in cognitive neuroscience. He argues that even though the brain is a highly differentiated organ, "high level cognitive functions" should not be localized in specific brain regions. First, he argues that psychological processes are not well-defined. Second, he criticizes the methods used to localize psychological processes, including imaging technology: he argues that variation among individuals compromises localization, and that the statistical methods used to construct activation maps are flawed. Neither (...) criticism is compelling. First, as we illustrate, there are behavioral measures which offer at least weak constraints on psychological attribution. Second, though imaging does face methodological difficulties associated with variation among individuals, these are broadly acknowledged; moreover, his specific criticisms of the imaging work, and in particular of fMRI, misrepresent the methodology. In concluding, we suggest a way of framing the issues that might allow us to resolve differences between localizationist models and more distributed models empirically. (shrink)
Reverse engineering is a matter of inferring adaptive function from structure. The utility of reverse engineering for evolutionary biology has been a matter of controversy. I offer a simple taxonomy of the uses of engineering design in assessing adaptation, with a variety of illustrations. The plausibility of applications of engineering design reflects the specific way the models are elaborated and derived.
Recent work on self organization promises an explanation of complex order which is independent of adaptation. Self-organizing systems are complex systems of simple units, projecting order as a consequence of localized and generally nonlinear interactions between these units. Stuart Kauffman offers one variation on the theme of self-organization, offering what he calls a ``statistical mechanics'' for complex systems. This paper explores the explanatory strategies deployed in this ``statistical mechanics,'' initially focusing on the autonomy of statistical explanation as it applies in (...) evolutionary settings and then turning to Kauffman's analysis. Two primary morals emerge as a consequence of this examination: first, the view that adaptation and self-organization should be seen as competing theories or models is misleading and simplistic; and second, while we need a synthesis treating self-organization and adaptation as geared toward different problems, at different levels of organization, and deploying different methods, we do not yet have such a synthesis. (shrink)
Developmental biology has resurfaced in recent years, often without a clearly central role for the organism. The organism is pulled in divergent directions: on the one hand, there is an important body of work that emphasizes the role of the gene in development, as executing and controlling embryological change; on the other hand, there are more theoretical approaches under which the organism disappears as little more than an instance for testing biological generalizations. I press here for the ineliminability of the (...) organism in developmental biology on explanatory grounds. I examine classical work concerned with growth and development, particularly in Drosophila and C. elegans. Some of this work is suggestive of modular development, and accordingly suggests a level below that of the organism as being explanatory. These are not the only type of case. There are other equally well-established results, which indicate greater integration in the developing organism. Though with a modular organization the organism can be thought of as made up of its constituent traits, and though the explanations of these traits may lie in terms of cells or genes, even with modular development the explanations of "genetic" differences require an appeal to the organism. With non-modular organization the organism has an even more central role. This does not mean that these genetic or cellular contributions are unreal in any way, or that development requires some sort of vitalistic contribution; but the genetic contributions make sense only as constituents of the organism, embedded in a larger organic context. (shrink)
John Bickle's Psychoneural reduction: the new wave (Cambridge, MA: MIT Press, 1998) aims to resurrect reductionism within philosophy of mind. He develops a new model of scientific reduction, geared to enhancing our understanding of how theories in neuroscience and cognitive science are interrelated. I put this discussion in context, and assess the prospects for new wave reductionism, both as a general model of scientific reduction and as an attempt to defend reductionism in the philosophy of mind.
Genetic regulatory networks are complex, involving tens or hundreds of genes and scores of proteins with varying dependencies and organizations. This invites the application of artificial techniques in coming to understand natural complexity. I describe two attempts to deploy artificial models in understanding natural complexity. The first abstracts from empirically established patterns, favoring random architectures and very general constraints, in an attempt to model developmental phenomena. The second incorporates detailed information concerning the genetic structure, organization, and dependencies in actual systems (...) in an attempt to explain developmental differences. The results offered by these models, pitched at these different levels of abstraction, are different. The more detailed models are more continuous with classical developmental approaches. (shrink)
Evolutionary psychology purports to explain human capacities as adaptations to an ancestral environment. A complete explanation of human language or human reasoning as adaptations depends on assessing an historical claim, that these capacities evolved under the pressure of natural selection and are prevalent because they provided systematic advantages to our ancestors. An outline of the character of the information needed in order to offer complete adaptation explanations is drawn from Robert Brandon (1990), and explanations offered for the evolution of language (...) and reasoning within evolutionary psychology are evaluated. Pinker and Bloom's (1992) defense of human language as an adaptation for verbal communication, Robert Nozick's (1993) account of the evolutionary origin of rationality, and Cosmides and Tooby's (1992) explanation of human reasoning as an adaptation for social exchange, are discussed in light of what is known, and what is not known, about the history of human evolution. In each case, though a plausible case is made that these capacities are adaptations, there is not enough known to offer even a semblance of an explanation of the origin of these capacities. These explanations of the origin of human thought and language are simply speculations lacking the kind of detailed historical information required for an evolutionary explanation of an adaptation. (shrink)
Pickering and Chater (P&C) maintain that folk psychology and cognitive science should neither compete nor cooperate. Each is an independent enterprise, with a distinct subject matter and characteristic modes of explanation. P&C''s case depends upon their characterizations of cognitive science and folk psychology. We question the basis for their characterizations, challenge both the coherence and the individual adequacy of their contrasts between the two, and show that they waver in their views about the scope of each. We conclude that P&C (...) do not so muchdiscover ascreate the gap they find between folk psychology and cognitive science. It is an artifact of their implausible and unmotivated attempt to demarcate the two areas, and of the excessively narrow accounts they give of each. (shrink)
Sober (1992) has recently evaluated Brandon's (1982, 1990; see also 1985, 1988) use of Salmon's (1971) concept of screening-off in the philosophy of biology. He critiques three particular issues, each of which will be considered in this discussion.
Optimization models treat natural selection as a process tending to produce maximal adaptedness to the environment, measured on some "criterion scale" defining the optimal phenotype. These models are descriptively adequate if they describe the outcomes of evolutionary processes. They are dynamically adequate if the variables which describe the outcomes also are responsible for those evolutionary outcomes. Optimality models can be descriptively adequate, but dynamically unrealistic. Relying on cases from evolutionary ecology, I provide reasons to question the dynamic adequacy of optimality (...) models, and offer reasons for distinguishing, at least at a theoretical level, between satisficing and optimizing. (shrink)
We offer a systematic examination of propensity interpretations of fitness, which emphasizes the role that fitness plays in evolutionary theory and takes seriously the probabilistic character of evolutionary change. We distinguish questions of the probabilistic character of fitness from the particular interpretations of probability which could be incorporated. The roles of selection and drift in evolutionary models support the view that fitness must be understood within a probabilistic framework, and the specific character of organism/environment interactions supports the conclusion that fitness (...) must be understood as a propensity rather than as a limiting frequency. (shrink)
The formal framework of Kauffman (1991) depicts the constraints of self-organization on the evolution of complex systems and the relation of self-organization to selection. We discuss his treatment of 'generic constraints' as sources of order (section 2) and the relation between adaptation and organization (section 3). We then raise a number of issues, including the role of adaptation in explaining order (section 4) and the limitations of formal approaches in explaining the distinctively biological (section 5). The principal question we pose (...) is the relation of generic constraints on evolution to more specific local constraints, imposed, for example, by the characteristic materials out of which organisms are constructed, the accidental features characteristic of the Bauplan of a lineage, and the local vicissitudes of adaptation. We offer no answer to this large question. (shrink)
Selection operates at many levels. Robert Brandon has distinguished the question of the level of selection from the unit of selection, arguing that the phenotype is commonly the target of selection, whatever the unit of selection might be. He uses "screening off" as a criterion for distinguishing the level of selection. Cave animals show a common morphological pattern which includes hypertrophy of some structures and reduction or loss of others. In a study of a cave dwelling crustacean, Gammarus minus, (...) we find evidence for selection for both increased antennal size and reduction of eyes. The genetic structure of the population does not support the view that the phenotype screens off the genotype in explaining the differences in fitness. Nonetheless, the results do indicate that the level of selection is at least at the level of the phenotype in both cases. (shrink)
The classic charge against Freudian theory is that the therapeutic success of psychoanalysis can be explained without appeal to the mechanisms of repression and insight. Whatever therapeutic success psychoanalysis might enjoy would then provide no support for the diagnostic claim that psychological disorders are due to repressed desires or for the therapeutic claim that the gains in psychoanalysis are due to insight into repressed causes. Adolf Grünbaum has repeated the charge in The Foundations of Psychoanalysis (1984), arguing that Freud's response (...) to it in what he calls the "Tally Argument" is woefully inadequate. Grünbaum claims that Freud's defense depends on the view that only psychoanalytic techniques can yield therapeutic effects, and therefore that the transience of some psychoanalytic "cures", the existence of alternative treatment modalities, and the frequency of spontaneous remission undermine Freud's defense of psychoanalysis. I argue that, whatever the merits of psychoanalysis, Freud is not logically committed to any view as extreme as that attributed to him by Grünbaum; and, furthermore, Grünbaum's rendering of Freud is historically inaccurate. (shrink)
The mutual influence of science and values in biology is exhibited in several cases from the biological literature. It is argued in a number of cases, from R. A. Fisher's argument for the optimality of a 50:50 sex ratio to A. Jensen's defense of a genetic basis for intelligence, and including work on the evolution of sexual dimorphism and muted aggression, that the credence accorded the views is disproportionate with their theoretical and empirical warrant. It is, furthermore, suggested that the (...) proper explanation for the attraction and persistence of such views lies in their conformity with ideological norms. There is thus an important, if circumscribed, role for ideological critique in the evaluation of scientific theories; in particular, it lies in the explanation of the acceptance and persistence of scientific views, given independent grounds for questioning their justifiability. (shrink)
Much recent work in sociobiology can be understood as designed to demonstrate the sufficiency of selection operating at lower levels of organization by the development of models at the level of the gene or the individual. Higher level units are accordingly viewed as artifacts of selection operating at lower levels. The adequacy of this latter form of argument is dependent upon issues of the complexity of the systems under consideration. A taxonomy is proposed elaborating a series of types, or grades, (...) of hierarchically organized systems. These range from aggregative systems, in which there is no organization relevant to systemic properties, through several graded variations reflecting various degrees of functional interdependence of components, to integrated systems, which manifest component specialization and diversification as well as a subordination of component function to systemic function. It is suggested that the most complex form of organization is plausibly treated as indicative of higher level units of selection. (shrink)
We have no schema for comprehending how a radical revision of our conceptual scheme such as that embraced by "eliminative materialism" could possibly be rationally justified. This general point is illustrated and pressed through an examination of richard rorty's classic defense of the "disappearance form of the identity theory." it is argued that 1) though more standard critiques of rorty fail, 2) rorty fails to make out the case for the view that incorrigibility" is the "mark of the mental" to (...) the exclusion of intentionality, And 3) the paradigmatic elimination of demons a explanatory entities cannot be extended to yield a justification for the elimination of the mental. (shrink)