This paper examines the nature of model-based reasoning in the interplay between theory and experiment in the context of biomedical engineering research laboratories, where problem solving involves using physical models. These “model systems” are sites of experimentation where in vitro models are used to screen, control, and simulate specific aspects of in vivo phenomena. As with all models, simulation devices are idealized representations, but they are also systems themselves, possessing engineering constraints. Drawing on research in contemporary cognitive science that construes cognition as occurring in a complex distributed system comprising people and artifacts, I argue that reasoning with model systems is a constraint satisfaction process involving co-construction, manipulation, and revision of mental and physical models.

In previous publications I have argued that much scientific activity should be thought of as involving the operation of distributed cognitive systems. Since these contributions to the cognitive study of science appear in venues not necessarily frequented by philosophers of science, I begin with a brief introduction to the notion of a distributed cognitive system. I then describe what I take to be an exemplary case of a scientific distributed cognitive system, the Hubble Space Telescope (HST). I do not here reargue the case for conceiving of systems like the HST as distributed cognitive systems. Rather, I examine a question that arises once one has adopted the perspective of distributed cognitive systems, namely, the role of agency in a distributed cognitive system. Here I argue, contrary to several advocates of distributed cognitive systems, that we should regard the human components of distributed cognitive systems as the only sources of agency within such systems. In particular, we should not extend notions of agency to such systems as a whole.

Some ecologists have argued that theoretical model building in population and community ecology has gone evidentially unconstrained. In the essay, I argue that “bottle experiments” offer ecological model building evidential constraints and illustrate this by considering work on chaotic models tested by the dynamics of flour beetles. Critics reply that these experiments are importantly unlike nonmanipulated natural systems and thus do not constitute genuine tests of the models. I conclude by considering two responses to this worry and a suggestion on how to move forward on this debate.

Modelers often rely on robustness analysis, the search for predictions common to several independent models. Robustness analysis has been characterized and championed by Richard Levins and William Wimsatt, who see it as central to modern theoretical practice. The practice has also been severely criticized by Steven Orzack and Elliott Sober, who claim that it is a nonempirical form of confirmation, effective only under unusual circumstances. This paper addresses Orzack and Sober's criticisms by giving a new account of robustness analysis and showing how the practice can identify robust theorems. Once the structure of robust theorems is clearly articulated, it can be shown that such theorems have a degree of confirmation, despite the lack of direct empirical evidence for their truth.

Initially, models of chemical systems displaying oscillatory behavior were judged successful if they could show how such behavior was even possible. Recently, however, reaction mechanisms for chemical oscillators have been subjected to more stringent experimental tests. I examine strategies for model testing that flow from theoretical considerations, in particular, the types of feedback relations between chemical species required to produce oscillatory behavior in mechanistic models. These theoretical considerations allow chemists to work around important practical considerations such as an inability to measure certain species in the experimental system. These sorts of testing strategies illuminate chemists’ desiderata for a “good model.”

In 1966, Richard Levins argued that there are different strategies in model building in population biology. In this paper, I reply to Orzack and Sober's (1993) critiques of Levins and argue that his views on modeling strategies apply also in the context of evolutionary genetics. In particular, I argue that there are different ways in which models are used to ask and answer questions about the dynamics of evolutionary change, prospectively and retrospectively, in classical versus molecular evolutionary genetics. Further, I argue that robustness analysis is a tool for, if not confirmation, then something near enough, in this discipline.

Both Henri Poincaré and (more recently) Roger Shepard have argued that the geometry and topology of physical space are internalized by the mind in the form, not (or not only) of a Euclidean manifold, but in terms of the group of rigid Euclidean transformations. Since this issue can have bearing on various metaphysical and epistemological questions, we explore the different reasons they offer for holding this view. In this context, we show how most commentators misunderstand Poincaré's ‘heated sphere/plate’ model and introduce Shepard's ideas to the philosophy of science community.

I maintain that quantum mechanics is fundamentally about a system of N particles evolving in three-dimensional space, not the wave function evolving in 3N-dimensional space.

The biological effects of low doses of toxic and carcinogenic chemicals are currently a matter of significant scientific controversy. This paper argues that philosophers of science can contribute to alleviating this controversy by examining it with the aid of a novel account of scientific anomaly. Specifically, analysis of contemporary research on chemical hormesis (i.e., alleged beneficial biological effects produced by low doses of substances that are harmful at higher doses) suggests that scientists may initially describe anomalous phenomena in terms of multiple distinct “characterizations,” each of which is compatible with current empirical evidence. By focusing attention on this feature of scientific anomalies, philosophers of science can alleviate the controversy over low-dose chemical effects in at least two ways: (1) they can pinpoint the significant ways in which particular characterizations frame the controversy, and (2) they can identify the methodological value judgments at stake in researchers’ choice of characterizations.

We argue that a responsible analysis of today's evidence-based risk assessments and risk debates in biology demands a critical or metascientific scrutiny of the uncertainties, assumptions, and threats of error along the manifold steps in risk analysis. Without an accompanying methodological critique, neither sensitivity to social and ethical values, nor conceptual clarification alone, suffices. In this view, restricting the invitation for philosophical involvement to those wearing a “bioethicist” label precludes the vitally important role philosophers of science may be able to play as bioevidentialists. The goal of this paper is to give a brief and partial sketch of how a metascientific scrutiny of risk evidence might work.

Comparing alternative scientific theories obviously is relevant to theory assessment, but are comparativists (like Laudan) correct when they also make it necessary? This paper argues that they are not. Defining rationality solely in terms of theories’ comparative problem-solving strengths, comparativist philosophers of science like Laudan subscribe to what I call the irrelevance claim (IC) and the necessity claim (NC). According to IC, a scientific theory's being well or poorly confirmed is “irrelevant” to its acceptance; NC is the claim that “all evaluations of research traditions and theories must be made within a comparative context,” how any theory “compares with its competitors” (Laudan 1977, 21, 120). Using current competing theories (T1 and T2) of population viability assessment (PVA) for the Florida panther, the paper investigates IC/NC. In part because dominant T2 panther biologists accept IC/NC (which T1 theorists reject), the paper argues that they appear both to have accepted flawed T2 and to have contributed to flawed panther science and policy. Correcting Laudan's Comparativist Philosophy of Science (LCPS), underlying the T1-versus-T2 debate, thus may hold promise for helping resolve both the scientific and policy controversy over panther PVA.

The Aristotelian distinction between actual and potential presence of a substance in a mixture forms part of a conception of mixture which stands in contrast to atomist and Stoic theories as propounded by the ancients. But the central ideas on which these theories are built need not be combined and opposed to one another in precisely the ways envisaged by these ancient theories. This is well illustrated by Duhem, who maintained the Aristotelian idea that the original ingredients are only potentially, and not actually, present in a mixture, but who sided with the Stoics and against Aristotle on the possibility of co-occupancy. I have argued that the Stoic theory cannot dispense with some such notion as the Aristotelian conception of potentiality in allowing the elements to be actually present in a mixture. Here I suggest that some such Aristotelian notion must be at work in a more modern atomic conception of matter if this is to allow elemental substances to be actually present in compounds, which I think is how compounds are usually understood. Analogous issues arise regarding the status of solutions and their components.

The main scientific problems of chemical bonding were solved half a century ago, but adequate philosophical understanding of chemical combination is yet to be achieved. Chemists routinely use important terms (“element,” “atom,” “molecule,” “substance”) with more than one meaning. This can lead to misunderstandings. Eliminativists claim that what seems to be a baseball breaking a window is merely the action of “atoms, acting in concert.” They argue that statues, baseballs, and similar macroscopic things “do not exist.” When macroscopic objects like baseballs move, exceedingly large numbers (∼1025) of microscopic components coordinate their activities. Understanding how this happens requires attention to the interactions that link parts into larger units. Eliminativists say that everything that truly exists has causal relationships in addition to those of its components—“nonredundant causality.” This paper holds that if a number of entities interact in such a way that the effect of that collection on test objects is different than it would have been in the absence of the interaction, then identification of that collection as a single composite agent is warranted, for purposes to which that difference is relevant. Ordinary “chemical substances” (both elementary materials such as dihydrogen and compounds such as water) fulfill this version of the requirement of nonredundant causality. Other sorts of chemical coherences, including chemical dissipative structures (e.g., flames), also fulfill that criterion. All these types of coherences qualify as “substances” (as that term is used in philosophy) even though they are not all “chemical substances.”

This article will explore whether there are arguments for Aristotle's concept mixis which can aid our current discussions within the philosophy of chemistry. We remain troubled by the way and extent to which chemical substance in bulk can be identified with or reduced to the stability and structure of molecules, and whether these in turn can be identified with or reduced to elemental atoms and the quantum theoretical characterization of their electrons. Aristotle was as determined as we are to think through the implications of substances comprised of constituents and to question their status in chemical compounds.

In this article I assess the problems and prospects of a microstructural approach to chemical substances. Saul Kripke and Hilary Putnam famously claimed that to be gold is to have atomic number 79 and to be water is to be H2O. I relate the first claim to the concept of element in the history of chemistry, arguing that the reference of element names is determined by atomic number. Compounds are more difficult: water is so complex and heterogeneous at the molecular level that `water is H2O’ seems false under some interpretations. I sketch a response to this problem.

Many of the arguments against reductionism and fundamental theory as a method for explaining physical phenomena focus on the role of models as the appropriate vehicle for this task. While models can certainly provide us with a good deal of explanatory detail, problems arise when attempting to derive exact results from approximations. In addition, models typically fail to explain much of the stability and universality associated with critical point phenomena and phase transitions, phenomena sometimes referred to as “emergent.” The paper examines the connection between theoretical principles like spontaneous symmetry breaking and emergent phenomena and argues that new ways of thinking about emergence and fundamentalism are required in order to account for the behavior of many phenomena in condensed matter and other areas of physics.

This paper considers the relationship between continuum hydrodynamics and discrete molecular dynamics in the context of explaining the behavior of breaking droplets. It is argued that the idealization of a fluid as a continuum is actually essential for a full explanation of the drop breaking phenomenon and that, therefore, the less “fundamental,” emergent hydrodynamical theory plays an ineliminable role in our understanding.

The linear sequence specification of a gene product is not provided by the target DNA sequence alone but by the mechanisms of gene expressions. The main actors of these mechanisms, proteins and functional RNAs, relay environmental information to the genome with important consequences to sequence selection and processing. This ‘postgenomic’ reality has implications for our understandings of development not as predetermined by genes but as an epigenetic process. Critics of genetic determinism have long argued that the activity of ‘genes’ and hence their contribution to the phenotype depends on intra- and extraorganismal ‘environmental’ elements. As will be shown here, even the mere physical existence of a `gene' is dependent on its phenotypic context.

Although the construction of neo-Darwinism grew out of Thomas Hunt Morgan's melding of Darwinism and Mendelism, his evidence did not soley support a model of gradual change. To the contrary, he was confronted with observations that could have led him to a more “evo-devo” understanding of the emergence of novel features. Indeed, since Morgan was an embryologist before he became a fruit-fly geneticist, one would have predicted that the combination of these two lines of research would have resulted in early formulations of concepts relevant to evolutionary developmental biology. It is thus of interest to review Morgan's thought processes and arguments for at first rejecting both Darwinism and Mendelism, and then for later dismissing data that would have yielded a model of rapid morphological change in favor of a model of change based on the accumulation of minor mutations and their morphological consequences.

Radically new or unexpected findings in a science demand an openness to new concepts and styles of explanation. The time is more than ripe for asking ourselves what we have learned from the research program of comparative genomics. Where not long ago the human genome was expected to reveal a close association of complexity with the quantitative expansion of the roster of unique genes, more recent findings, especially in relation to comparisons between human and chimp, have raised the bracing possibility that when it comes to complexity, it may be that `less is more'. But `less is more' is not the only observation or inference that follows from the data. The idea of `progressive detachment' will be introduced and set forth as the most perspicuous conceptual resource for unifying and interpreting the overall findings from comparative genomics to date.