The distinction between causal role and selected effect functions is typically framed in terms of their respective explanatory roles. However, much of the controversy over functions in genomics takes place in an investigative, not an explanatory context. Specifically, the process of component-driven functional investigation begins with the designation of some genetic or epigenetic element as functional —i.e. not junk— because it possesses properties that, arguably, suggest some biologically interesting organismal effect. The investigative process then proceeds, in a bottom-up fashion, to (...) search for those effects. I argue that this process encounters a problem reminiscent of one that Gould and Lewontin associated with the adaptationist program. Just as their stereotypical adaptationst became trapped in the myopic pursuit of one selectionist hypothesis after another, so can the investigation of CR functions in genomics lead to an unending series putative organism-level CR functions for junk DNA. This is an acute problem for genomics, because eukaryotic genomes are littered with transposable elements and their deactivated descendants which often masquerade as interesting CR-functional components and it is experimentally onerous to determine whether they lack such a function. I further argue that selectionist reasoning about TE-host coevolutionary dynamics can greatly streamline the investigative process. Importantly, selectionist hypotheses need not be well confirmed to be illuminating in this context. Informed selectionist reasoning about the strategic roles of TEs in the genome offers a corrective to the idea that most of our DNA is somehow CR functional for the organism. (shrink)

While the term “reactivity” has come to be associated with specific phenomena in the social sciences, having to do with subjects’ awareness of being studied, this paper takes a broader stance on this concept. I argue that reactivity is a ubiquitous feature of the psychological subject matter and that this fact is a precondition of experimental research, while also posing potential problems for the experimenter. The latter are connected to the worry about distorted data and experimental artifacts. But what are (...) experimental artifacts and what is the most productive way of dealing with them? In this paper, I approach these questions by exploring the ways in which experimenters in psychology simultaneously exploit and suppress the reactivity of their subject matter in order to produce experimental data that speak to the question or subject matter at hand. Highlighting the artificiality of experimental data, I raise the question of what distinguishes a genuine experimental result from an experimental artifact. My analysis construes experimental results as the outcomes of inferences from the data that take material background assumptions as auxiliary premises. Artifacts occur when one or more of these background assumptions are false, such that the data do not reliably serve the purposes they were generated for. I conclude by laying out the ways in which my analysis of data quality is relevant to, and informed by, recent debates about the replicability of experimental results. (shrink)

According to the hypothesis-generator account, valid extrapolations from a source to a target system are circular, since they rely on knowledge of relevant similarities and differences that can onl...

The new mechanists and the autonomy approach both aim to account for how biological phenomena are explained. One identifies appeals to how components of a mechanism are organized so that their activities produce a phenomenon. The other directs attention towards the whole organism and focuses on how it achieves self-maintenance. This paper discusses challenges each confronts and how each could benefit from collaboration with the other: the new mechanistic framework can gain by taking into account what happens outside individual mechanisms, (...) while the autonomy approach can ground itself in biological research into how the actual components constituting an autonomous system interact and contribute in different ways to realize and maintain the system. To press the case that these two traditions should be constructively integrated we describe how three recent developments in the autonomy tradition together provide a bridge between the two traditions: (1) a framework of work and constraints, (2) a conception of function grounded in the organization of an autonomous system, and (3) a focus on control. (shrink)

Many of the most important social institutions—e.g., law and language—are thought to be normative in some sense. And philosophers have been puzzled by how this normativity can be explained in terms of the social, descriptive states of affairs that presumably constitute them. This paper attempts to solve this sort of puzzle by considering a simpler and less contentious normative social practice: table manners. Once we are clear on the exact sense in which a practice is normative, we see that some (...) practices can be normative in an interesting and non-trivial sense, but also explicable with merely descriptive resources. In addition to arguing that it is possible to explain normative practices with descriptive resources, this paper presents and defends just such an explanation—an account of the nature of table manners that appeals only to descriptive states of affairs. (shrink)

The history of developmental biology is interwoven with debates as to whether mechanistic explanations of development are possible or whether alternative explanatory principles or even vital forces need to be assumed. In particular, the demonstrated ability of embryonic cells to tune their developmental fate precisely to their relative position and the overall size of the embryo was once thought to be inexplicable in mechanistic terms. Taking a causal perspective, this Element examines to what extent and how developmental biology, having turned (...) molecular about four decades ago, has been able to meet the vitalist challenge. It focuses not only on the nature of explanations but also on the usefulness of causal knowledge – including the knowledge of classical experimental embryology – for further scientific discovery. It also shows how this causal perspective allows us to understand the nature and significance of some key concepts, including organizer, signal and morphogen. This title is also available as Open Access on Cambridge Core. (shrink)

This MPhil dissertation presents a novel account of teleological explanations in biology. I outline the “shorthand approach” to such explanations, on which they are taken to convey implicit evolutionary explanations. “Selected effects” accounts of teleological explanation dominate recent literature, but they struggle to accommodate teleological explanations of complex traits built through cumulative selection. I articulate the general notion of a landscape explanation, which, applied to biology, explains the evolution of complex features in a population by citing salient features of the (...) population’s fitness landscape. I show that such explanations lend themselves to a teleological shorthand. I close with remarks concerning when a teleological explanation of a trait is legitimate, and why teleological language strikes us as appropriate when we give evolutionary explanations. (shrink)

Against those who identify genealogy with reductive genealogical debunking or deny it any evaluative and action-guiding significance, I argue for the following three claims: that although genealogies, true to their Enlightenment origins, tend to trace the higher to the lower, they need not reduce the higher to the lower, but can elucidate the relation between them and put us in a position to think more realistically about both relata; that if we think of genealogy’s normative significance in terms of a (...) triadic model that includes the genealogy’s addressee, we can see that in tracing the higher to the lower, a genealogy can facilitate an evaluation of the higher element, and where the lower element is some important practical need rather than some sinister motive, the genealogy can even be vindicatory; and finally, that vindicatory genealogies can offer positive guidance on how to engineer better concepts. (shrink)

There are two traditions of thinking about idealization offering almost opposite views on their functioning and epistemic status. While one tradition views idealizations as epistemic deficiencies, the other one highlights the epistemic benefits of idealization. Both of these, however, identify idealization with misrepresentation. In this article, we instead approach idealization from the artifactual perspective, comparing it to the distortion-to-reality accounts of idealization, and exemplifying it through the case of the Hodgkin and Huxley model of nerve impulse. From the artifactual perspective, (...) the epistemic benefits and deficiencies introduced by idealization frequently come in a package due to the way idealization draws together different resources in model construction. Accordingly, idealization tends to be holistic in that it is not often easily attributable to just some specific parts of the model. Instead, the idealizing process tightly embeds theoretical concepts and formal tools into the construction of a model. (shrink)

The use of multiple means of determination to “triangulate” on the existence and character of a common phenomenon, object, or result has had a long tradition in science but has seldom been a matter of primary focus. As with many traditions, it is traceable to Aristotle, who valued having multiple explanations of a phenomenon, and it may also be involved in his distinction between special objects of sense and common sensibles. It is implicit though not emphasized in the distinction between (...) primary and secondary qualities from Galileo onward. It is arguably one of several conceptions involved in Whewell’s method of the “consilience of inductions” (Laudan 1971) and is to be found in several places in Peirce. (From M. Brewer and B. Collins, eds., (1981); Scientific Inquiry in the Social Sciences (a festschrift for Donald T. Campbell), San Francisco: Jossey-Bass, pp. 123–162.). (shrink)

One of the defining features of the classical gene was its position. In molecular genetics, positions are defined instead as nucleotide numbers and there is no clear correspondence with its classical counterpart. However, the classical gene position did not simply disappear with the development of the molecular approach, but survived in the lab associated to different genetic practices. The survival of classical gene position would illustrate Waters’ view about the practical persistence of the genetic approach beyond reductionism and anti-reductionist claims. (...) We show instead that at the level of laboratory practices there are also reductive processes, operating through the rise and fall of different techniques. Molecular markers made the concept of classical gene position practically dispensable, leading us to rethink whether it had any causal role or was just a mere heuristic. (shrink)

This article argues for the explanatory autonomy of psychology drawing on cases from the multilevel modeling practice. This is done by considering a multilevel linear model in personality and social psychology, and discussing its philosophical implications for the reductionism debate in philosophy of psychology. I argue that this practice challenges the reductionist position in philosophy of psychology, and supports the explanatory autonomy of psychology.

Multidisciplinary models aggregating ‘lower-level’ biological and ‘higher-level’ psychological and social determinants of a phenomenon raise a puzzle. How is the interaction between the physical, the psychological and the social conceptualized and explained? Using biopsychosocial models of pain as an illustration, I argue that these models are in fact level-neutral compilations of empirical findings about correlated and causally relevant factors, and as such they neither assume, nor entail a conceptual or ontological stratification into levels of description, explanation or reality. If inter-level (...) causation is deemed problematic or if debates about the superiority of a particular level of description or explanation arise, these issues are fueled by considerations other than empirical findings. (shrink)

We characterize access to empirical objects in biology from a theoretical perspective. Unlike objects in current physical theories, biological objects are the result of a history and their variations continue to generate a history. This property is the starting point of our concept of measurement. We argue that biological measurement is relative to a natural history which is shared by the different objects subjected to the measurement and is more or less constrained by biologists. We call symmetrization the theoretical and (...) often concrete operation which leads to considering biological objects as equivalent in a measurement. Last, we use our notion of measurement to analyze research strategies. Some strategies aim to bring biology closer to the epistemology of physical theories, by studying objects as similar as possible, while others build on biological diversity. (shrink)

Waters’s (2007) actual difference making and Weber’s (2013, 2017) biological normality approaches to causal selection have received many criticisms, some of which miss their target. Disagreement about whether Waters’s and Weber’s views succeed in providing criteria that uniquely singles out the gene as explanatorily significant in biology has led philosophers to overlook a prior problem. Before one can address whether Waters’s and Weber’s views successfully account for the explanatory significance of genes, one must ask whether either view satisfactorily meets the (...) necessary conditions for causal selection in the first place. An adequate defense of causal selection must meet two desiderata. First, there must be an explanatory property that sets some causes apart from others. Second, the property identified must be one that is recognized by biologists as relevant to their domain(s) of inquiry. I argue that both fall short of meeting the second condition. I demonstrate this by showing how many of the biological technologies crucial to experimentation do not fit either view very well. I offer a more adequate proposal that accommodates non-actual and artificial causal variables. A consequence of my view is the following: When analyzing the causal selection practices of biologists, philosophers should consider the explanatory targets relevant to a research program – including ones whose explanans must appeal to biological technologies. I then explain how this proposal can inform the existing debate between Weber (2017) and Griffiths et al. (2015). (shrink)

This book addresses key conceptual issues relating to the modern scientific and engineering use of computer simulations. It analyses a broad set of questions, from the nature of computer simulations to their epistemological power, including the many scientific, social and ethics implications of using computer simulations. The book is written in an easily accessible narrative, one that weaves together philosophical questions and scientific technicalities. It will thus appeal equally to all academic scientists, engineers, and researchers in industry interested in questions (...) related to the general practice of computer simulations. (shrink)

This article describes contrasting ideas for a set of topics in epidemiological thinking. The premise underlying this contribution to the special edition is that researchers develop their epidemiological thinking over time through interactions with other researchers who have a variety of in-practice commitments, such as to kinds of cases and methods of analysis, and not simply to a philosophical framework for explanation. I encourage discussants from philosophy and epidemiology to draw purposefully from across a range of topics and contrasting positions, (...) and thereby pursue critical thinking in the sense of understanding ideas and practices better when we examine them in relation to alternatives. After an initial topic concerning practices for developing epidemiological literacy, a number of conceptual steps follow—the characterization of the very phenomena we might be concerned with, the scope and challenges of the field of epidemiology, the formulation of categories—before linking associations, predictions, causes and interventions and examining the confounding of purported links. Building on that conceptual basis, the remaining topics consist of issues or angles of analysis related to the complexities of inequalities within and between populations, context, and changes over the life course. The organization of topics derives from a graduate course that I teach that aims for epidemiological literacy, not technical ability in statistical formulas and data analysis, and shares the underlying premise and critical thinking goals of this article. During the topic-by-topic description, some assertions about explanation and intervention emerge, notably, that epidemiological–philosophical discussion about causality often leaves unclear or unexamined whether a modifiable factor shown to have been associated with a difference in the data from past observations should be thought of as factor that, when modified, would generate that difference going forward. The article concludes with a “Limitations of this Study” section that teases out different kinds of description–prescription relationship that are implied in undertaking philosophy of epidemiology and identifies some other considerations that are implied but not emphasized by this article. (shrink)

The paper analyzes the early theory building process of Thomas Hunt Morgan from the 1910s to the 1930s and the introduction of the invisible gene as a main explanatory unit of heredity. Morgan’s work marks the transition between two different styles of thought. In the early 1900s, he shifted from an embryological study of the development of the organism to a study of the mechanism of genetic inheritance and gene action. According to his contemporaries as well as to historiography, Morgan (...) separated genetics from embryology, and the gene from the whole organism. Other scholars identified an underlying embryological focus in Morgan’s work throughout his career. Our paper aims to clarify the debate by concentrating on Morgan’s theory building—characterized by his confidence in the power of experimental methods, and carefully avoiding any ontological commitment towards the gene—and on the continuity of the questions to be addressed by both embryology and genetics. (shrink)

Ongoing empirical discoveries in molecular biology have generated novel conceptual challenges and perspectives. Philosophers of biology have reacted to these trends when investigating the practice of molecular biology and contributed to scientific debates on methodological and conceptual matters. This article reviews some major philosophical issues in molecular biology. First, philosophical accounts of mechanistic explanation yield a notion of explanation in the context of molecular biology that does not have to rely on laws of nature and comports well with molecular discovery. (...) Second, reductionism continues to be debated and increasingly be rejected by scientists. Philosophers have likewise moved away from reduction toward integration across fields or integrative explanations covering several levels of organization. Third, although the gene concept has undergone substantial transformation and even fragmentation, it still enjoys widespread use by molecular biologists, which has prompted philosophers to understand the empirical reasons for this. At the same time, it has been argued the notion of ‘genetic information’ is largely an empty metaphor, which generates the illusion of explanatory understanding without offering an adequate explanation of molecular and developmental mechanisms. (shrink)

The historical debate on representation in cognitive science and neuroscience construes representations as theoretical posits and discusses the degree to which we have reason to posit them. We reject the premise of that debate. We argue that experimental neuroscientists routinely observe and manipulate neural representations in their laboratory. Therefore, neural representations are as real as neurons, action potentials, or any other well-established entities in our ontology.

Over the last 20 years, several philosophers have developed a new approach to biological functions, the organizational approach. This is not a single theory but a family of theories based on the idea that a trait token can acquire a function by virtue of the way it contributes to a complex, organized system and thereby to its own continued persistence as a token. I argue that the organizational approach faces a serious liberality objection. I examine three different ways organizational theorists (...) have tried to avoid that objection and show how they fail. (shrink)

I present and defend the generalized selected effects theory (GSE) of function. According to GSE, the function of a trait consists in the activity that contributed to its bearer’s differential reproduction, or differential retention, within a population. Unlike the traditional selected effects (SE) theory, it does not require that the functional trait helped its bearer reproduce; differential retention is enough. Although the core theory has been presented previously, I go significantly beyond those presentations by providing a new argument for GSE (...) and defending it from a recent objection. I also sketch its implications for teleosemantics and philosophy of medicine. (shrink)

John Searle has argued that functions owe their existence to the value that we put into life and survival. In this paper, I will provide a critique of Searle’s argument concerning the ontology of functions. I rely on a standard analysis of functional predicates as relating not only a biological entity, an activity that constitutes the function of this entity and a type of system but also a goal state. A functional attribution without specification of such a goal state has (...) no truth-value. But if completed with a goal state, functional attributions understood as four-place relations attain a truth-value. The truth conditions of all attributions of function involve a dependence claim of the goal state on the function bearer’s activity. The nature of this dependence may differ; I consider five different possibilities: causality, mechanistic constitution, mereology, supervenience and metaphysical grounding. If these dependency relations are objective, Searle’s central ontological thesis fails. What he ought to have said is that our valuing survival or other goal states may be the reason why biology seeks functional knowledge, but this has nothing to do with ontology. I will show further that Searle also raised an interesting challenge concerning the relationship of functional and causal truths, but it does not threaten the objectivity of functions either. At best, it could show that functional vocabulary is eliminable. However, I will show that functional vocabulary is not so eliminable. (shrink)

Multidisciplinary models aggregating ‘lower-level’ biological and ‘higher-level’ psychological and social determinants of a phenomenon raise a puzzle. How is the interaction between the physical, the psychological and the social conceptualized and explained? Using biopsychosocial models of pain as an illustration, I argue that these models are in fact level-neutral compilations of empirical findings about correlated and causally relevant factors, and as such they neither assume, nor entail a conceptual or ontological stratification into levels of description, explanation or reality. If inter-level (...) causation is deemed problematic or if debates about the superiority of a particular level of description or explanation arise, these issues are fueled by considerations other than empirical findings. (shrink)

Which domains of biology do philosophers of biology primarily study? The fact that philosophy of biology has been dominated by an interest for evolutionary biology is widely admitted, but it has not been strictly demonstrated. Here I analyse the topics of all the papers published in Biology & Philosophy, just as the journal celebrates its thirtieth anniversary. I then compare the distribution of biological topics in Biology & Philosophy with that of the scientific journal Proceedings of the National Academy of (...) Science of the USA, focusing on the recent period 2003–2015. This comparison reveals a significant mismatch between the distributions of these topics. I examine plausible explanations for that mismatch. Finally, I argue that many biological topics underrepresented in philosophy of biology raise important philosophical issues and should therefore play a more central role in future philosophy of biology. (shrink)

The Realist that investigates questions of ontology by appeal to the quantificational structure of language assumes that the semantics for the privileged language of ontology is externalist. I argue that such a language cannot be (some variant of) a natural language, as some Realists propose. The flexibility exhibited by natural language expressions noted by Chomsky and others cannot obviously be characterized by the rigid models available to the externalist. If natural languages are hostile to externalist treatments, then the meanings of (...) natural language expressions serve as poor guides for ontological investigation, insofar as their meanings will fail to determine the referents of their constituents. This undermines the Realist’s use of natural languages to settle disputes in metaphysics. (shrink)

Recently the functional model of reduction has become something like the standard model of reduction in philosophy of mind. In this paper, I argue that the functional model fails as an account of reduction due to problems related to three key concepts: functionalization, realization and causation. I further argue that if we try to revise the model in order to make it more coherent and scientifically plausible, the result is merely a simplified version of what in philosophy of science is (...) known as mechanistic explanation. Hence, instead of analyzing reduction in philosophy of mind in terms of functional reduction, it should be analyzed in terms of mechanistic explanation. (shrink)

This paper looks at an appeal to the authority of biomedical research that has recently been used by empirical economists to motivate and justify their methods. I argue that those who make this appeal mistake the nature of biomedical research. Randomised trials, which are said to have revolutionised biomedical research, are a central methodology, but according to only one paradigm. There is another paradigm at work in biomedical research, the inferentialist paradigm, in which randomised trials play no special role. I (...) outline the inferentialist alternative in broad strokes, apply it to a recent controversy in econometrics and draw some general conclusions concerning econometric methodology. (shrink)

We outline a framework of multilevel neurocognitive mechanisms that incorporates representation and computation. We argue that paradigmatic explanations in cognitive neuroscience fit this framework and thus that cognitive neuroscience constitutes a revolutionary break from traditional cognitive science. Whereas traditional cognitive scientific explanations were supposed to be distinct and autonomous from mechanistic explanations, neurocognitive explanations aim to be mechanistic through and through. Neurocognitive explanations aim to integrate computational and representational functions and structures across multiple levels of organization in order to explain (...) cognition. To a large extent, practicing cognitive neuroscientists have already accepted this shift, but philosophical theory has not fully acknowledged and appreciated its significance. As a result, the explanatory framework underlying cognitive neuroscience has remained largely implicit. We explicate this framework and demonstrate its contrast with previous approaches. (shrink)

Intertheoretic relations are an important topic in the philosophy of science. However, since their classical discussion by Ernest Nagel, such relations have mostly been restricted to relations between pairs of theories in the natural sciences. In this paper, we present a model of a new type of intertheoretic relation, called 'Montague Reduction', which is assumed in Montague's framework for the analysis and interpretation of natural language syntax. To motivate the adoption of our new model, we show that this model extends (...) the scope of application of the Nagelian (or related) models, and that it shares the epistemological advantages of the Nagelian model. The latter is achieved in a Bayesian framework. (shrink)

Griffiths and Stotz’s Genetics and Philosophy: An Introduction offers a very good overview of scientific and philosophical issues raised by present-day genetics. Examining, in particular, the questions of how a “gene” should be defined and what a gene does from a causal point of view, the authors explore the different domains of the life sciences in which genetics has come to play a decisive role, from Mendelian genetics to molecular genetics, behavioural genetics, and evolution. In this review, I highlight what (...) I consider as the two main theses of the book, namely: genes are better conceived as tools; genes become causes only in a context. I situate these two theses in the wider perspective of developmental systems theory. This leads me to emphasize that Griffiths and Stotz reflect very well an on going process in genetics, which I call the “epigenetization” of genetics, i.e., the growing interest in the complex processes by which gene activation is regulated. I then make a factual objection, which is that Griffiths and Stotz have almost entirely neglected the perspective of ecological developmental biology, and more precisely recent work on developmental symbioses, and I suggest that this omission is unfortunate in so far as an examination of developmental symbioses would have considerably strengthened Griffiths and Stotz’s own conclusions. (shrink)

Consensus conferences are social techniques which involve bringing together a group of scientific experts, and sometimes also non-experts, in order to increase the public role in science and related policy, to amalgamate diverse and often contradictory evidence for a hypothesis of interest, and to achieve scientific consensus or at least the appearance of consensus among scientists. For consensus conferences that set out to amalgamate evidence, I propose three desiderata: Inclusivity, Constraint, and Evidential Complexity. Two examples suggest that consensus conferences can (...) readily satisfy Inclusivity and Evidential Complexity, but consensus conferences do not as easily satisfy Constraint. I end by discussing the relation between social inclusivity and the three desiderata. (shrink)

In this contribution, I comment on Raffaella Campaner’s defense of explanatory pluralism in psychiatry (in this volume). In her paper, Campaner focuses primarily on explanatory pluralism in contrast to explanatory reductionism. Furthermore, she distinguishes between pluralists who consider pluralism to be a temporary state on the one hand and pluralists who consider it to be a persisting state on the other hand. I suggest that it would be helpful to distinguish more than those two versions of pluralism – different understandings (...) of explanatory pluralism both within philosophy of science and psychiatry – namely moderate/temporary pluralism, anything goes pluralism, isolationist pluralism, integrative pluralism and interactive pluralism. Next, I discuss the pros and cons of these different understandings of explanatory pluralism. Finally, I raise the question of how to implement or operationalize explanatory pluralism in scientific practice; how to structure the “genuine dialogue” or shape “the pluralistic attitude” Campaner is referring to. As tentative answers, I explore a question-based framework for explanatory pluralism as well as social-epistemological procedures for interaction among competing approaches and explanations. (shrink)

This article examines a metaphilosophical issue, namely existing disagreements in philosophy of science about the significance of using multiple means of determination in scientific practice. We argue that this disagreement can, in part, be resolved by separating different questions that can be asked about the use of multiple means of determination, including the following: what can be concluded from the convergence of data or the convergence of claims about phenomena? Are the conclusions drawn from the convergence of data and of (...) statements about phenomena of special importance to the debate about realism and antirealism? Do inferences based on multiple means of determination have stronger epistemic force than inferences that are secured in other ways? Is the epistemic goal of deploying multiple means of determination well entrenched within the scientific community? Most of these questions can be discussed both in a formal and in an empirical perspective. If the differences in perspective are taken into account, some disagreements can be easily resolved. In part, however, the disagreements reflect historiographical challenges that are very difficult, if not impossible to meet. (shrink)

In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning (...) the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk. (shrink)

Experimental modeling in biology involves the use of living organisms (not necessarily so-called "model organisms") in order to model or simulate biological processes. I argue here that experimental modeling is a bona fide form of scientific modeling that plays an epistemic role that is distinct from that of ordinary biological experiments. What distinguishes them from ordinary experiments is that they use what I call "in vivo representations" where one kind of causal process is used to stand in for a physically (...) different kind of process. I discuss the advantages of this approach in the context of evolutionary biology. (shrink)

This paper examines causal theories of reference with respect to how plausible an account they give of non-physical natural kind terms such as ‘gene’ as well as of the truth of the associated theoretical claims. I first show that reference fixism for ‘gene’ fails. By this, I mean the claim that the reference of ‘gene’ was stable over longer historical periods, for example, since the classical period of transmission genetics. Second, I show that the theory of partial reference does not (...) do justice to some widely held realist intuitions about classical genetics. This result is at loggerheads with the explicit goals usually associated with partial theories of reference, which is to defend a realist semantics for scientific terms. Thirdly, I show that, contrary to received wisdom and perhaps contrary to physics and chemistry, neither reference fixism nor partial reference are necessary in order to hold on to scientific realism about biology. I pinpoint the reasons for this in the nature of biological kinds, which do not even remotely resemble natural kinds (i.e., Lockean real essences) as traditionally conceived. (shrink)

I describe two traditions of philosophical accounts of evidence: one characterizes the notion in terms of signs of success, the other characterizes the notion in terms of conditions of success. The best examples of the former rely on the probability calculus, and have the virtues of generality and theoretical simplicity. The best examples of the latter describe the features of evidence which scientists appeal to in practice, which include general features of methods, such as quality and relevance, and general features (...) of evidence, such as patterns in data, concordance with other evidence, and believability of the evidence. Two infamous episodes from biomedical research help to illustrate these features. Philosophical characterization of these latter features—conditions of success—has the virtue of potential relevance to, and descriptive accuracy of, practices of experimental scientists. (shrink)

Amalgamating evidence of different kinds for the same hypothesis into an overall confirmation is analogous, I argue, to amalgamating individuals’ preferences into a group preference. The latter faces well-known impossibility theorems, most famously “Arrow’s Theorem”. Once the analogy between amalgamating evidence and amalgamating preferences is tight, it is obvious that amalgamating evidence might face a theorem similar to Arrow’s. I prove that this is so, and end by discussing the plausibility of the axioms required for the theorem.

Laudan famously argued that neither truth nor approximate truth can be part of an explanation of a scientific theory's predictive success because in the history of science there were theories that enjoyed some limited success but now are considered outright false. The power of his argument lay in the many historic examples he listed . Realists have disputed that all theories on Laudan's list can be regarded as predictively successful but let's suppose momentarily that at least some exist that support (...) his point. In this case, there are historic false theories that made some true predictions. We are aiming for a general explanation of a theory's predictive success and hence these false theories necessarily are on board. Now, Laudan also argues that historic false theories – the downright false ones and the ones we nowadays judge as strictly false, but approximately true – do not in any principled sense differ from the ones we presently accept. These theories seem to present a good basis for inductively inferring that any presently accepted scientific theory is actually false. Many presently accepted theories certainly are predictively successful to a great extent and certainly their success should be covered by an acceptable explanation. Since there seems to be inductive support for the conclusion that …. (shrink)

Kenneth Waters and Marcel Weber argue that the joint use of distinct gene concepts and the transfer of knowledge between classical and molecular analyses in contemporary scientific practice is possible because classical and molecular concepts of the gene refer to overlapping chromosomal segments and the DNA sequences associated with these segments. However, while pointing in the direction of coreference, both authors also agree that there is a considerable divergence between the actual sequences that count as genes in classical genetics and (...) molecular biology. The thesis advanced in this paper is that the referents of classical and molecular gene concepts are coextensive to a higher degree than admitted by Waters and Weber, and therefore coreference can provide a satisfactory account of the high level of integration between classical genetics and molecular biology. In particular, I argue that the functional units/cistrons identified by classical techniques overlap with functional elements entering the composition of molecular transcription units, and that the precision of this overlap can be improved by conducting further experimentation. (shrink)

It is customary to distinguish experimental from purely observational sciences. The former include physics and molecular biology, the latter astronomy and palaeontology. Experiments involve actively intervening in the course of nature, as opposed to observing events that would have happened anyway. When a molecular biologist inserts viral DNA into a bacterium in his laboratory, this is an experiment; but when an astronomer points his telescope at the heavens, this is an observation. Without the biologist’s handiwork the bacterium would never have (...) contained foreign DNA; but the planets would have continued orbiting the sun whether or not the astronomer had directed his telescope skyward. The observational/experimental distinction would probably be difficult to make precise 1, as the notion of an ‘intervention’ is not easily defined, but it is intuitively fairly clear, and is frequently invoked by scientists and historians of science. Experimentation, or ‘putting questions to nature’, is often cited as a hallmark of the modern scientific method, something that permitted the enormous advances of the last 350 years. And it is sometimes said that the social sciences lag behind the natural because controlled experiments cannot be done so readily in the former. Moreover in certain sciences, e.g. epidemiology, students are explicitly taught that experimental data is preferable to observational data, particularly for doing causal inference. So the distinction between observational and experimental science has quite wide currency, and is often regarded as methodologically significant. Surprisingly, mainstream philosophy of science has had rather little to say about the observational/experimental distinction. 2 For example, discussions of confirmation usually invoke a notion of ‘evidence’, to be contrasted with ‘theory’ or ‘hypothesis’; the aim is to understand how the evidence bears on the hypothesis. But whether this ‘evidence’ comes from observation or experiment generally plays no role in the discussion; this is true …. (shrink)

Accounts of mechanistic explanation have emphasized the importance of looking down—decomposing a mechanism into its parts and operations. Using research on visual processing as an exemplar, I illustrate how productive such research has been. But once multiple components of a mechanism have been identified, researchers also need to figure out how it is organized—they must look around and determine how to recompose the mechanism. Although researchers often begin by trying to recompose the mechanism in terms of sequential operations, they frequently (...) find that the components of a mechanism interact in complex ways involving positive and negative feedback and that the organization often exhibits highly interactive local networks linked by a few long-range connections (small-worlds organization) and power law distributions of connections. The mechanisms are themselves active systems that are perturbed by inputs but not set in motion by them. Researchers also need to look up —situate a mechanism in its context, which may be a larger mechanism that modulates its behavior. When looking down is combined with looking around and up, mechanistic research results in an integrated, multi-level perspective. (shrink)