Due to the variation, contingency and complexity of living systems, biology is often taken to be a science without fundamental theories, laws or general principles. I revisit this question in light of the quest for design principles in systems biology and show that different views can be reconciled if we distinguish between different types of generality. The philosophical literature has primarily focused on generality of specific models or explanations, or on the heuristic role of abstraction. This paper takes (...) a different approach in emphasizing a theory-constituting role of general principles. Design principles signify general dependency-relations between structures and functions, given a set of formally defined constraints. I contend that design principles increase our understanding of living systems by relating specific models to general types. The categorization of types is based on a delineation of the scope of biological possibilities, which serves to identify and define the generic features of classes of systems. To characterize the basis for general principles through generic abstraction and reasoning about possibility spaces, I coin the term constraint-based generality. I show that constraint-based generality is distinct from other types of generality in biology, and argue that general principles play a unifying role that does not entail theory reduction. (shrink)

The comparison between biological and social macroevolution is a very important (though insufficiently studied) subject whose analysis renders new significant possibilities to comprehend the processes, trends, mechanisms, and peculiarities of each of the two types of macroevolution. Of course, there are a few rather important (and very understandable) differences between them; however, it appears possible to identify a number of fundamental similarities. One may single out at least three fundamental sets of factors determining those similarities. First of all, those similarities (...) stem from the fact that in both cases we are dealing with very complex non-equilibrium (but rather stable) systems whose principles of functioning and evolution are described by the General Systems' Theory, as well as by a number of cybernetic principles and laws. -/- Secondly, in both cases we do not deal with isolated systems; in both cases we deal with a complex interaction between systems of organic systems and external environment, whereas the reaction of systems to external challenges can be described in terms of certain general principles (that, however, express themselves rather differently within the biological reality, on the one hand, and within the social reality, on the other). -/- Thirdly, it is necessary to mention a direct ‘genetic’ link between the two types of macroevolution and their mutual influence. -/- It is important to emphasize that the very similarity of the principles and regularities of the two types of macroevolution does not imply their identity. Rather significant similarities are frequently accompanied by enormous differences. For example, genomes of the chimpanzees and the humans are very similar – with differences constituting just a few per cent; however, there are enormous differences with respect to intellectual and social differences of the chimpanzees and the humans hidden behind the apparently ‘insignificant’ difference between the two genomes. Thus, in certain respects it appears reasonable to consider the biological and social macroevolution as a single macroevolutionary process. This implies the necessity to comprehend the general laws and regularities that describe this process, though their manifestations may display significant variations depending on properties of a concrete evolving entity (biological, or social one). An important notion that may contribute to the improvement of the operationalization level as regards the comparison between the two types of macroevolution is the one that we suggested some time ago – the social aromorphosis (that was developed as a counterpart to the notion of biological aromorphosis well established within Russian evolutionary biology). We regard social aromorphosis as a rare qualitative macrochange that increases in a very significant way complexity, adaptability, and mutual influence of the social systems, that opens new possibilities for social macrodevelopment. In our paper we discuss a number of regularities that describe biological and social macroevolution and that employ the notions of social and biological aromorphosis such as ones of the module evolution (or the evolutionary ‘block assemblage’), ‘payment for arogenic progress’ etc. (shrink)

Due to the variation, contingency and complexity of living systems, biology is often taken to be a science without fundamental theories, laws or general principles. I revisit this question in light of the quest for design principles in systems biology and show that different views can be reconciled if we distinguish between different types of generality. The philosophical literature has primarily focused on generality of specific models or explanations, or on the heuristic role of abstraction. This paper takes (...) a different approach in emphasizing a theory-constituting role of general principles. Design principles signify general dependencyrelations between structures and functions, given a set of formally defined constraints. I contend that design principles increase our understanding of living systems by relating specific models to general types. The categorization of types is based on a delineation of the scope of biological possibilities, which serves to identify and define the generic features of classes of systems. To characterize the basis for general principles through generic abstraction and reasoning about possibility spaces, I coin the term constraint-based generality. I show that constraintbased generality is distinct from other types of generality in biology, and argue that general principles play a unifying role that does not entail theory reduction. (shrink)

We argue that broad, simplegeneralizations, not specifically linked tocontingencies, will rarely approach truth in ecologyand evolutionary biology. This is because mostinteresting phenomena have multiple, interactingcauses. Instead of looking for single universaltheories to explain the great diversity of naturalsystems, we suggest that it would be profitable todevelop general explanatory frameworks. A frameworkshould clearly specify focal levels. The process orpattern that we wish to study defines our level offocus. The set of potential and actual states at thefocal level interacts with conditions (...) at thecontiguous lower and upper levels of organization,through sets of many-to-one and one-to-manyconnections. The number of initiating conditions andtheir permutations at the lower level define thepotential states at the focal level, whereas theactual state is constrained by the upper-levelboundary conditions. The most useful generalizationsare explanatory frameworks, which are road maps tosolutions, rather than solutions themselves. Suchframeworks outline what is understood about boundaryconditions and initiating conditions so that aninvestigator can pick and choose what is required toeffectively understand a specific event or situation. We discuss these relationships in terms of examplesinvolving sex ratio and mating behavior, competitivehierarchies, insect life-histories and the evolutionof sex. (shrink)

Asking and answering questions is the cornerstone of science yet formal training in understanding this key process is often overlooked. "Asking Questions in Biology" unpacks this crucial process of enquiry, from a biological perspective, at its various stages. It begins with an overview of scientific question-asking in general, before moving on to demonstrate how to derive hypotheses from unstructured observations. It then explains in the main sections of the book, how to use statistical tests as tools to analyse data (...) and answer those questions before, finally, showing the best practice in presenting scientific reports. As such, it is an indispensable companion to all students of biology, but particularly those enrolled in courses concerning experimental design; data analysis; hypothesis testing; research methods; or any practical project work. The late Chris Barnard was Professor of Animal Behaviour at Nottingham University. Francis Gilbert is Associate Professor of Ecology at Nottingham University. Peter McGregor isa Reader in Applied Zoologyat Cornwall College. ". (shrink)

This paper presents an alternative conceptual foundation for biological evolution. First the causal and statistical perspectives on evolutionary fitness are analyzed, finding them to implicitly depend on each other, and hence cannot be individually fundamental. It is argued that this is an instance of a relativistic perspective over evolutionary phenomena. New accounts of fitness, the struggle for life, and Natural Selection are developed under this interpretation. This biological relativism is unique in that it draws from General Relativity in physics, unlike (...) previous theories that drew upon statistical mechanics or Newtonian dynamics. A mathematical law of evolutionary change, as well as new theoretical biological concepts to underpin it, are likewise developed. The law and theory are then applied to give examples of how both cornerstones and edge cases can be understood using these new methods. Using General Relativistic Biology provides fresh insight into evolution, all while preserving the core, canonical scientific research program. (shrink)

Homology is a biological sameness relation that is purported to hold in the face of changes in form, composition, and function. In spite of the centrality and importance of homology, there is no consensus on how we should understand this concept. The two leading views of homology, the genealogical and developmental accounts, have significant shortcomings. We propose a new account, the hierarchical-dependency account of homology, which avoids these shortcomings. Furthermore, our account provides for continuity between special, general, and serial homology.

The behavior of an organism, according to Merleau-Ponty, lays out a milieu through which significant phenomena of varying degrees of optimality elicit adjustment. This leads to the dialectical co-emergence of milieu and aptitude that is both the product and the condition of life. What is present as a norm soliciting optimization is species-specific, but it also depends on the needs of the organism and its prior experience. Although a rich entry point into biological phenomenology, Merleau-Ponty’s work does not adequately describe (...) milieu–aptitude development in interactions between organisms, but it can be assisted through employing Husserl’s three levels of analysis identified by Steinbock, extending all three modes into the biological world. In particular, generative analyses can address inter-organismal behavioral structures slighted in Merleau-Ponty’s work. Generative phenomenology is concerned with the cultural, historical, and intersubjective constitution of human experience and is generally thought to be solely of value in examining the structure of human phenomenality. However, the possibility of human generativity presupposes structures produced widely in the biological world. Ecological, embryogenic, and evolutionary development already depend on protocultural and historical processes creating and created through intercorporeal interaction. After developing the concept of biological generativity through a consideration of plant ecology, mammalian embryology, and insect mimicry, I conclude with implications for humans, who can participate in biological generativity not merely phenomenally, but phenomenologically. (shrink)

In 1979 Harvard biologists Stephen Jay Gould and Richard C. Lewontin published an essay entitled “The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme.” The target of their critique is a style of thinking rooted in “the near omnipotence of natural selection in forging organic design and fashioning the best among possible worlds.” According to Gould and Lewontin, adaptationists assume that all traits of an organism are products of natural selection, and that the traits (...) were favored by natural selection because they were optimal solutions to problems posed by the environment. Gould and Lewontin called the adaptationist program the Panglossian paradigm because they saw strong parallels between the arguments of Dr. Pangloss in Voltaire’s Candide and the arguments of adaptationists and optimality theorists in biology. (shrink)

This paper develops an account of explanation in biology which does not involve appeal to laws of nature, at least as traditionally conceived. Explanatory generalizations in biology must satisfy a requirement that I call invariance, but need not satisfy most of the other standard criteria for lawfulness. Once this point is recognized, there is little motivation for regarding such generalizations as laws of nature. Some of the differences between invariance and the related notions of stability and (...) resiliency, due respectively to Sandra Mitchell and Brian Skyrms, are explored. (shrink)

Frank E. Zachos offers a comprehensive review of one of today's most important and contentious issues in biology: the species problem. After setting the stage with key background information on the topic, the book provides a brief history of species concepts from antiquity to the Modern Synthesis, followed by a discussion of the ontological status of species with a focus on the individuality thesis and potential means of reconciling it with other philosophical approaches. More than 30 different species concepts (...) found in the literature are presented in an annotated list, and the most important ones, including the Biological, Genetic, Evolutionary and different versions of the Phylogenetic Species Concept, are discussed in more detail. Specific questions addressed include the problem of asexual and prokaryotic species, intraspecific categories like subspecies and Evolutionarily Significant Units, and a potential solution to the species problem based on a hierarchical approach that distinguishes between ontological and operational species concepts. A full chapter is dedicated to the challenge of delimiting species by means of a discrete taxonomy in a continuous world of inherently fuzzy boundaries. Further, the book outlines the practical ramifications for ecology and evolutionary biology of how we define the species category, highlighting the danger of an apples and oranges problem if what we subsume under the same name ("species") is in actuality a variety of different entities. A succinct summary chapter, glossary and annotated list of references round out the coverage, making the book essential reading for all biologists looking for an accessible introduction to the historical, philosophical and practical dimensions of the species problem. (shrink)

We defend the fundamental ontological-pragmatic principle that where there are continua in reality science is often forced to make partly fiat terminological delimitations. In particular, this principle applies when it comes to describing biological organisms, their parts, properties, and relations. Human-made fiat delimitations are indispensable at the level of both individuals and the natural kinds which they instantiate. The kinds of pragmatically based ‘fiatness’ that we describe can create incompatibilities and lack of interoperability even between properly designed ontologies, if not (...) appropriately handled. (shrink)

It is widely assumed that functional and dispositional properties are not identical to their physical base, but that there is some kind of asymmetrical ontological dependence between them. In this regard, a popular idea is that the former are realized by the latter, which, under the non-identity assumption, is generally understood to be a non-causal, constitutive relation. In this paper we examine two of the most widely accepted approaches to realization, the so-called ‘flat view’ and the ‘dimensioned view’, and we (...) analyze their explanatory relevance in the light of a number of examples from the life sciences, paying special attention to developmental phenomena. Our conclusion is that the emphasis placed by modern-day biology on such properties as variability, evolvability, and a whole collection of phenomena like modularity, robustness, and developmental constraint or developmental bias requires the adoption of a much more dynamic perspective than traditional realization frameworks are able to capture. (shrink)

In the first part of my analysis, I wish briefly to clarify the different modes of relation found in the living being, and point out the multiplicity of disciplines in which biologists use (explicitly or implicitly) the notion of laws. In the second part, I shall analyse the notion of universal laws in biology and examine successively: (1) accidental generalizations; (2) non-causal biological correlations; (3) the meaning of 'necessity' in these correlations; and (4) causal connections. Finally, in the (...) third part, I shall examine statistical laws and probabilistic laws in biology, in particular: (1) chance in biology; (2) probabilistic theories; and (3) relations between logical probability and statistical probability. (shrink)

In this paper the authors give a survey of biological phenomena , for which the term ‘differentiation’, used in the widest sense, has a meaningful application. The last chapter deals with some general aspects of differentiation and connected phenomena, such as polarity, symmetry, loss of potencies, dedifferentiation, redifferentiation, adifferentiation, regulation and integration.To prevent this article becoming too voluminous, the authors had to refrain from extending the treatment of differentiation to non-living matter and to human society.

Does biology have general laws that apply to all levels of biological organisation, across all evolutionary time? In their book “Biology’s first law: the tendency for diversity and complexity to increase in evolutionary systems” (2010), Daniel McShea and Robert Brandon propose that the most fundamental law of biology is that all levels of biological organisation have an underlying tendency to become more complex and diverse over time. A range of processes, most notably selection, can prevent the expression (...) of this tendency, but they predict that, on average, we should see that lineages tend toward greater diversity and complexity, driven by fundamentally neutral processes. Their hypothesis can be summarised as “diversity is easy, stasis is hard”. Here, I consider evidence for this “zero force evolutionary law”. It provides a fair description of evolutionary change at the genomic level, but the predictions of the proposed law are not met for broad scale patterns in the evolution of the animal kingdom. (shrink)

Are there laws in evolutionary biology? Stephen J. Gould has argued that there are factors unique to biological theorizing which prevent the formulation of laws in biology, in contradistinction to the case in physics and chemistry. Gould offers the problem of complexity as just such a fundamental barrier to biological laws in general, and to Dollos Law in particular. But I argue that Gould fails to demonstrate: (1) that Dollos Law is not law-like, (2) that the alleged failure (...) of Dollos Law demonstrates why there cannot be laws in biological science, and (3) that complexity is a fundamental barrier to nomologicality. (shrink)

In this paper I shall discuss the concept of reduction—ontological, methodological, and epistemological or theoretical—in the biological sciences, with special emphasis on genetics and evolutionary biology. I suggest that perhaps, because the biological world has a form different from the non-biological world, it is appropriate to think of terms or metaphors different from those we would use when trying to understand the inorganic world. As such, the attempt to show that the biological is simply a deductive consequence of the (...) physicochemical is doomed to failure. The philosophical complexity of reductionism on the one hand and its potential for advancing the study of biology on the other thus requires continuing the ongoing dialogue between philosophers and biologists. (shrink)

Unlike in physics, the category of thought experiment is not very common in biology. At least there are no classic examples that are as important and as well-known as the most famous thought experiments in physics, such as Galileo’s, Maxwell’s or Einstein’s. The reasons for this are far from obvious; maybe it has to do with the fact that modern biology for the most part sees itself as a thoroughly empirical discipline that engages either in real natural history (...) or in experimenting on real organisms rather than fictive ones. While theoretical biology does exist and is recognized as part of biology, its role within biology appears to be more marginal than the role of theoretical physics within physics. It could be that this marginality of theory also affects thought experiments as sources of theoretical knowledge. Of course, none of this provides a sufficient reason for thinking that thought experiments are really unimportant in biology. It is quite possible that the common perception of this matter is wrong and that there are important theoretical considerations in biology, past or present, that deserve the title of thought experiment just as much as the standard examples from physics. Some such considerations may even be widely known and considered to be important, but were not recognized as thought experiments. In fact, as we shall see, there are reasons for thinking that what is arguably the single most important biological work ever, Charles Darwin’s On the Origin of Species, contains a number of thought experiments. There are also more recent examples both in evolutionary and non-evolutionary biology, as we will show. Part of the problem in identifying positive examples in the history of biology is the lack of agreement as to what exactly a thought experiment is. Even worse, there may not be more than a family resemblance that unifies this epistemic category. We take it that classical thought experiments show the following characteristics: They serve directly or indirectly in the non-empirical epistemic evaluation of theoretical propositions, explanations or hypotheses. Thought experiments somehow appeal to the imagination. They involve hypothetical scenarios, which may or may not be fictive. In other words, thought experiments suppose that certain states of affairs hold and then try to intuit what would happen in a world where these suppositions are true. We want to examine in the following sections if there are episodes in the history of biology that satisfy these criteria. As we will show, there are a few episodes that might satisfy all three of these criteria, and many more if the imagination criterion is dropped or understood in a lose sense. In any case, this criterion is somewhat vague in the first place, unless a specific account of the imagination is presupposed. There will also be issues as to what exactly “non-empirical” means. In general, for the sake of discussion we propose to understand the term “thought experiment” here in a broad rather than a narrow sense here. We would rather be guilty of having too wide a conception of thought experiment than of missing a whole range of really interesting examples. (shrink)

Three metascientific concepts that have been object of philosophical analysis are the concepts oflaw, model and theory. The aim ofthis article is to present the explication of these concepts, and of their relationships, made within the framework of Sneedean or Metatheoretical Structuralism (Balzer et al. 1987), and of their application to a case from the realm of biology: Population Dynamics. The analysis carried out will make it possible to support, contrary to what some philosophers of science in general and (...) of biology in particular hold, the following claims: a) there are "laws" in biological sciences, b) many of the heterogeneous and different "models" of biology can be accommodated under some "theory", and c) this is exactly what confers great unifying power to biological theories. (shrink)

Levels of organization are structures in nature, usually defined by part-whole relationships, with things at higher levels being composed of things at the next lower level. Typical levels of organization that one finds in the literature include the atomic, molecular, cellular, tissue, organ, organismal, group, population, community, ecosystem, landscape, and biosphere levels. References to levels of organization and related hierarchical depictions of nature are prominent in the life sciences and their philosophical study, and appear not only in introductory textbooks and (...) lectures, but also in cutting-edge research articles and reviews. In philosophy, perennial debates such as reduction, emergence, mechanistic explanation, interdisciplinary relations, natural selection, and many other topics, also rely substantially on the notion. -/- Yet, in spite of the ubiquity of the notion, levels of organization have received little explicit attention in biology or its philosophy. Usually they appear in the background as an implicit conceptual framework that is associated with vague intuitions. Attempts at providing general and broadly applicable definitions of levels of organization have not met wide acceptance. In recent years, several authors have put forward localized and minimalistic accounts of levels, and others have raised doubts about the usefulness of the notion as a whole. -/- There are many kinds of ‘levels’ that one may find in philosophy, science, and everyday life—the term is notoriously ambiguous. Besides levels of organization, there are levels of abstraction, realization, being, analysis, processing, theory, science, complexity, and many others. In this article, the focus will be on levels of organization and debates associated with them, and other kinds of levels will only be discussed when they are relevant to this main topic. (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)

Biosemiotics is a growing fi eld that investigates semiotic processes in the living realm in an attempt to combine the fi ndings of the biological sciences and semiotics. Semiotic processes are more or less what biologists have typically referred to as “ signals, ” “ codes, ”and “ information processing ”in biosystems, but these processes are here understood under the more general notion of semiosis, that is, the production, action, and interpretation of signs. Thus, biosemiotics can be seen as (...) class='Hi'>biology interpreted as a study of living sign systems — which also means that semiosis or sign process can be seen as the very nature of life itself. In other words, biosemiotics is a field of research investigating semiotic processes (meaning, signification, communication, and habit formation in living systems) and the physicochemical preconditions for sign action and interpretation. -/- (...). (shrink)

Das allgemeine Prinzip der „Relativität der Begriffe” — vom Verfasser a. a. O. dargelegt — behauptet, dass ein und dieselbe Situation der Wirklichkeit auf verschiedene Weisen beschrieben werden kann, die sprachlich und begrifflich zwar verschieden sein mögen, doch grundsätzlich die gleichen bleiben. Die verbalen oder begrifflichen Unterschiede führen uns zu der falschen Annahme, dass den Elementen, welchen im Denken oder im sprachlichen Ausdruck weniger Bedeutung zugemessen wird, auch weniger Bedeuten in Wirklichkeit zukommen, oder dass sie weniger real sind.Die bedeutendste Anwendung (...) dieser Lehre auf die Biologie betrifft die Interpretation des „Individuellen”. Soll man das Individuum als eine Einheit verstehen, oder kommt der Begriff der Einheit einerseits den Teilen zu, wie z. B. Zellen, Molekülen und Atomen, oder andererseits höheren und synthetischen Einheiten wie z.B. Klassen, Arten, dem „élan vital”, u.s.w. ? Alle diese drei Ansichten haben etwas für sich, doch stehen auch jeder entscheidende Gegengründe gegenüber, so dass die einzig-mögliche Schlussfolgerung die Annahme der Begriffsrelativität ist. Jeder der drei Standpunkte ist nur in so weit wahr, als er etwas Positives beibringt, falsch jedoch solange er nur die beiden andern leugnet.Le principe de la relativité des concepts, ayant une application générale dans toutes: parties de la philosophie et de la science, est développé ailleurs par l'auteur. Ce principe propose qu'une situation quelconque peut être discutée dans plusieurs manières, se différant entre elles dans le choix des mots ou des concepts, tout en étant au fond indentiques. Les differences linguistiques ou conceptuelles nous mènent à l'assomption fausse que les éléments moins importants dans la pensée ou dans le langage sont moins importants dans la nature, ou même que ces éléments sont moins réels.En biologie, ce principe a une importance notable en ce qui concerne l'interprétation de l'individu. Doit-on entendre par l'individu les cellules, les molécules, les atomes, et les autres éléments qui le composent; ou bien l'individu même; ou encore doit-on oublier et l'individu et les éléments qui le composent, et baser sa philosophie sur les entités synthétiques telles que les espèces, les genres, et l'élan vital ? Chacune de ces trois opinions a des considérations en sa faveur; mais chacune d'elles se bute à des objections plus considérables encore qui l'empêchent d'être acceptée. La seule conclusion qui semble être possible est l'adoption du principe de la relativité des concepts, et l'assomption que chaque manière d'envisager l'individu est valide tant qu'elle a quelque chose de positif à dire; chaque manière est fausse quand elle nie Ja validité des autres points de vue. (shrink)

Propositions alone are not constitutive of science. But is the "non-propositional" side of science theoretically superfluous: must philosophy of science consider it in order to adequately account for science? I explore the boundary between the propositional and non-propositional sides of biological theory, drawing on three cases: Grinnell's remnant models of faunas, Wright's path analysis, and Weismannism's role in the generalization of evolutionary theory. I propose a picture of material model-building in biology in which manipulated systems of material objects function (...) as theoretical models. In each of the cases, material systems such as diagrams play important generative as well as presentational roles. (shrink)

It is often argued that biological generalizations have a distinctive and special status by comparison with the generalizations of other natural sciences, such as that biological generalizations are riddled with exceptions defying systematic and simple treatment. This special status of biology is used as a premise in arguments that posit a deprived explanatory, nomological, or methodological status in the biological sciences. I will discuss the traditional and still almost universally held idea that the biological sciences cannot (...) deal with exceptions and application conditions of their generalizations with their own distinctive and proprietary explanantia, but need the help of lower-level sciences to carry out this task. The idea of lower-level explanations of exceptions is connected to the idea that the biological sciences need lower-level sciences to better themselves and to the idea that biological sciences cannot provide reliable and extrapolatable results or explanations by themselves. I present counterexamples to the idea of lower-level explanations of exceptions in biology. I also discuss and refute more general arguments why the idea of lower-level explanations of exceptions has been held to hold in the special sciences, such as the screening-off and openness arguments. This suggest that there might be nothing special about the biological sciences vis-à-vis the more fundamental natural sciences, such as physics insofar as explanations of exceptions are concerned, and that the biological sciences can provide reliable and extrapolatable results or explanations by themselves. (shrink)

In his article Forme et Fonction Barge wrote in 1936 that living matter cannot be totally understood in terms of causality. In this paper we argue on the contrary that this is in principle possible.In order to develop our arguments, we discuss some basic and derived concepts used in morphology and functional anatomy. We also formulate comments on the so-called formal, functional and final elucidations.

In this paper we present a new framework of idealization in biology. We characterize idealizations as a network of counterfactual and hypothetical conditionals that can exhibit different "degrees of contingency". We use this idea to say that, in departing more or less from the actual world, idealizations can serve numerous epistemic, methodological or heuristic purposes within scientific research. We defend that, in part, this structure explains why idealizations, despite being deformations of reality, are so successful in scientific practice. For (...) illustrative purposes, we provide an example from population genetics, the Wright-Fisher Model. (shrink)

The emphasis of systems and synthetic biology on quantitative understanding of biological objects and their eventual re-design has raised the question of whether description and construction standards that are commonplace in electric and mechanical engineering are applicable to live systems. The tuning of genetic devices to deliver a given activity is generally context-dependent, thereby undermining the re-usability of parts, and predictability of function, necessary for manufacturing new biological objects. Tolerance and allowance are key aspects of standardization that need to (...) be brought to biological design. These should endow functional building blocks with a pre-specified level of confidence for bespoke biosystems engineering. However, in the absence of more fundamental knowledge, fine-tuning necessarily relies on evolutionary/combinatorial gravitation toward a fixed objective. (shrink)

There has been a significant amount of uncertainty and controversy over the prospects for general knowledge in ecology. Environmental decision makers have begun to despair of ecology's capacity to provide anything more than case by case guidance for the shaping of environmental policy. Ecologists themselves have become suspicious of the pursuit of the kind of genuine nomothetic knowledge that appears to be the hallmark of other scientific domains. Finally, philosophers of biology have contributed to this retreat from generality by (...) suggesting that there really are no laws in biology. This paper addresses these issues by providing a framework for thinking about general knowledge claims in ecology. It introduces a philosophical taxonomy that classifies generalizations into three broad categories – phenomenological, causal and theoretical. It then turns to the difficult problem of laws, arguing that, while there are probably no laws as that term has been understood in philosophy of science, it doesn't follow that everything in ecology is equally contingent. A mechanism for recognizing degrees of contingency in ecological generalizations is developed. The paper concludes by examining the implications of the analysis for the controversies noted at the outset. (shrink)

The prelims comprise: Nuclear Transfer at Present Potential Applications Implications of the Present Inadequacies General Conclusions.

This article considers claims that biology should seek general theories similar to those found in physics but argues for an alternative framework for biological theories as collections of prototypical interlevel models that can be extrapolated by analogy to different organisms. This position is exemplified in the development of the Hodgkin‐Huxley giant squid model for action potentials, which uses equations in specialized ways. This model is viewed as an “emergent unifier.” Such unifiers, which require various simplifications, involve the types of (...) heuristics discussed in Wimsatt’s writings on reduction, but with a twist. Here, the heuristics are used to generate emergent rather than reductive explanations. †To contact the author, please write to: Department of History and Philosophy of Science, University of Pittsburgh, 1017 Cathedral of Learning, Pittsburgh, PA 15260; e‐mail: [email protected]. (shrink)

In this paper we present a new framework of idealization in biology. We characterize idealizations as a network of counterfactual and hypothetical conditionals that can exhibit different “degrees of contingency”. We use this idea to say that, in departing more or less from the actual world, idealizations can serve numerous epistemic, methodological or heuristic purposes within scientific research. We defend that, in part, this structure explains why idealizations, despite being deformations of reality, are so successful in scientific practice. For (...) illustrative purposes, we provide an example from population genetics, the Wright-Fisher Model. (shrink)

This paper sets out to analyze how causation works by focusing on biology, as represented by epidemiology and by scientific information on how the body works (“physiology”). It starts by exploring the specificity of evolved physiological systems, in which evolutionary, developmental and proximal causes all fit together, and the concept of function is meaningful; in contrast, this structure does not apply in epidemiology (or outside biology). Using these two contrasting branches of biology, I examine the role both (...) of mechanism and of difference making in causation. I find that causation necessarily involves both mechanism and difference making, and that they play complementary roles. Both are seen as ontologically necessary, even if the evidence is not always available for both. Influential monist accounts that focus on one of these, at the expense of ignoring the other, are found to be inadequate on these and on other grounds. Recent attempts to combine them are reviewed, notably that of Russo and Williamson (Int Stud Philos Sci 21:157–170, 2007), and it is argued that their epistemic view requires there to be a source of the different types of evidence that a rational agent would consider, and that this source must be ontic. I then analyze how causal relationships work in evolved physiological systems and in those studied by epidemiology, with a particular focus on how mechanism interacts with input. Finally, I consider this concept of causation from the perspective of everyday language, and of its possible generalisability outside biology. (shrink)

Interdisciplinary integration has fundamental limitations. This is not sufficiently realized in science and in philosophy. Concerning scientific theories there are many examples of pseudo-integration which should be unmasked by elementary philosophical analysis. For example, allegedly over-arching theories of stress which are meant to unite biology and psychology, upon analysis, turn out to represent terminological rather than substantive unity. They should be replaced by more specific, local theories. Theories of animal orientation, likewise, have been formulated in unduly general terms. A (...) natural history approach is more suitable for the study of animal orientation. The tendency to formulate overgeneral theories is also present in evolutionary biology. Philosophy of biology can only deal with these matters if it takes a normative turn. Undue emphasis on interdisciplinary integration is a modern variant of the old unity of science ideal. The replacement of the ideal by a better one is an important challenge for the philosophy of science. (shrink)

The present essay aims at integrating different concepts of meaning developed in semiotics, biology, and cognitive science, in a way that permits the formulation of issues involving evolution and development. The concept of sign in semiotics, just like the notion of representation in cognitive science, have either been used too broadly, or outright rejected. My earlier work on the notions of iconicity and pictoriality has forced me to spell out the taken-forgranted meaning of the sign concept, both in the (...) Saussurean and the Peircean tradition. My work with the evolution and development of semiotic resources such as language, gesture, and pictures has proved the need of having recourse to a more specified concept of sign. To define the sign, I take as point of departure the notion of semiotic function (by Piaget), and the notion of appresentation (by Husserl). In the first part of this essay, I compare cognitive science and semiotics, in particular as far as the parallel concepts of representation and sign are concerned. The second part is concerned with what is probably the most important attempt to integrate cognitive science and semiotics that has been presented so far, The Symbolic Species, by Terrence Deacon. I criticize Deacon’s use of notions such as iconicity, indexicality, and symbolicity. I choose to separate the sign concept from the notions of iconicity, indexicality, and symbolicity, which only in combination with the sign give rise to icons, indices, and symbols, but which, beyond that, have other, more elemental, uses in the world of perception. In the third part, I discuss some ideas about meaning in biosemiotics, which I show not to involve signs in the sense characterised earlier in the essay. Instead, they use meaning in the general sense of selection and organisation, which is a more elementary sense of meaning. Although I admit that there is a possible interpretation of Peirce, which could be taken to correspond to Uexküll’s idea of functional circle, and to meaning as function described by Emmeche and Hoffmeyer, I claim thatthis is a different sense of meaning than the one embodied in the sign concept. Finally, I suggest that more thresholds of meaning than proposed, for instanceby Kull, are necessary to accommodate the differences between meaning (in the broad sense) and sign (as specified in the Piaget–Husserl tradition). (shrink)

What follows is a discussion of three sets of experimental results that deal with various aspects of universal biological understanding among American and Maya children and adults. The first set of experiments shows that by the age of four-to-five years urban American and Yukatek Maya children employ a concept of innate species potential, or underlying essence, as an inferential framework for understanding the affiliation of an organism to a biological species, and for projecting known and unknown biological properties to organisms (...) in the face of uncertainty. The second set of experiments shows that the youngest Maya children do not have an anthropocentric understanding of the biological world. Children do not initially need to reason about non-human living kinds by analogy to human kinds. The third set of results show that the same taxonomic rank is cognitively preferred for biological induction in two diverse populations: people raised in the Mid-western USA and Itza' Maya of the Lowland Meso-american rainforest. This is the generic species  the level of oak and robin. These findings cannot be explained by domain-general models of similarity because such models cannot account for why both cultures prefer species-like groups in making inferences about the biological world, although Americans have relatively little actual knowledge or experience at this level. The implication from these experiments is that folk biology may well represent an evolutionary design: universal taxonomic structures, centred on essence-based generic species, are arguably routine products of our ‘habits of mind,' which may be in part naturally selected to grasp relevant and recurrent ‘habits of the world.' The science of biology is built upon these domain-specific cognitive universals: folk biology sets initial cognitive constraints on the development of any possible macro-biological theory, including the initial development of evolutionary theory. Nevertheless, the conditions of relevance under which science operates diverge from those pertinent to folk biology. For natural science, the motivating idea is to understand nature as it is ‘in itself,' independently of the human observer. From this standpoint, the species-concept, like taxonomy and teleology, may arguably be allowed to survive in science as a regulative principle that enables the mind to readily establish stable contact with the surrounding environment, rather than as an epistemic concept that guides the search for truth. (shrink)

This paper consists of four parts. Part 1 is an introduction. Part 2 evaluates arguments for the claim that there are no strict empirical laws in biology. I argue that there are two types of arguments for this claim and they are as follows: (1) Biological properties are multiply realized and they require complex processes. For this reason, it is almost impossible to formulate strict empirical laws in biology. (2) Generalizations in biology hold contingently but laws (...) go beyond describing contingencies, so there cannot be strict laws in biology. I argue that both types of arguments fail. Part 3 considers some examples of biological laws in recent biological research and argues that they exemplify strict laws in biology. Part 4 considers the objection that the examples in part 3 may be strict laws but they are not distinctively biological laws. I argue that given a plausible account of what distinctively biological means, such laws are distinctively biological. (shrink)

Since the early 20th century underdetermination has been one of the most contentious problems in the philosophy of science. In this article I relate the underdetermination problem to models in biology and defend two main lines of argument: First, the use of models in this discipline lends strong support to the underdetermination thesis. Second, models and theories in biology are not determined strictly by the logic of representation of the studied phenomena, but also by other constraints such as (...) research traditions, backgrounds of the scientists, aims of the research and available technology. Convincing evidence for the existence of underdetermination in biology, where models abound, comes both from the fact that for a natural phenomenon we can create a number of candidate models but also from the fact that we do not have a universal rule that would adjudicate among them. This all makes a strong case for the general validity of underdetermination thesis. (shrink)

The problem of synthesis in biology may have reference to the evolutionary origin of living organisms in past time, a process not directly observable but conceivably reconstructible in broad outline: thus to the biochemist this evolution may appear as the evolution of the special biological compounds, to the psychologist as the evolution of “mind”—or at least of types of behavior. Or the problem may refer to the synthesis of the individual animal or plant, a process of construction which typically (...) starts from a detached portion of a parent organism, such as an egg or seed; this is the problem of individual development or ontogeny and is not essentially different from the general problem of growth. But it is clear that the processes of phyletic evolution and of ontogeny must be considered together, since evolutionary history is in reality the history of a succession of individual organisms, each developing from its germ, i.e. of ontogenies; and the ontogenetic process, so faithfully repeated in each individual as it comes into existence, is itself a product of evolution, having originated in the remote past. The succession of individuals has undergone progressive diversification, culminating in the present condition. We may describe our problem, then, as the problem of the factors underlying the synthesis of a highly special process, that by which the diffusely distributed nonliving materials and energies of nature are brought together in a special kind of unification and transformed into a living organism. (shrink)

Evolutionary convergence is often appealed to in support of claims about multiple realization. The idea is that convergence shows that the same function can be realized by different kinds of structures. I argue here that the nature of convergence is more complicated than it might appear at first look. Broad claims about convergence are made by biologists during general discussions of the mechanisms of evolution. In their specialized work, though, biologists are often more limited in the claims they make. I (...) will examine a standard example to show how claims about convergence can be oversimplified. (shrink)

In discussion of mechanisms, philosophers often debate about whether quantitative descriptions of generalizations or qualitative descriptions of operations are explanatorily fundamental. I argue that these debates have erred by conflating the explanatory roles of generalizations and patterns. Patterns are types of variations within or between quantities in a mechanism over time or across conditions. While these patterns must often be represented in addition to descriptions of operations in order to explain a phenomenon, they are not equivalent to (...) class='Hi'>generalizations because their explanatory role does not depend on any specific facts about their scope or domain of invariance. (shrink)

Durante las últimas décadas, la biología ha sido objeto de una considerable proliferación teórica y subdisciplinar, hecho que suscita la pregunta acerca de su unidad. Por ello, a partir del abandono del reduccionismo como estrategia unificadora, el interrogante filosófico es qué otras formas alternativas de relaciones subdisciplinares son posibles, y si dichas relaciones logran dar unidad a la biología. En el presente artículo, a partir de una breve consideración de algunos de los problemas que el programa reduccionista ha tenido en (...) biología, analizaremos diferentes tipos de relaciones que se encuentran entre las subdisciplinas de la biología contemporánea. En particular, indagaremos cuatro de las principales propuestas que pueden encontrarse en la literatura filosófica especializada; ofrecemos entonces dos nuevas propuestas de relación interdisciplinar: el isomorfismo de la biología evolutiva, e la importación/exportación de cuerpos teóricos, propia de la relación entre la ecología y la fisiología. Finalmente, presentaremos algunas consideraciones en torno al objetivo de la unidad de la ciencia en general, como también acerca de la clase de cohesión que creemos posible para la biología a partir de nuestros análisis, defendiendo la idea de un pluralismo de las relaciones interdisciplinares y de la unidad como un fenómeno local. Over the last decades, in biology there has been a proliferation of subdisciplines and theories, and this poses a question about its unity. Consequently, after reductionism was abandoned as a unifying strategy, philosophical questions have been raised about the possibility of alternative forms of relations among the subdisciplines, and whether they can effectively accomplish a unity of biology. This article starts with a brief consideration of some of the problems that the reductionist program confronts in biology, and then analyzes different kind of relations that are present among the subdisciplines of contemporary biology. In particular, we investigate four of the main proposals that can be found in the specialized philosophical literature; and then we propose two models of inter-disciplinary relations: isomorphism in evolutionary biology, and import/export of theoretical corpus, present in the relation between ecology and physiology. Finally, we offer a few ideas on unity as a goal for science in general, and also about the kind of cohesion that we think to be possible for biology based on our analysis. Thus, we defend the idea of pluralism of inter-disciplinary relations and of unity as a local phenomenon. (shrink)