The use of informational terms is widespread in molecular and developmental biology. The usage dates back to Weismann. In both protein synthesis and in later development, genes are symbols, in that there is no necessary connection between their form (sequence) and their effects. The sequence of a gene has been determined, by past natural selection, because of the effects it produces. In biology, the use of informational terms implies intentionality, in that both the form of the signal, and the response (...) to it, have evolved by selection. Where an engineer sees design, a biologist sees natural selection. (shrink)

The concept of information tempts us as a theoretical primitive, partly because of the respectability lent to it by highly successful applications of Shannon’s information theory, partly because of its broad range of applicability in various domains, partly because of its neutrality with respect to what basic sorts of things there are. This versatility, however, is the very reason why information cannot be the theoretical primitive we might like it to be. “Information,” as it is (...) variously used, is systematically ambiguous between whether it involves continuous or discrete quantities, causal or noncausal relationships, and intrinsic or relational properties. Many uses can be firmly grounded in existing theory, however. Continuous quantities of information involving probabilities can be related to information theory proper. Information defined relative to systems of rules or conventions can be understood relative to the theory of meaning . A number of causal notions may possibly be located relative to standard notions in physics. Precise specification of these distinct properties involved in the common notion of information can allow us to map the relationships between them. Consequently, while information is not in itself the kind of single thing that can play a significant unifying role, analyzing its ambiguities may facilitate headway toward that goal. (shrink)

The history of the idea of biological progress shows that it is not a selfexplanatory category, so a clear definition is required. Biological progress exists if: “more progressive” is defined as “more complex” – in that case evolution is synonymous with progress, i.e. development from simple to complex, from homogeneous to heterogeneous; we perceive the expression “more progressive” as more successful in relation to the environment, in these terms some groups in the history of life were more progressive (...) because/so that they survived, while others were retrogressive or less progressive because/so that they died out; on the other hand, within their ecological niches, certain forms of life are perfectly adapted to their environment as long as it is stable ; we take the span or reach of a potential adaptation of populations as a measure. However, there is no active, innovative problem solving in relation to the environment either with plants or animals – only the variability mechanism / selection is in place, automatism, instinct. In the light of the above-mentioned biological criteria, man is the most complex living creature by his constitution, he is the least dependent on the environment and can be innovative in relation to the environment. Man is the only living creature capable of establishing an active relationship with the environment through his special tool – culture. Considering the level of organization and quantity of information, the mammal genome is more progressive than the bacterium genome, while the human genome comprises most information which makes man the most progressive living thing. We can talk about biological progress if we define progressiveness as advancement toward complexity of organisation, but sometimes the simplification of structure enables survival. It seems that we can talk about progressivenessin biology only if we accept the anthropic principle – that is why only cultural progress is possible. Information is the link between biological and cultural-anthropological successfulness. Biological information is a “complete” piece of information to an animal. To a human being, it is only a condicio sine qua non for the reality of human spirit which receives, keeps and generates information. Progress can be measured according to the capability of establishing an active and innovative relationship with the environment, but only within some sort of anthropocentric outlook which is a criterion of value. It is not possible to talk about progressiveness of life if man is not the measure of all things. (shrink)

Chapter 1 First Person Access to Mental States. Mind Science and Subjective Qualities -/- Abstract. The philosophy of mind as we know it today starts with Ryle. What defines and at the same time differentiates it from the previous tradition of study on mind is the persuasion that any rigorous approach to mental phenomena must conform to the criteria of scientificity applied by the natural sciences, i.e. its investigations and results must be intersubjectively and publicly controllable. In Ryle’s view, philosophy (...) of mind needs to adopt an antimentalist stance to achieve this aim. Antimentalism not only definitively rejects the idea that mind is a substance separated from the body, it also denies that mental phenomena radically differ from physical phenomena by virtue of several unique features. Most problematically, mental phenomena have a conscious character (mental states are related to specific qualitative feelings) and are accessible only to the first-person (only the subject knows directly what s/he is experiencing inside his/her mind). Ryle takes a strong stance on antimentalism going so far as to maintain that an approach to mind which aims to meet the criteria of scientificity set by the natural sciences must avoid any reference to internal, unobservable mental states. In his view (which is considered a specifically philosophical version of psychological behaviorism and also addresses questions put forward in psychological research), mental states can be redescribed in terms of behavioral dispositions. In this chapter, we address the historical roots of the antimentalist view and analyze its relation to the later tradition of research on mind. We show that, compared to the antimentalist stance, functionalism and cognitivism take a step back when they maintain that direct reference to mental states is necessary since mental states cause and therefore explain human behavior. This step backwards is often interpreted as a return to mentalism. However, this is only partially true. Indeed, we suggest that these later traditions retain one important element of Ryle’s antimentalism, i.e. the idea that mental states must be uniquely identified using external and publicly observable criteria, while excluding any reference to introspection and those qualitative dimensions of a mental state, which are accessible only to the first-person. According to the perspective we put forward, this epistemological stance has continued to influence contemporary research on mind and current philosophical and psychological theories which both tend to exclude the subjective qualities of human experience from their accounts of how the mind works. The issue we raise here is whether this is legitimate or whether subjective qualities do play a role with respect to the way our mind works. The conclusion of this chapter anticipates the argument the book makes in in favor of this latter position, starting from a particular angle, i.e. the problem of how we categorize concepts related to our internal states. -/- Chapter 2 The Misleading Aspects of the Mind/Computer Analogy. The Grounding Problem and the Thorny Issue of Propriosensitive Information -/- Abstract. After the crisis of behaviorism, cognitivism and functionalism became the predominant models in the field of psychology and of philosophy, respectively. Their success is mainly due to the new key they use for interpreting mental processes: the mind/computer analogy. On the basis of this analogy, mental operations are seen as cognitive processes based on computations, i.e. on manipulations of abstract symbols which are in turn understood as informational unities (representations). This chapter identifies two main problems with this model. The first is how these symbols can relate to and communicate with perception and thus allow us to identify and classify what we perceive through the senses. Here we limit ourselves to presenting this issue in relation to the classical symbol grounding problem originally put forward by Harnad on the basis of Searle’s Chinese room argument. An attempt to address the problem raised here will be made in chap. 3. The second point we discuss in relation to the mind/computer analogy concerns the idea of information it fosters. Indeed, following this analogy, information is something available in the external world which can be captured by the senses and transmitted to the central system without being influenced or modified by the procedures of transmission. This perspective does not take into account that – unlike computers – in living beings information is acquired by means of the body. As Ulric Neisser has already pointed out, the body is itself an informational source that provides us with additional sensory experience that influences (modifies or complements) the information extracted from the external world by the senses. To develop this line of analysis and to determine exactly what information is provided by the body and how this might influence cognition, we examine Sherrington’s and Gibson’s positions. Moving on from their views, we qualify bodily information in terms of ‘proprioception’. We use ‘proprioception’ in a broad sense to describe any kind of experience we have of our internal states (including postural information as well as sensations related to the general state of the body and its parts). Following Damasio’s and Craig’s studies, we further elaborate this position, arguing that living beings are equipped with an internal propriosensitive monitoring system which maps all the changes that constantly occur in our body and that give us perceptual (‘proprioceptive’ or propriosensitive) information about what happens inside us. Moreover, relying on Goldie’s and Ratcliffe’s view, we show that emotional information can also be considered as a form of ‘proprioception’ which contributes to determining everything we perceive. This analysis leads us to the second main thesis of this book: ‘proprioception’ is a form of internal perception and it is an essential component of the sensory information we can access and use for all cognitive purposes. -/- Chapter 3 Semantic Competence from the Inside: Conceptual Architecture and Composition -/- Abstract. Concepts are essential constituents of thought: they are the instruments we use to categorize our experience, i.e. to classify things and group them together in homogeneous sets. Here we define concepts as the internal mental information (representations) that allows us, among other things, to master words in natural language. By analyzing the way in which individuals master word meanings we explore a number of hypotheses regarding the nature of concepts. Following Diego Marconi’s research, we differentiate between two kind of abilities that underpin lexical competence – so-called ‘referential’ and ‘inferential competence’ – and we suggest that, in order to support these abilities, concepts must also include two corresponding kinds of information, i.e. inferential and referential information. We point out that the most widely used and acknowledged theories of concepts do not make this distinction, instead broadly characterizing the information used for categorization in terms of propositionally described feature lists. However, we show that while feature lists can explain inferential competence, they do not account for referential competence. To address the issue of referential competence we examine Ray Jackendoff’s hypothesis that to account for the possibility of linking perceptual and conceptual information we need to assume the existence of a (visual) representation that encodes the geometric and topological properties of objects and bridges the gap between the percept and the concept. Furthermore, we analyze the extension of this work by Jesse Prinz who introduced the notion of a proxytype, a perceptual representation of a class of objects that incorporates structural and parametric information related to their appearance. However, as we point out, proxytypes can only explain the relationship between perception and concepts with respect to instances that can be perceived through the senses and that belong to the same class by virtue of their physical similarity. We suggest that this notion be extended to include larger conceptual classes. To accomplish this, we further develop Mark Johnson, George Lakoff and Jean Mandler’s idea of a schematic image and argue that conceptual representations include a perceptual schema. Perceptual schemata are non-linguistic, structured experiential gestalts (patterns or maps) that make use of information taken from all sensory modalities, including body perception. They accomplish a quasi-conceptual function: they allow us to recognize and to classify different instances. In this work, we hypothesize that perceptual schemata are an essential component of concepts, but not identical to them. Instead, we suggest that concepts include both perceptual and propositional information with perceptual schemata providing the ‘perceptual core concept’ that grounds related propositional information. -/- Chapter 4 In the Beginning There Were Categories. The Bodily Origin of Prelinguistic Categorical Organization: The Example of Folkbiological Taxonomies -/- Abstract. Studies of categorization in psychology and the cognitive sciences have made use of the notions of ‘category’ and ‘concept’ without precisely defining what is meant by either; in fact, often these terms have been used as synonyms, making it difficult to address specific issues related to conceptual development. This chapter begins by discussing the definitions of, as well as the distinctions between, ‘categories’ and ‘concepts’ in the classical philosophical tradition (Aristotle, Kant and Husserl). We introduce our view of categories with reference to Husserl. Categorization is defined as the way in which our experience is originally (pre-linguistically) organized in a passive and fully unconscious manner on the basis of universal structuring principles. Conceptualization is explained as a later process in which the earlier categorical macro-classes are further subdivided into more specific and detailed sets; this later process also relies on linguistic learning and exposure to culture. On the basis of Ray Jackendoff, Jean Mandler, George Lakoff and Mark Johnson’s work, we hypothesize that categorization is a two-step process that begins with the formation of homogeneous sets of entities partitioned into regions that describe the ontological boundaries of the objects that humans perceive (categories) and continues at a later stage with the development of more specific classifications (concepts). In this chapter, we mainly address three related issues: Why should we assume that there is categorical organization which precedes the development of a conceptual system? How do categories and concepts relate to each other? Shall we hypothesize that categories are innate or that they are formed before concepts on the basis of information and organizational structure available at a very early developmental stage? We show that categorical partitions are necessary for categorization and, following Mandler, that the general categories we form at an early age do not match our adult superordinate concepts. As for the third issue, we argue that there might be no need to assume that categories are innately present in the human mind, since their formation can be explained – at least in certain cases – by basic mechanisms that work on body (propriosensitive) information. This hypothesis will not be discussed in general, but in relation to a particularly relevant example of categorical partition, i.e. the folk-biological dichotomy between ANIMATE/INANIMATE. This is compared with other dichotomies that derive from it, but are not directly categorical such as LIVING/NON-LIVING and BIOLOGICAL/NON-BIOLOGICAL. -/- Chapter 5 Internal States: From Headache to Anger. Conceptualization and Semantic Mastery -/- Abstract. Here we ask if we can also apply the distinction between referential and inferential competence we introduced in Chapter 3 to words that do not refer to things that are perceived using the external senses, especially to words/concepts that denote bodily experiences (such as pain, thirst, hunger, etc.) or emotions. We introduce and discuss the hypothesis that – even though such words/concepts do not refer to intersubjectively identifiable entities in the external world – they do have a kind of referent that can be accessed via direct perception, more specifically ‘proprioception’, as we have defined it in terms of all propriosensitive information we can consciously access. In the first part of the chapter, we specifically consider terms denoting bodily experiences such as ‘pain’ or ‘hunger’ and argue that their referents are identified and classified from a first-personal point of view on the basis of four main characteristics: their specific intensity, their localization in the body, their co-occurrence with other signals and above all their specific qualitative sensations. Emotions are addressed in the second part of the chapter. We suggest that there is a continuity between bodily experiences and emotions. In particular, we argue for a perceptual theory of emotions in line with that proposed by James and Lange at the end of the 19th century and developed more recently by authors such as Damasio (see also chap. 2§5, §6). The hypothesis we put forward is that the referential information that supports the categorization of emotions and therefore also our mastery of terms referring to emotions consists in the perception (i.e. the ‘proprioception’) of those bodily states and changes in bodily states which constitute our emotional experience. In the context of this discussion we examine some objections to this line of reasoning that arise from a cognitivist perspective and following authors such as Oatley, Johnson-Laird and Frijda, we distinguish between basic emotions that can be identified and classified solely on the basis on how they feel and complex emotions whose identification and classification additionally depends on cognitive factors. To describe how emotions are identified and classified on the basis of how they feel, we rely on Marcel and Lambie’s distinction between an ‘emotion state’ and an ‘emotion experience’. Both notions indicate kinds of feelings that we consciously experience. However, they describe first-order and second order emotion awareness respectively. The emotion state is the feeling we have of the bodily states and changes that occur when we are experiencing an emotion, while the emotion experience is the fully developed and integrated emotion we both experience and are, with reflection, aware of experiencing. On the basis of this differentiation, we also show that the same characteristics that aid in the identification and classification of bodily experiences (specific qualitative sensations; somatic localization; specific intensity; presence/absence of specific concomitant sensations) can also be used for the identification and classification of emotions – at least basic emotions. In the last two sections of the chapter we present some clinical evidence on the semantic competence of people who suffer from Alexithymia and Autism Spectrum Disorder which supports the conclusions of our preceding analyses. -/- Chapter 6 The ‘Proprioceptive’ Component of Abstract Concepts -/- Abstract. In this chapter, we address the issue of whether the mastery of abstract words requires only inferential knowledge and thus, if the concepts that support the mastery of abstract words include only linguistic information. We start by differentiating the notions of ‘abstract’ and ‘general’ which are often erroneously confused. We then identify a strict definition of abstract, as contrasted with ‘concrete’, that applies to words or concepts whose referent cannot be experienced by the senses. We argue that abstract words/concepts would be better described as theoretical, because they are usually conceived as structured sets of inferential knowledge expressed linguistically; that is, as small theories. Pointing out parallels with Carnap’s analysis of this issue in philosophy of science, we hypothesize that words/concepts denoting non-observable entities are not all ‘equally theoretical’, because their link to sensory experience can be stronger or weaker. We revive the distinction, inspired by Quine, between theoretical and intertheoretical concepts/words. This distinction relies on the fact that the former – unlike the latter – retains a strong, although indirect, connection with perception. In Quine’s discussion, perception is understood uniquely in terms of observability, i.e. of external sensory experience. Here we argue, however, that bodily, ‘proprioceptive’ (i.e. propriosensitive) experience can also serve to referentially ground theoretical (i.e. abstract) concepts/words. We frame this issue using the example of the theoretical concept ‘freedom’ and Lakoff’s hypothesis that this concept is developed on the basis of bodily information. We contrast this with the example of ‘democracy’ which more closely resembles an intertheoretical concept/word. Furthermore, we show that one of the classical views put forward in psycholinguistic research to explain how abstract concepts are mentally represented – i.e. Paivio’s Dual Coding Theory – points in the same direction as our analysis. The same is true of Barsalou’s work suggesting that we use internal information to understand at least some abstract words. To sustain this position, we put forward two lines of evidence: the first comes from psycholinguistic studies while the second examines deficits of semantic competence exhibited by people with Autism Spectrum Disorder. On the basis of our analysis, we put forward a classification that distinguishes between different kinds of concreteness and different degrees of abstraction: concepts/words referring to body experiences and basic emotions are described as analogous to concrete concepts/words because they are grounded in perceptual (i.e. propriosensitive) experience, while abstract concepts/words are considered more or less abstract depending on whether they are intratheoretical (and rely entirely on inferential information) or theoretical (and are partially grounded in perceptual – or more often in propriosensitive perceptual – information). In the last section of the chapter we consider two scales that have been used in psycholinguistic research to measure the degree of concreteness vs. abstractness of words and we show that – used conjointly – they can provide a measure of the internal vs. external grounding of specific words. (shrink)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction (...) between form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

Maynard Smith notes that he provides a natural history and not a philosophical analysis of the use of concepts of information in contemporary biology. Just a natural history, however rich, would do little to resolve the ongoing controversy about the role of these concepts in biology. None of the disputants deny that the biological use of these concepts is pervasive. The dispute is about whether these concepts—and the framework in which they are embedded—continue to be of explanatory value (...) in contemporary biology. Fortunately, Maynard Smith does much more than provide a natural history: his contribution is also a sustained attempt to justify many of the uses of information in biology. (shrink)

Progress has become a suspect concept in evolutionary biology, not the least because the core concepts of neo-Darwinism do not support the idea that evolution is progressive. There have been a number of attempts to account for directionality in evolution through additions to the core hypotheses of neo-Darwinism, but they do not establish progressiveness, and they are somewhat of an ad hoc collection. The standard account of fitness and adaptation can be rephrased in terms of information theory. From (...) this, an information of adaptation can be defined in terms of a fitness function. The information of adaptation is a measure of the mutual information between biota and their environment. If the actual state of adaptation lags behind the state of optimal adaptation, then it is possible for the information of adaptation to increase indefinitely. Since adaptations are functional, this suggests the possibility of progressive evolution in the sense of increasing adaptation. Keywords: evolution, information, adaptation, fitness, entropy, progress.. (shrink)

In this chapter we examine the relationship between biological information, the key biological concept of specificity, and recent philosophical work on causation. We begin by showing how talk of information in the molecular biosciences grew out of efforts to understand the sources of biological specificity. We then introduce the idea of ‘causal specificity’ from recent work on causation in philosophy, and our own, information theoretic measure of causal specificity. Biological specificity, we argue, (...) is simple the causal specificity of certain biological processes. This, we suggest, means that causal relationships in biology are ‘informational’ relationships simply when they are highly specific relationships. Biological information can be identified with the storage, transmission and exercise of biological specificity. It has been argued that causal relationships should not be regarded as informational relationship unless they are ‘arbitrary’. We argue that, whilst arbitrariness is an important feature of many causal relationships in living systems, it should not be used in this way to delimit biological information. Finally, we argue that biological specificity, and hence biological information, is not confined to nucleic acids but distributed among a wide range of entities and processes. (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)

The concept of information has acquired a strikingly prominent role in contemporary biology. This trend is especially marked within genetics, but it has also become important in other areas, such as evolutionary theory and developmental biology, particularly where these fields border on genetics. The most distinctive biological role for informational concepts, and the one that has generated the most discussion, is in the description of the relations between genes and the various structures and processes that genes play (...) a role in causing. For many biologists, the causal role of genes should be understood in terms of their carrying information about their various products. That information might require the cooperation of various environmental factors before it can be "expressed," but the same can be said of other kinds of message. An initial response might be to think that this mode of description is entirely anchored in a set of well-established facts about the role of DNA and RNA within protein synthesis, summarized in the familiar chart representing the "genetic code," mapping DNA base triplets to amino acids. However, informational enthusiasm in biology predates even a rudimentary understanding of these mechanisms (Schrodinger 1944). And more importantly, current applications of informational concepts extend far beyond anything that can receive an obvious justification in terms of the familiar facts about the specification of protein molecules by DNA. This includes: 1 (i) The description of whole-organism phenotypic traits (including complex behavioral traits) as specified or coded for by information contained in the genes, (ii) The treatment of many causal processes within cells, and perhaps of the wholeorganism developmental sequence, in terms of the execution of a program stored in the genes, (iii) The idea that genes themselves, for the purpose of evolutionary theorizing, should be seen as, in some sense, "made" of information.. (shrink)

Communication is an important feature of the living world that mainstream biology fails to adequately deal with. Applying two main disciplines can be contemplated to fill in this gap: semiotics and information theory. Semiotics is a philosophical discipline mainly concerned with meaning; applying it to life already originated in biosemiotics. Information theory is a mathematical discipline coming from engineering which has literal communication as purpose. Biosemiotics and information theory are thus concerned with distinct and complementary possible meanings (...) of the word ‘communication’. Since literal communication needs to be secured so as to enable semantics being communicated, information theory is a necessary prerequisite to biosemiotics. Moreover, heredity is a purely literal communication process of capital importance fully relevant to literal communication, hence to information theory. A short introduction to discrete information theory is proposed, which is centred on the concept of redundancy and its use in order to make sequences resilient to errors. Information theory has been an extremely active and fruitful domain of researches and the motor of the tremendous progress of communication engineering in the last decades. Its possible connections with semantics and linguistics are briefly considered. Its applications to biology are suggested especially as regards error-correcting codes which are mandatory for securing the conservation of genomes. Biology needs information theory so biologists and communication engineers should closely collaborate. (shrink)

The question that probably emerges when the title of this work is read is if it is possible to establish any relation between philosophy and a scientific discipline such as molecular biology. The common opinion, shared even by many renowned biologists and philosophers, is that each of these disciplines has got its own without taking into account the results of the other. However, the relation between science and philosophy is nowadays one of the most challenging topics, where philosophers and biologists (...) meet and each other to better understand what life is and how it works. Philosophical concepts such as information, causality, semiotics and function can be seen as instruments for a philosophical approach to biological topics. The aim of this work is to see if, studying a biological example in depth, there are elements that fit with the informational paradigm that is proposed as a philosophical framework. Biology has been considered as a discipline in which objects can be reduced to the laws of physics and chemistry. A different approach can be seen in this work. The philosophy of Charles Sanders Peirce can help us to see biological systems as informational systems, where molecules are more than their chemical structure, indeed, the cell can deal with them from a semiotic point of view; that is, treating them as signs that stand for other molecules or processes, allowing the system to canalize all this information to its own benefit. (shrink)

This paper discussses various concepts of biological information with particular attention being paid to genetic information.

In a recent essay in this journal, John Maynard Smith argues that the often expressed idea that the genome is the repository of meaningful information is not merely a heuristically useful metaphor. Instead, he contends, it is a central idea in contemporary microbiology. While I am in general agreement with Maynard Smith on this issue, his account suffers, I believe, from using an inappropriate concept of ‘information.’ One result of this is that the concept of genomic (...) information becomes burdened by a conceptual load that the biological facts cannot support. When, however, the appropriate concept of information is used, then these burdens are shed, and the result is an account that is in substantial agreement with the heart of Maynard Smith's thesis. (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)

One of the major impediments to understanding the concept of information is that the term is used to describe a number of disparate things, including a property of organized matter and messages sent from a sender to a receiver. Information is essentially an attribute of the form that matter and energy take, not of matter and energy themselves. Intrinsic information is a theoretical measure of the degree to which an entity is organized, the opposite of entropy. (...) Meaningful information, however, involves the detection of a pattern of organized matter or energy by an animate or a man-made receptor, which triggers a change in the behavior, function, or organizational structure of the receiving entity. The ability to detect and respond to meaningful information is one of the defining characteristics of living entities; the process that enables cells and organisms to receive their genetic heritage, regulate their internal milieu, and respond to changes in their environment. Although energy and information are the two fundamental causal agents in the natural world, they bring about change through completely different mechanisms. The energy involved in physical interactions is supplied by the originating entity, while the energy involved in informational interactions is provided by the recipient. There is no predictable relationship between the nature of the informational stimulus and the response it engenders, for this is primarily determined by the pattern of connections between the involved receptors and effectors that evolution and learning have fashioned. As a result, a living entity’s response to information cannot be predicted on a purely mechanical basis. The laws that describe the physical interaction of organized matter apply to the transfer of energy, not to the transfer of information. This is why biology cannot be reduced to physics. (shrink)

The term ‘information’ is used extensively in biology, cognitive science and the philosophy of consciousness in relation to the concepts of ‘meaning’ and ‘causation’. While ‘information’ is a term that serves a useful purpose in specific disciplines, there is much to the concept that is problematic. Part 1 is a critique of the stance that information is an independently existing entity. On this view, and in biological contexts, systems transmit, acquire, assimilate, decode and manipulate it, (...) and in so doing, generate meaning. I provide a detailed proposal in Part 2 that supports the claim that it is the dynamic form of a system that qualifies the informational nature of meaningful interactive engagement, that is, that information is dependent on dynamic form rather than that it exists independently. In Part 3, I reflect on the importance of the distinction between the independent and dependent stances by looking specifically at the implications for how we might better interpret causation and emergence. (shrink)

Integrating concepts of maintenance and of origins is essential to explaining biological diversity. The unified theory of evolution attempts to find a common theme linking production rules inherent in biological systems, explaining the origin of biological order as a manifestation of the flow of energy and the flow of information on various spatial and temporal scales, with the recognition that natural selection is an evolutionarily relevant process. Biological systems persist in space and time by transfor (...) ming energy from one state to another in a manner that generates structures which allows the system to continue to persist. Two classes of energetic transformations allow this; heat-generating transformations, resulting in a net loss of energy from the system, and conservative transformations, changing unusable energy into states that can be stored and used subsequently. All conservative transformations in biological systems are coupled with heat-generating transformations; hence, inherent biological production, or genealogical proesses, is positively entropic. There is a self-organizing phenomenology common to genealogical phenomena, which imparts an arrow of time to biological systems. Natural selection, which by itself is time-reversible, contributes to the organization of the self-organized genealogical trajectories. The interplay of genealogical (diversity-promoting) and selective (diversity-limiting) processes produces biological order to which the primary contribution is genealogical history. Dynamic changes occuring on times scales shorter than speciation rates are microevolutionary; those occuring on time scales longer than speciation rates are macroevolutionary. Macroevolutionary processes are neither redicible to, nor autonomous from, microevolutionary processes. (shrink)

In this paper I analyze the process by which modelers in systems biology arrive at an adequate representation of the biological structures thought to underlie data gathered from high-throughput experiments. Contrary to views that causal claims and explanations are rare in systems biology, I argue that in many studies of gene regulatory networks modelers aim at a representation of causal structure. In addressing modeling challenges, they draw on assumptions informed by theory and pragmatic considerations in a manner that is (...) guided by an interventionist conception of causal structure. While doubts have been raised about the applicability of this notion of causality to complex biological systems, it is here seen to be an adequate guide to inquiry. (shrink)

The key assumption behind evolutionary epistemology is that animals are active learners or ‘knowers’. In the present study, I updated the concept of natural learning, developed by Henry Plotkin and John Odling-Smee, by expanding it from the animal-only territory to the biosphere-as-a-whole territory. In the new interpretation of natural learning the concept of biological information, guided by Peter Corning’s concept of “control information”, becomes the ‘glue’ holding the organism–environment interactions together. The control information (...) guides biological systems, from bacteria to ecosystems, in the process of natural learning executed by the universal algorithm. This algorithm, summarized by the acronym IGPT (information-gain-process-translate) incorporates natural cognitive methods including sensing/perception, memory, communication, and decision-making. Finally, the biosphere becomes the distributed network of communicative interactions between biological systems termed the interactome. The concept of interactome is based on Gregory Bateson’s natural epistemology known as the “ecology of mind”. Mimicking Bateson’s approach, the interactome may also be designated “physiology of mind”—the principle behind regulating the biosphere homeostasis. (shrink)

Many philosophers are skeptical about the scientific value of the concept of biological information. However, several have recently proposed a more positive view of ascribing information as an exercise in scientific modeling. I argue for an alternative role: guiding empirical data collection for the sake of theorizing about the evolution of semantics. I clarify and expand on Bergstrom and Rosvall’s suggestion of taking a “diagnostic” approach that defines biological information operationally as a procedure for (...) collecting empirical cases. The more recent modeling-based accounts still perpetuate a theory-centric view of scientific concepts, which motivated philosophers’ misplaced skepticism in the first place. (shrink)

The concept of biological information, and information in general, usually presupposes a purely quantitative view of reality. Even though actualist quantification has an important place in the description of the world, a nominalistic stance that tries to simplify reality in purely actualist terms inevitably runs into inconsistencies; these inconsistencies have been pointed out by the critical assessments of the notion of biological information. Rather than calling for an abandonment of the informational terminology, we try (...) to rethink information as a part of an event, the description of which cannot be exhausted by a physicalist, mechanistic, temporally static view of reality. Reconceptualizing the notion of biological information in terms of a process of interpretation rather than as an informational object allows us to transcend the limitations imposed by an analysis of reality that depends on a fixed, finite structure of outcome. Thus, we argue that measuring biological information is intrinsically problematic. (shrink)

The general concept of information does not belong in the category of universal and inexorable physical laws but in the category of initial conditions and boundary conditions. Boundary conditions formed by local structures are often called constraints. Informational structures such as symbol vehicles are a special type of constraint. It should be clear that the concepts of initial conditions and constraints in physics make no sense outside the context of the law-based physical dynamics to which they apply. This (...) is also the case for the concept of information. -/- . (shrink)

We argue that living systems process information such that functionality emerges in them on a continuous basis. We then provide a framework that can explain and model the normativity of biological functionality. In addition we offer an explanation of the anticipatory nature of functionality within our overall approach. We adopt a Peircean approach to Biosemiotics, and a dynamical approach to Digital-Analog relations and to the interplay between different levels of functionality in autonomous systems, taking an integrative approach. We (...) then apply the underlying biosemiotic logic to a particular biological system, giving a model of the B-Cell Receptor signaling system, in order to demonstrate how biosemiotic concepts can be used to build an account of biological information and functionality. Next we show how this framework can be used to explain and model more complex aspects of biological normativity, for example, how cross-talk between different signaling pathways can be avoided. Overall, we describe an integrated theoretical framework for the emergence of normative functions and, consequently, for the way information is transduced across several interconnected organizational levels in an autonomous system, and we demonstrate how this can be applied in real biological phenomena. Our aim is to open the way towards realistic tools for the modeling of information and normativity in autonomous biological agents. (shrink)

Over the last two decades, network-focused approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While the network approach continues to grow very rapidly, some of its conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organisational and descriptive levels of networks can be applied universally across biological sciences. Consequently, the central focus of this theme issue will be (...) on the definition, motivation and application of key concepts in biological network science, such as levels, hierarchies, and explanatory directionality. A unification will be achieved by formulating norms for delimiting the distinctively network-topological class of explanations that connect general as well as very specific biological research questions. The impact of this theme issue is broad and encompassing, as it is highly interdisciplinary and opens a uniquely normative perspective on the foundational aspects of network-based explanations and modelling. This theme issue is intended to become a landmark publication for practical research as well as funding policy decisions, by unifying network approaches in biological sciences in terms of fundamental concepts and informing the public understanding of the network science. (shrink)

Much of the debate surrounding the concept of information in biology centers on the question of whether or not biological systems ‘really’ carry information. The criterion for determining if a system “really” carries information is whether or not there is a principled, theoretical account of information that captures the relevant biological usages. If biological systems do not carry information in this sense, information talk is termed merely heuristic and dismissed as (...) philosophically uninteresting. To date, all three proposed theoretical accounts of information—mathematical, causal and teleosemantic—fail to capture the meaning of biologists. Details of other biological practices that utilize informational concepts are often lost because the debate is too focused on one instance of information talk—genetic information and because biological representations are thought to need a certain kind of theoretical foundation. The problem with this methodology is that it takes the failure of philosophical accounts of information to capture current biological practices as conclusive evidence that informational representations in biology are incoherent. This approach is backwards. A better strategy is to get a clear understanding of biological practice and then to use it to shape our understanding of the philosophical significance of biological information. In this paper, I shift attention from abstract reasoning about information in the philosophical literature to concrete reasoning about informational models in biology. The current debate pays too little attention to the biologically prominent concept of signal. I develop a contextualized understanding of signaling models in biological practice. I argue that biologists use the concept of signal to model distinct functional roles in biological systems and not in any of the theoretical senses of information found in the current philosophical literature. For cell biologists, a signal causally indicates the state of a system at a given point and is used in the context of a style of functional explanation generally known as ‘causal role function,’ in which a mechanism or entity has a function if its behavior explains a contribution to a capacity of interest. I support this analysis with an example drawn from cell biology and reframe the debate over the significance of informational terms in biology. The focus on signal recasts the debate by highlighting examples of information talk which are central to active research programs in biology. The advantage of looking at these models is that their centrality to biological practice forces us to reconsider the adequacy of a methodology that dismisses biological models because we lack a particular kind of philosophical understanding of them. Standard philosophical accounts of information rely on assumptions appropriate for the needs of philosophers but are ill-suited for capturing biological practice. A contextualized understanding of the role of signal in biological practice allows us to work out from the details of practice to tackle broader philosophical issues. On this view, the significance of information talk in biology hinges more on our understanding of how biologists represent function than on our understanding of philosophical accounts of information. (shrink)

Many of the current comparisons of taxic phylogenetic and biological homology in the context of morphology focus on what are seen as categorical distinctions between the two concepts. The first, it is claimed, identifies historical patterns of conservation and variation relating taxa; the second provides a causal framework for the explanation of this conservation and variation. This leads to the conclusion that the two need not be placed in conflict and are in fact compatible, having non-competing epistemic purposes or (...) mapping the same extensions in the form of monophyletic groupings (see Roth, The biological basis of homology 1–26, 1988; Sluys, J Zool Syst Evol Res 34:145–152, 1996; Abouheif, Trends Ecol Evol 12:405–408, 1997; Brigandt, J Exp Zool 299:9–17, 2003, Biol Philos 22:709–725, 2007; Assis and Brigandt, Evol Biol 36:248–255, 2009). This article argues that moves in this direction miss the essential disagreement between these concepts as they have been developed in the context of the debate concerning the best concept for evolutionary investigation. We should rather see these concepts employing a common fundamental methodological approach to homology, but disagreeing about how to apply the methodology effectively. Both concepts employ class reasoning, which pursues homologies as units of generalization—more precisely, as sources of reliable and relevant group-bound information in the form of shared underlying causes. The dispute can be better understood by two poles that structure such reasoning: the need for a reliable basis for projections about the causal history of shared structures, and the desire to identify homologous characters with more informative and specific causal information relevant to generalizing about evolutionary processes. Judgments in favor of one or the other in turn have affected the scope or extension of these competing homology concepts. (shrink)

The Modern Synthesis has received criticism for its purported gene-centrism. That criticism relies on a concept of the gene as a unit of instructional information. In this paper I discuss information concepts and endorse one, developed from Floridi, that sees information as a functional relationship between data and context. I use this concept to inspect developmental criticisms of the Modern Synthesis and argue that the instructional gene arose as an idealization practice when evolutionary biologists made (...) comment on development. However, a closer inspection of key claims shows that at least some associated with the Modern Synthesis were in fact adopting the data led definition I favour and made clear arguments for the role of developmental processes beyond genetic input. There was no instructional gene. (shrink)

The genetic code appeared on Earth at the origin of life, and the codes of culture arrived almost four billion years later. For a long time it has been assumed that these are the only codes that exist in Nature, and if that were true we would have to conclude that codes are extraordinary exceptions that appeared only at the beginning and at the end of the history of life. In reality, various other organic codes have been discovered in the (...) past few decades and it is likely that more will come to light in the future. The existence of many organic codes in Nature is therefore an experimental fact, but also more than that. It is one of those facts that have extraordinary implications. In this book it is shown that the genetic code was a precondition for the origin of the first cells, the signal transduction codes divided the first cells into three primary kingdoms (Archaea, Bacteria and Eukarya), the splicing codes were instrumental to the origin of the eukaryotic nucleus, the histone code provided a new regulation system in eukaryotic genomes, and the cytoskeleton codes allowed the Eukarya to perform internal movements, including those of mitosis and meiosis. It is shown, furthermore, that organic codes had a key role in multicellular life, in particular in the origin of animals, the origin of mind and the origin of language. The great events of macroevolution, in other words, were associated with the appearance of new organic codes, and we can easily understand why. The reason is that a new code brings into existence something that has never existed before because it creates arbitrary associations, relationships that are not determined by physical necessity. Another outstanding implication is the fact that codes involve meaning and we need therefore to introduce in biology, with the standard methods of science, not only the concept of biological information but also that of biological meaning. The research on biological codes, in conclusion, is bringing to light new mechanisms in evolution and new fundamental concepts in science. This research is the field of Code Biology, the study of all codes of life, from the genetic code to the codes of culture, from the origin of life to the origin of man. (shrink)

The necessary but not sufficient conditions for biological informational concepts like signs, symbols, memories, instructions, and messages are (1) an object or referent that the information is about, (2) a physical embodiment or vehicle that stands for what the information is about (the object), and (3) an interpreter or agent that separates the referent information from the vehicle’s material structure, and that establishes the stands-for relation. This separation is named the epistemic cut, and explaining clearly how (...) the stands-for relation is realized is named the symbol-matter problem. (4) A necessary physical condition is that all informational vehicles are material boundary conditions or constraints acting on the lawful dynamics of local systems. It is useful to define a dependency hierarchy of information types: (1) syntactic information (i.e., communication theory), (2) heritable information acquired by variation and natural selection, (3) non-heritable learned or creative information, and (4) measured physical information in the context of natural laws. High information storage capacity is most reliably implemented by discrete linear sequences of non-dynamic vehicles, while the execution of information for control and construction is a non-holonomic dynamic process. The first epistemic cut occurs in self-replication. The first interpretation of base sequence information is by protein folding; the last interpretation of base sequence information is by natural selection. Evolution has evolved senses and nervous systems that acquire non-heritable information, and only very recently after billions of years, the competence for human language. Genetic and human languages are the only known complete general purpose languages. They have fundamental properties in common, but are entirely different in their acquisition, storage and interpretation. (shrink)

In many texts on evolution the reader will find a characteristic depiction of inheritance and evolution, one showing the generations of an evolving population linked only by a causal flow from genotype to genotype. On this view, the genotype of each organism in this population plays a dual role as both the motor of individual development and as the sole causal channel across the generations. This picture is known to be literally false. In many species, parents exert direct causal influence (...) on their offspring, and some of those influences cause the offspring to resemble the parent. For example, a butterfly that lays her eggs on the same plant host on which she hatched thereby exerts a causal influence on her offspring, and one apt to cause them to resemble her more than they would, had she chosen a plant of a different species. None of this is at all controversial, but it poses a puzzle. If the “Weissmanian” conception is literally false, why is it seen as a perspicacious representation of evolution? (shrink)

When dealing with biological communication and information, unifying concepts are necessary in order to couple the different “codes” that are being inductively “cracked” and defined at different emergent and “deemergent” levels of the biological hierarchy. In this paper I compare the type of biological information implied by genetic information with that implied in the concept of “quorum sensing” (which refers to a prokaryotic cell-to-cell communication system) in order to explore if such integration is (...) being achieved. I use the Lux operon paradigm and the Vibrio fischeri – Euprymna scolopes symbiotic partnership to exemplify the emergence of informational contexts along the biological hierarchy (from molecules to ecologies). I suggest that the biosemiotic epistemological framework can play an integrative role to overcome the limits of dyadic mechanistic descriptions when relating the different emergent levels. I also emphasise that the realisation ofbiology as being a “science of sensing” and the new importance that is being ascribed to the “context” in experimental biology corroborate past claims ofbiosemioticians about a shift from a focus on information (as a material agent of causality) towards a focus on the world of signification. (shrink)

In spite of being ubiquitous in life sciences, the concept of information is harshly criticized. Uses of the concept other than those derived from Shannon's theory are denounced as pernicious metaphors. We perform a computational experiment to explore whether Shannon's information is adequate to describe the uses of said concept in commonplace scientific practice. Our results show that semantic sequences do not have unique complexity values different from the value of meaningless sequences. This result suggests (...) that quantitative theoretical frameworks do not account fully for the complex phenomenon that the term “information” refers to. We propose a restructuring of the concept into two related, but independent notions, and conclude that a complete theory of biological information must account completely not only for both notions, but also for the relationship between them. (shrink)

Purpose : The purpose of this paper is to bring the concept of a 'hierarchy of action', as it is currently being used in other fields, into library and information science . Design/methodology/approach Hierarchy theory is adopted to describe three hierarchies of action, which include the human processes of semantic and social innovation, as well as a system of biological interpretence, from which human processes are thought to have evolved as a development of biosemiosis in nature. By (...) way of example, it is argued that a text is a complex achievement, and hierarchy theory shows how to account for this complexity; the everyday definition of text is augmented with accounts from different levels of observation. Findings: The concept of a hierarchy of action enables a person to account for a text as a meaning/symbolic product; include in that account the processes whereby texts are produced and used; and say why these processes are important to the health of the biosphere that is called home. Originality/value Hierarchy of action has been developed as a concept in biology and ecology; it belongs to a way of thinking whereby human reality, like nature, is construed as dynamical processes operating in symbiotic relationship with each other; it has not yet been adopted in LIS with reference to hierarchy theory and its potential is yet to be explored. Keywords Hierarchy theory, Complexity theory, Process philosophy, Natural philosophy, Hierarchies of action, Complex systems, Libraries, Information science Paper type Conceptual paper. (shrink)

Many scientists regard mass and energy as the primary currency of nature. In recent years, however, the concept of information has gained importance. In this book, eminent scientists, philosophers, and theologians chart various aspects of information, from quantum information to biological and digital information, in order to understand how nature works. Beginning with a historical treatment of the topic, the book also examines physical and biological approaches to information, and the philosophical, theological, (...) and ethical implications. (shrink)

The semantic concept of information is one of the most important, and one of the most problematical concepts in biology. I suggest a broad definition of biological information: a source becomes an informational input when an interpreting receiver can react to the form of the source (and variations in this form) in a functional manner. The definition accommodates information stemming from environmental cues as well as from evolved signals, and calls for a comparison between (...) class='Hi'>information‐transmission in different types of inheritance systems—the genetic, the epigenetic, the behavioral, and the cultural‐symbolic. This comparative perspective highlights the different ways in which information is acquired and transmitted, and the role that such information plays in heredity and evolution. Focusing on the special properties of the transfer of information, which are very different from those associated with the transfer of materials or energy, also helps to uncover interesting evolutionary effects and suggests better explanations for some aspects of the evolution of communication. (shrink)

Animals and robots perceiving and acting in a world require an ontology that accommodates entities, processes, states of affairs, etc., in their environment. If the perceived environment includes information - processing systems, the ontology should reflect that. Scientists studying such systems need an ontology that includes the first - order ontology characterising physical phenomena, the second - order ontology characterising perceivers of physical phenomena, and a third order ontology characterising perceivers of perceivers, including introspectors. We argue that second - (...) and third - order ontologies refer to contents of virtual machines and examine requirements for scientific investigation of combined virtual and physical machines, such as animals and robots. We show how the CogAff architecture schema, combining reactive, deliberative, and meta - management categories, provides a first draft schematic third - order ontology for describing a wide range of natural and artificial agents. Many previously proposed architectures use only a subset of CogAff, including subsumption architectures, contention - scheduling systems, architectures with Ôexecutive functionsÕ and a variety of types of ÔOmegaÕ architectures. Adding a multiply - connected, fastacting ÔalarmÕ mechanism within the CogAff framework accounts for several varieties of emotions. H - CogAff, a special case of CogAff, is postulated as a minimal architecture specification for a human - like system. We illustrate use of the CogAff schema in comparing H - CogAff with Clarion, a well known architecture. One implication is that reliance on concepts tied to observation and experiment can harmfully restrict explanatory theorising, since what an information processor is doing cannot, in general, be determined by using the standard observational techniques of the physical sciences or laboratory experiments. Like theoretical physics, cognitive science needs to be highly speculative to make progress. Ó 2004 Published by Elsevier B. V. (shrink)

Some biological processes move from step to step in a way that cannot be completely understood solely in terms of causes and correlations. This paper develops a notion of mechanistic information that can be used to explain the continuities of such processes. We compare them to processes that do not involve information. We compare our conception of mechanistic information to some familiar notions including Crick’s idea of genetic information, Shannon-Weaver information, and Millikan’s biosemantic (...) class='Hi'>information. (shrink)

The notion of the value of information is discussed. The value one attributes to information is determined by the result of its reception by an open nonequilibrium system. Qualitative reasoning shows that the concept of value of information makes sense only in nonequilibrium situations, and is directly connected with the nonredundancy of information. In biology it is the value and not the amount of information that is important. The value of information is especially (...) high if there are instabilities in the system; these are connected with the notions of purpose and of freedom of will. The notion of selective value, introduced by Eigen in the theory of the prebiological evolution of macromolecules, is discussed. The amount of information in various codons is calculated and the conventional definition of its value is given based on the determination of the danger of the replacement of one amino acid by another with a different value of hydrophobicity. It is shown that the relative probability of transversion is considerably lower than that of transition. As most nonsense mutations are transversions, the genetic code provides decreased probability for the most dangerous mutations. It is shown that the information of the codonUGG(Trp) is highest in both amount and value. (shrink)

Maynard Smith is right that one of the most striking features of contemporary biology is the ever-increasing prominence of the concept of information, along with related concepts like representation, programming, and coding. Maynard Smith is also right that this is surely a phenomenon which philosophers of science should examine closely. We should try to understand exactly what sorts of theoretical commitment are made when biological systems are described in these terms, and what connection there is between semantic (...) descriptions in biology and in other domains. (shrink)

Epigenetics is currently one of the fastest-growing fields in the sciences. Epigenetic information not only controls DNA expression but links genetic factors with the environmental experiences that influence the traits and characteristics of an individual. What we eat, where we work, and how we live affects not only the activity of our genes but that of our offspring as well. This discovery has imposed a revolutionary theoretical shift on modern biology, especially on evolutionary theory. It has helped to uncover (...) the developmental processes leading to cancer, obesity, schizophrenia, alcoholism, and aging, and to facilitate associated medial applications such as stem cell therapy and cloning. Above the Gene, Beyond Biology explores how biologists in this booming field investigate and explain living systems. Jan Baedke offers the first comprehensive philosophical discussion of epigenetic concepts, explanations, and methodologies so that we can better understand this "epigenetic turn" in the life sciences from a philosophical perspective. (shrink)

The concept of genetic information is controversial because it attributes semantic properties to what seem to be ordinary biochemical entities. I argue that nucleic acids contain information in a semantic sense, but only about a limited range of effects. In contrast to other recent proposals, however, I analyze genetic information not in terms of a naturalized account of biological functions, but instead in terms of the way in which molecules determine their products during processes known (...) as template-directed syntheses. I argue that determining an outcome in a certain way is constitutive for being an instruction. On this account, the content of genetic information is identified with the template's properties, which determine the product in the way constitutive for instructions. (shrink)

The theory of evolution, which provides the conceptual framework for all modern research in organismal biology and informs research in molecular bi- ology, has gone through several stages of expansion and refinement. Darwin and Wallace (1858) of course proposed the original idea, centering on the twin concepts of natural selection and common descent. Shortly thereafter, Wallace and August Weismann worked toward the complete elimination of any Lamarckian vestiges from the theory, leaning in particular on Weismann’s (1893) concept of the (...) separation of soma and germ, resulting in what is some- times referred to as “neo-Darwinism”. (shrink)

This book is a critical survey of and guidebook to the literature on biological functions. It ties in with current debates and developments, and at the same time, it looks back on the state of discourse in naturalized teleology prior to the 1970s. It also presents three significant new proposals. First, it describes the generalized selected effects theory, which is one version of the selected effects theory, maintaining that the function of a trait consists in the activity that led (...) to its differential persistence or reproduction in a population, and not merely its differential reproduction. Secondly, it advances “within-discipline pluralism” (as opposed to between-discipline pluralism) a new form of function pluralism, which emphasizes the coexistence of function concepts within diverse biological sub-disciplines. Lastly, it provides a critical assessment of recent alternatives to the selected effects theory of function, namely, the weak etiological theory and the systems-theoretic theory. The book argues that, to the extent that functions purport to offer causal explanations for the existence of a trait, there are no viable alternatives to the selected effects view. -/- The debate about biological functions is still as relevant and important to biology and philosophy as it ever was. Recent controversies surrounding the ENCODE Project Consortium in genetics, the nature of psychiatric classification, and the value of ecological restoration, all point to the continuing relevance to biology of philosophical discussion about the nature of functions. In philosophy, ongoing debates about the nature of biological information, intentionality, health and disease, mechanism, and even biological trait classification, are closely related to debates about biological functions. (shrink)

John Maynard Smith has defended against philosophical criticism the view that developmental biology is the study of the expression of information encoded in the genes by natural selection. However, like other naturalistic concepts of information, this ‘teleosemantic’ information applies to many non-genetic factors in development. Maynard Smith also fails to show that developmental biology is concerned with teleosemantic information. Some other ways to support Maynard Smith’s conclusion are considered. It is argued that on any definition of (...) information the view that development is the expression of genetic information is misleading. Some reasons for the popularity of that view are suggested. (shrink)