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)

We often hear how scientists have discovered that a certain human trait – or a trait of another type of organism – is innate, genetic, heritable, inherited, naturally selected etc. All these claims have something in common: they all declare a trait to have significant organism internal (for instance genetic) causes that are present in the organism at its birth. I call claims like these “nativist claims”. Nativist claims are important. They shape our overall understanding of what we are, what (...) we can do and what is good for us. They also impact our practical decision making. For instance, we know that certain types of genes increase the risk of certain diseases, and increasingly this has an effect on healthcare practices. Many people believe that in the matter of children’s education we should consider the fact that many cognitive abilities are highly heritable. Associations between genetics and aggressive behavior have been taken to be alleviating circumstances in criminal sentencing. It is therefore important to correctly understand the content and implications of nativist claims. In this doctoral thesis I analyze, by philosophical means, the content of different kinds of nativist claim. What does it mean that some psychological tendency is innate? What does it mean that intelligence is 50% heritable? How (if at all) do genes come to carry information about the traits of an organism – they are nothing like the information carriers familiar to us, such as newspapers, e-mails, secret codes, and audio files. This thesis emphasizes two things. Firstly, I demonstrate, that in different scientific contexts these words ('innate', 'genetically caused' etc.) can mean very different things. Therefore, the implications of a given nativist claim in one scientific context can be remarkably different from another nativist claim’s implications in some other scientific context. Secondly, I explain how the development of innate, heritable and genetically caused traits can be determined in different and often unexpected ways by our environment and experiences. I demonstrate that the content of a concept that is considered innate by cognitive scientists can be determined by what the organism that possesses the concept has experienced. I also show that even a trait which is 100% heritable can at the same time be a socially constructed trait. (shrink)

This paper introduces the reconstitutor as a comprehensive unit of heredity within the context of evolutionary research. A reconstitutor is the structure resulting from a set of relationships between different elements or processes that are actively involved in the recreation of a specific phenotypic variant in each generation regardless of the biomolecular basis of the elements or whether they stand in a continuous line of ancestry. Firstly, we justify the necessity of introducing the reconstitutor by showing the limitations of other (...) evolutionary conceptions of the unit of heredity, such as the replicator, the reproducer, and the Darwinian individual. We argue that these conceptions are based on the requirement of lineage formation, which we argue to be unnecessary for the existence of evolutionary heredity. In the second part, we introduce the reconstitutor, which we base on the concept of Stability of Traits, and illustrate how it covers cases of hereditary phenomena not covered by the previous accounts. Secondly, we illustrate how the reconstitutor could serve as a platform to rethink ecological inheritance and other forms of inheritance that have been recently introduced under the song/singer model of evolution. (shrink)

In the history of genetics, the information-theoretical description of the gene, beginning in the early 1960s, had a significant effect on the concept of the gene. Information is a highly complex metaphor which is applicable in view of the description of substances, processes, and spatio-temporal organisation. Thus, information can be understood as a functional particle of many different language games (some of them belonging to subdisciplines of genetics, as the biochemical language game, some of them belonging to linguistics and informatics). (...) It is this wide covering of different language games that justifies the common description of genes x, y, z as containing information for the phenotypic traits X, Y, Z (or the genome as storage for the information of a whole organism). However, if information is taken as the explanans and phenotypic traits or organisms as the explananda, then a description of the explanandum is of prior importance before the explanans can be characterised. This way of thinking could be useful for future discussions on the strikingly dominant information -metaphor, and the different gene concepts as well. The article illustrates this in two steps. First, a condensed overview on the history of genetics is given, which can be divided into three parts: (1) genetics without genes, (2) genetics with genes, but without information, (3) genetics with genes and information. It is assumed that this provides not only some historical knowledge about the origin of genetics and the introduction of technical terms, but offers at least preliminary insight into the methodological structure of genetic descriptions. In a second step, we redraw Spemann’s disturbation experiments to discuss our thesis that genetic information is not a natural entity, but part of a causality-language game which is secondarily added to the descriptions of interventionalistic practices, viz. experimental approaches. (shrink)

An assessment is offered of the recent debate on information in the philosophy of biology, and an analysis is provided of the notion of information as applied in scientific practice in molecular genetics. In particular, this paper deals with the dependence of basic generalizations of molecular biology, above all the ‘central dogma’, on the so-called ‘informational talk’ (Maynard Smith [2000a]). It is argued that talk of information in the ‘central dogma’ can be reduced to causal claims. In that respect, the (...) primary aim of the paper is to consider a solution to the major difficulty of the causal interpretation of genetic information: how to distinguish the privileged causal role assigned to nucleic acids, DNA in particular, in the processes of replication and protein production. A close reading is proposed of Francis H. C. Crick's On Protein Synthesis (1958) and related works, to which we owe the first explicit definition of information within the scientific practice of molecular biology. Introduction 1.1 The basic questions of the information debate 1.2 The causal interpretation (CI) of biological information and Crick's ‘central dogma’ Crick's definitions of genetic information The main requirement for (CI) Types of causation in molecular biology 4.1 Structural causation in molecular biology 4.2 Nucleic acids as correlative causal factors The ‘central dogma’ without the notion of information Concluding remarks This is a new version of this article as there were errors in the abstract and full text in the previous version. (shrink)

The main purpose of this article is to consider the significance of different types of memory and non-genetic inheritance and different biosemiotic systems for the origin and evolution of language. It presents language and memory as distributed, heteronomous and system-determined processes implemented in biological and social domains. The article emphasises that language and other sign systems are both ecological and inductive systems that were caused by and always correlate with the environment and deductive systems that are inherited by and depend (...) on the internal development of organisms, individuals, and societies. The article also claims that the origin, re-occurrence and evolution of naturally-emerging sign systems presuppose their retention and accumulation in physical, biological, individual, and social types of memory and reinforcement and maintenance by conventional and deliberate social regulation and accumulation. All of this allows language and other sign systems to be situation-relevant and to be transmitted through generations without their constant reinvention. The novelty of the proposed theory of language origin and evolution is in interdisciplinary integration of biosemiotic studies, systems approaches to language and studies of inheritance systems presented by ‘Extended evolutionary synthesis’. (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)

Hutto and Satne identify three research traditions attempting to explain the place of intentional agency in a wholly natural world: naturalistic reduction; sophisticated behaviourism, and pragmatism, and suggest that insights from all three are necessary. While agreeing with that general approach, I develop a somewhat different package, offering an outline of a vindicating genealogy of our interpretative practices. I suggest that these practices had their original foundation in the elaboration of much more complex representation-guided control structures in our lineage and (...) the support and amplification of those control structures through external resources. Cranes became increasingly important in the explanation of systematically successful action. These more complex representational engines coevolved with selection to detect and respond to the control structures of others. Since much of that selection was driven by the advantages of cooperation and coordination, in part these control structures were co-opted as external signals and guarantees, in cooperation and coordination. As the time depth of cooperation and co-ordination extended, these public signals of belief and intent acquired secondary functions, as mechanisms to stabilise and structure control systems, making humans not just more transparent to one another at a time, but more predictable over time. Mindshaping, not just mindreading, became increasingly important in our lineage. (shrink)

There is ongoing controversy as to whether the genome is a representing system. Although it is widely recognised that DNA carries information, both correlating with and coding for various outcomes, neither of these implies that the genome has semantic properties like correctness or satisfaction conditions, In the Scope of Logic, Methodology, and the Philosophy of Sciences, Vol. II. Kluwer, Dordrecht, pp. 387–400). Here a modified version of teleosemantics is applied to the genome to show that it does indeed have semantic (...) properties – there is representation in the genome. The account differs in three respects from previous attempts to apply teleosemantics to genes. It emphasises the role of the consumer of representations. It rejects the standard assumption that genetic representation can be used to explain the course of an organism’s development. And it identifies the explanatory role played by representational properties of the genome. A striking consequence of this account is that other inheritance systems could also be representational. Thus, a version of the parity thesis is accepted. However, the criteria for being an inheritance system are demanding, so semantic properties are not ubiquitous. (shrink)

Recent theoretical work has identified a tightly-constrained sense in which genes carry representational content. Representational properties of the genome are founded in the transmission of DNA over phylogenetic time and its role in natural selection. However, genetic representation is not just relevant to questions of selection and evolution. This paper goes beyond existing treatments and argues for the heterodox view that information generated by a process of selection over phylogenetic time can be read in ontogenetic time, in the course of (...) individual development. Recent results in evolutionary biology, drawn both from modelling work, and from experimental and observational data, support a role for genetic representation in explaining individual ontogeny: both genetic representations and environmental information are read by the mechanisms of development, in an individual, so as to lead to adaptive phenotypes. Furthermore, in some cases there appears to have been selection between individuals that rely to different degrees on the two sources of information. Thus, the theory of representation in inheritance systems like the genome is much more than just a coherent reconstruction of information talk in biology. Genetic representation is a property with considerable explanatory utility. (shrink)

The concept of innateness is used to make inferences between various better-understood properties, like developmental canalization, evolutionary adaptation, heritability, species-typicality, and so on (‘innateness-related properties’). This article uses a recently-developed account of the representational content carried by inheritance systems like the genome to explain why innateness-related properties cluster together, especially in non-human organisms. Although inferences between innateness-related properties are deductively invalid, and lead to false conclusions in many actual cases, where some aspect of a phenotypic trait develops in reliance on (...) a genetic representation it will tend, better than chance, to have many of the innateness-related properties. The account also shows why inferences between innateness-related properties sometimes fail and argues that such inferences are especially misleading when applied to human psychology and behaviour because human psychological development is especially reliant on non-genetic inherited representations. (shrink)

Developmental Systems Theory (DST) emphasises the importance of non-genetic factors in development and their relevance to evolution. A common, deflationary reaction is that it has long been appreciated that non-genetic factors are causally indispensable. This paper argues that DST can be reformulated to make a more substantive claim: that the special role played by genes is also played by some (but not all) non-genetic resources. That special role is to transmit inherited representations, in the sense of Shea (2007: Biology and (...) Philosophy, 22, 313-331). Formulating DST as the claim that there are non-genetic inherited representations turns it into a striking, empirically-testable hypothesis, driving the sort of investigations that are only now beginning to appear in the scientific literature. DST’s characteristic rejection of a gene vs. environment dichotomy is preserved, but without dissolving all potentially explanatory distinctions into an interactionist causal soup, as some have alleged. (shrink)

The question of whether “genetic information” is a merely causal factor in development or can be made sense of semantically, in a way analogous to a language or other type of representation, has generated a long debate in the philosophy of biology. It is intimately connected with another intense debate, concerning the limits of genetic determinism. In this paper I argue that widespread attempts to draw analogies between genetic information and information contained in books, blueprints or computer programs, are fundamentally (...) inadequate. In development, gene exons are the central part of an intricate and densely ramified semantic Genetic Informational Network. DNA in the entire genome is in a state of continuous positive and negative feedback with itself and with its ‘environment’, and is ‘read’ and acted upon by the cell in various alternative and complementary ways. The linear combinatorial coding relation between codons and amino acids is but one aspect of semantic genetic information, which is, when considered in its entirety, a far wider and richer concept. (shrink)

The philosophy of biology literature offers several arguments aimed at showing that information theory is conceptually unsuited to capture the informational talk in molecular biology. Such arguments led to the consensus that, if the informational talk in biology can be defended and explained at all, we need a different strategy. The debate, in fact, developed mostly along this line. However, recent contributions seem to (and even claim to) challenge the consensus and thus to vindicate the role and relevance of information (...) theory to this particular debate. In this paper, I examine the main arguments leading to such a consensus and I analyze the extent to which those recent accounts actually succeed in vindicating the invocation of information theory. I argue that these attempts fail to vindicate the information-theoretic strategy and, therefore, the consensus remains unaffected by them. (shrink)

This essay employs Charles Peirce’s triadic semiotics in order to develop a biosemiotic theory of life that is capable of illuminating the function of information in living systems. Specifically, I argue that the relationship between biological information structures , selecting environments, and the adapted bodily processes of living organisms is aptly modelled by the irreducibly triadic relationship between Peirce’s sign, object, and interpretant, respectively. In each instance of information-based semiosis, the information structure is a complex informational sign that represents the (...) informational object ; and the bodily, behavioral, mental, or intellectual processes that are organized by the informational sign to more or less accurately interpret the present environment constitute a complex informational interpretant—a living, interpreting organism. The essay begins by discussing the precise sense in which this biosemiotic theory is based upon Charles Peirce’s semiotic theory. Next, the theory is developed at length in relation to genetic information structures. Finally, I present a brief outline of how the theory applies to neural and linguistic information structures. The essay concludes with a reflection upon the anti-reductionist implications of the theory. (shrink)

More than one researcher is currently proposing that the notion of information become an important element for defining living systems as well as for explaining conditions that make their origins possible. During the pre-biotic era, the type of compounds encountered would mainly have been very simple in nature and might have been immersed in the natural dynamic of the physical world and in processes of self-organization. It is furthermore quite possible that they formed a relationship between and among certain types (...) of processes that here we are specifically proposing as central for the emergence of cell organization. Consequently, an important initial step towards constructing a theory of biological information is to ask ourselves the question: how do biological systems process information? In this way, we will be contributing to the proposals of this paper where we seek to identify general principles that govern biological computing and that deal with biosemiotic approaches as they are defended in naturalistic normative terms. (shrink)

Any description of the emergence and evolution of different types of meaning processes (semiosis, sensu C.S.Peirce) in living systems must be supported by a theoretical framework which makes it possible to understand the nature and dynamics of such processes. Here we propose that the emergence of semiosis of different kinds can be understood as resulting from fundamental interactions in a triadically-organized hierarchical process. To grasp these interactions, we develop a model grounded on Stanley Salthe's hierarchical structuralism. This model can be (...) applied to establish, in a general sense, a set of theoretical constraints for explaining the instantiation of different kinds of meaning processes (iconic, indexical, symbolic) in semiotic systems. We use it to model a semiotic process in the immune system, namely, B-cell activation, in order to offer insights into the heuristic role it can play in the development of explanations for specific semiotic processes. (shrink)

The paper outlines the contours of an organizational perspective on extended inheritance. Based on theoretical studies about biological organization and extended physiology, this perspective allows for the conception of extended biological legacies while keeping a theoretically indispensable distinction between biological systems and their environment. In this context, the line of demarcation between these systems and their surroundings is modelled on an organizational criterion and on the related conceptual distinction between organizational constraints, whose specific role is to harness flows of matter (...) and energy across generations of composite biological systems, and resources exploited by those systems. Biological legacies are restricted to persisting constitutive elements responsible for the reoccurrence of organizational constraints in a given environment. The case of symbiotic transmission is presented as a paradigmatic system illustrating the main proposed conceptual clarifications. (shrink)

In this paper, I argue that the increasing data about non-genetic inheritance requires the construction of a new conceptual framework that should complement the inclusive approaches already discussed in the literature. More precisely, I hold that this framework should be epistemologically relevant for evolutionary biologists in capturing the limits of extended inheritance and in reassessing the boundaries of biological systems that transmit traits to their offspring. I outline the first elements of an organizational account of extended inheritance. In this account, (...) the category of inherited factors is neither restricted to genes nor extended to stable resources related to trans-generational similarities. Instead, it includes persisting constitutive elements appearing as difference makers for heterogeneous organizational constraints, namely for heterogeneous constitutive parts whose specific role is to harness flows of matter and energy across generations of clearly delimited extended organized systems. This both inclusive and restrictive framework opens an additional way to apprehend how extended inheritance may affect evolutionary trajectories. (shrink)

A causal approach to biological information is outlined. There are two aspects to this approach: information as determining a choice between alternative objects and information as determining the construction of a single object. The first aspect has been developed in earlier work to yield a quantitative measure of biological information that can be used to analyze biological networks. This article explores the prospects for a measure based on the second aspect and suggests some applications for such a measure. These two (...) aspects are not suggested to exhaust all the facets of biological information. (shrink)

With an increasing number of ways to ‘assist’ reproduction, some bioethicists have started to wonder what it takes to become a genetic parent. It is widely agreed that sharing genes is not enough to substantiate the parent–offspring relation, but what is? Without a better understanding of the concept of reproduction, our thinking about parent–offspring relations and the ethical issues surrounding them risk being unprincipled. Here, I address that problem by offering a principled account of reproduction—the Overlap, Development and Persistence account—which (...) I believe best captures the meaning of ‘genetic parenthood’. (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)

The relational structure of RNA, DNA, and protein bears an interesting similarity to the determination problem in category theory. In this paper, we present this deep-structure similarity and use it as a springboard for discussing some abstract properties of coding in various systems. These abstract properties, in turn, may shed light on the evolution of the DNA world from a semiotic perspective. According to the perspective adopted in this paper, living systems are not information processing systems but “meaning-making” systems. Therefore, (...) what flows in the genetic system is not “information” but “value.” We define meaning, meaning-making, and value and then use these terms to explain the abstract dynamics of coding, which can illuminate many forms of sign-mediated activities in biosystems. (shrink)

We develop a conceptual framework that connects biological heredity and organization. We refer to heredity as the cross-generation conservation of functional elements, defined as constraints subject to organizational closure. While hereditary objects are functional constituents of biological systems, any other entity that is stable across generations—and possibly involved in the recurrence of phenotypes—belongs to their environment. The central outcome of the organizational perspective consists in extending the scope of heredity beyond the genetic domain without merging it with the broad category (...) of cross-generation stability. After discussing some implications, we conclude with a reflection on the relationship between stability and variation. 1Introduction2From Extended Heredity to Cross-generation Stability 2.1Extending the scope of heredity: A brief state of the art2.2Rethinking heredity: Conceptual challenges3Biological Heredity in Light of Organization 3.1Biological organization within organisms and beyond3.2Extending organization in time3.3What is biological heredity?4Implications and Objections 4.1Heredity as a specific kind of cross-generation stability4.2Heredity at various levels of description4.3Non-functional and dysfunctional objects5Conclusions: From Conservation to Variation. (shrink)

Gary Marcus has written a very interesting book about mental development from a nativist perspective. For the general readership at which the book is largely aimed, it will be interesting because of its many informative examples of the development of cognitive structures and because of its illuminating explanations of ways in which genes can contribute to these developmental processes. However, the book is also interesting from a theoretical point of view. Marcus tries to make nativism compatible with the central arguments (...) that anti-nativists use to attack nativism and with many recent discoveries about genetic activity and brain development. In so doing, he reconfigures the nativist position to a considerable extent. (shrink)

Shannon information is commonly assumed to be the wrong way in which to conceive of information in most biological contexts. Since the theory deals only in correlations between systems, the argument goes, it can apply to any and all causal interactions that affect a biological outcome. Since informational language is generally confined to only certain kinds of biological process, such as gene expression and hormone signalling, Shannon information is thought to be unable to account for this restriction. It is often (...) concluded that a richer, teleosemantic sense of information is needed. I argue against this view, and show that a coherent and sufficiently restrictive theory of biological information can be constructed with Shannon information at its core. This can be done by paying due attention some crucial distinctions: between information quantity and its fitness value, and between carrying information and having the function of doing so. From this I construct an account of how informational functions arise, and show that the “subject matter” of these functions can easily be seen as the natural information dealt with by Shannon’s theory. (shrink)

This article is arranged around two general claims and a thought experiment. I begin by suggesting that the genome should be studied as a developmental system, and that genes supervene on genomes (rather than the other way around). I move on to present a thought experiment that illustrates the implications a dynamic view of the genome has for central concepts in biology, in particular the information content of the genome, and the notion of responses to stress.

‘Information’ and ‘code’ originated as technical terms within linguistics and information theory but are now widely used in genetics and developmental biology. Against this background, it is examined if coded information distinguishes genes from other information carriers, i.e., whether there are genetic words or sentences by virtue of the genetic code, and, if so, whether they have any semantic content. It is concluded that there is no genetic language with semantic content, but that the genetic code still enables unique language-like (...) modes of transmission and interpretation of causal information. (shrink)

The teleosemantic theory of representational content is held by some philosophers to imply that genes carry semantic information about whole-organism phenotypes. In this paper, I argue that this position is not supported by empirical findings. I focus on one of the most elaborate defenses of this position: Shea’s view that genes represent whole-organism phenotypes. I distinguish between two ways of individuating genes in contemporary biological science as possible vehicles of representational content—as molecular genes and as difference-maker genes. I show that (...) given either of these ways of individuating genes, genes fail to meet conditions which the teleosemantic theory requires an entity to meet if that entity is to qualify as a representational vehicle that represents a whole-organism phenotype. The considerations I present against Shea’s view generalize to other attempts to use the teleosemantic theory in support of the claim that genes represent whole-organism phenotypes. (shrink)

Over the last couple of decades, a call has begun to resound in a number of distinct fields of inquiry for a reattachment of form to matter, for an understanding of ‘information’ as inherently embodied, or, as Jean-Marie Lehn calls it, for a “science of informed matter.” We hear this call most clearly in chemistry, in cognitive science, in molecular computation, and in robotics—all fields looking to biological processes to ground a new epistemology. The departure from the values of a (...) more traditional epistemological culture can be seen most clearly in changing representations of biological development. Where for many years now, biological discourse has accepted a sharp distinction between information and matter, software and hardware, data and program, encoding and enactment, a new discourse has now begun to emerge in which these distinctions have little meaning. Perhaps ironically, much of this shift depends on drawing inspiration from just those biological processes which the discourse of disembodied information was intended to describe. (shrink)

Throughout the history of molecular biology, the primary meaning of biological information has been taken from the image of a word-based linguistic code. I want to argue that the metaphor of such a code does not begin to capture either the variety or the richness of the processes by which nucleotide sequences inform biological processes. Current research demonstrates that nucleotide sequences inform not only development but also heredity and evolution, and they do so in all sorts of ways. Even though (...) they do not exhaust the varieties of biological information employed in these processes, I claim that the power of DNA sequences to inform these processes is richer and perhaps far greater than the conventional understanding of genetic information permits, indeed richer than what any of our images of simple linguistic codes or of senders and receivers permits. Rather than a tape in a Turing machine or a message or signal sent through the generations, DNA is first and foremost a physicochemical structure with a range of potential uses by the physicochemical arsenal of biological cells that is so large as to expose the poverty of our most familiar metaphors. Recognition of this fact leads us to conclude that DNA is both more and less than we thought—more because it carries both symbolic and non-symbolic information and less because accepting that fact undermines its radical distinction from other biological molecules. (shrink)

Prions, prion-related diseases and prion-like phenomena are not only the subjects of rapidly growing scientific research interests, but also appear to be interesting from a philosophical perspective. In this study, we first present a brief review of the current prion research that includes a conceptual expansion of the notion of “prion” as a pathogenic conformation of a specific mammalian protein, towards more general “prion-like phenomena”, that can sometimes assume important beneficial functions in a broad range of biological contexts. Next, we (...) introduce Gilbert Simondon’s theory of individuation, which is a philosophical framework applicable to all possible domains of becoming. In contrast to the common approach of dividing the realm of ontogenetic processes into distinct domains and treating them separately, Simondon distinguishes between different modes of the same process: i.e., the physical, vital, and psycho-collective modes. His theory thus appears relevant with regard to the notion of prion-like phenomena in the extended sense, which seems to provide a useful metaphor for better understanding different modes of individuation and transitions between them. In particular, the transition from the physical to the vital mode is closely related to some core questions of biosemiotics such as the emergence of life from non-life, as well as “how a molecule became a sign”, which today constitute blank spots where the classical specialised disciplines of natural sciences fall short of satisfactory explanations. When recent scientific findings on prion-related phenomena are interpreted in the context of Simondon’s ontogenetic framework, the question related to the origin of life in our provocative title gains a different meaning. (shrink)

In this paper, I discuss how information theory has been used in the study of animal communication, as well as how these uses are justified. Biologists justify their use of Shannon’s information measures by the work they do in allowing for comparisons between different organisms and because they measure a quantity that is purported to be important for natural selection. I argue that there are problems with both sorts of justification. To make these difficulties clear, I focus on the use (...) of Shannon’s information measures to quantify the amount of information transmitted by the fire ant’s odor trail and the honeybee’s waggle dance. Both of these systems are relatively simple and well understood, and the application of Shannon’s information measure to these systems initially seemed very promising and relatively straightforward. They are therefore particularly suitable for revealing the benefits and difficulties of applying Shannon’s information measures to biological systems in general, and animal communication systems in particular. (shrink)

In responding to three reviews of Evolution in Four Dimensions (Jablonka and Lamb, 2005, MIT Press), we briefly consider the historical background to the present genecentred view of evolution, especially the way in which Weismann’s theories have influenced it, and discuss the origins of the notion of epigenetic inheritance. We reaffirm our belief that all types of hereditary information—genetic, epigenetic, behavioural and cultural—have contributed to evolutionary change, and outline recent evidence, mainly from epigenetic studies, that suggests that non-DNA heritable variations (...) are not rare and can be quite stable. We describe ways in which such variations may have influenced evolution. The approach we take leads to broader definitions of terms such as ‘units of heredity’, ‘units of evolution’, and ‘units of selection’, and we maintain that ‘information’ can be a useful concept if it is defined in terms of its effects on the receiver. Although we agree that evolutionary theory is not undergoing a Kuhnian revolution, the incorporation of new data and ideas about hereditary variation, and about the role of development in generating it, is leading to a version of Darwinism that is very different from the gene-centred one that dominated evolutionary thinking in the second half of the twentieth century. (shrink)

The scientific study of consciousness or subjective experiencing is a rapidly expanding research program engaging philosophers of mind, psychologists, cognitive scientists, neurobiologists, evolutionary biologists and biosemioticians. Here we outline an evolutionary approach that we have developed over the last two decades, focusing on the evolutionary transition from non-conscious to minimally conscious, subjectively experiencing organisms. We propose that the evolution of subjective experiencing was driven by the evolution of learning and we identify an open-ended, representational, generative and recursive form of associative (...) learning, which we call Unlimited Associative Learning (UAL), as an evolutionary transition marker of minimal consciousness. This evolutionary marker provides evidence that the evolutionary transition to consciousness has gone to completion and allows reverse-engineering from this learning capacity to the system that enables it – making possible the construction of a toy model of UAL. The model allows us to identify some of the key processes and structures that constitute minimal consciousness, points its taxonomic distribution and the ecological context in which it first emerged, highlights its function and suggests a framework for exploring developmental and evolutionary modifications of consciousness. We point to ways of experimentally testing the relationship between UAL and consciousness in human and in non-human animals and discuss the theoretical and ethical implications of our approach. The framework we offer allows the exploration of the evolutionary changes in agency, value systems, selective processes and goals that were involved in the transition to subjective experiencing from a perspective that resonates with the approaches of bio-semioticians. (shrink)

In his theory of evolution, Darwin recognized that the conditions of life play a role in the generation of hereditary variations, as well as in their selection. However, as evolutionary theory was developed further, heredity became identified with genetics, and variation was seen in terms of combinations of randomly generated gene mutations. We argue that this view is now changing, because it is clear that a notion of hereditary variation that is based solely on randomly varying genes that are unaffected (...) by developmental conditions is an inadequate basis for evolutionary theories. Such a view not only fails to provide satisfying explanations of many evolutionary phenomena, it also makes assumptions that are not consistent with the data that are emerging from disciplines ranging from molecular biology to cultural studies. These data show that the genome is far more responsive to the environment than previously thought, and that not all transmissible variation is underlain by genetic differences. In Evolution in Four Dimensions (2005) we identify four types of inheritance (genetic, epigenetic, behavioral, and symbol-based), each of which can provide variations on which natural selection will act. Some of these variations arise in response to developmental conditions, so there are Lamarckian aspects to evolution. We argue that a better insight into evolutionary processes will result from recognizing that transmitted variations that are not based on DNA differences have played a role. This is particularly true for understanding the evolution of human behavior, where all four dimensions of heredity have been important. (shrink)

The commentaries on Evolution in Four Dimensions reflect views ranging from total adherence to gene-centered neo-Darwinism, to the acceptance of non-genetic and Lamarckian processes in evolution. We maintain that genetic, epigenetic, behavioral, and cultural variations have all been significant, and that the developmental aspects of heredity and evolution are an important bridge that can unite seemingly conflicting research programs and different disciplines.

The themes, problems and challenges of developmental systems theory as described in Cycles of Contingency are discussed. We argue in favor of a robust approach to philosophical and scientific problems of extended heredity and the integration of behavior, development, inheritance, and evolution. Problems with Sterelny's proposal to evaluate inheritance systems using his `Hoyle criteria' are discussed and critically evaluated. Additional support for a developmental systems perspective is sought in evolutionary studies of performance and behavior modulation of fitness.

In a short work called De conceptione appended to the end of his Exercitationes de generatione animalium , William Harvey developed a rather strange analogy. To explain how such marvelous productions as living beings were generated from the rather inauspicious ingredients of animal reproduction, Harvey argued that conception in the womb was like conception in the brain. It was mostly rejected at the time; it now seems a ludicrous theory based upon homonymy. However, this analogy offers insight into the structure (...) and function of analogies in early modern natural philosophy. In this essay I hope to not only describe the complex nature of Harvey’s analogy, but also offer a novel interpretation of his use of analogical reasoning, substantially revising the account offered by Guido Giglioni . I discuss two points of conceptual change and negotiation in connection with Harvey’s analogy, understanding it as both a confrontation between the border of the natural and the supernatural, as well as a moment in the history of psychology. My interpretation touches upon a number of important aspects, including why the analogy was rejected, how Harvey systematically deployed analogies according to his notions of natural philosophical method, how the analogy fits into contemporary discussions of analogies in science, and finally, how the analogy must be seen in the context of changing Renaissance notions of the science of the soul, ultimately confronting the problem of how to understand final causality in Aristotelian science. In connection with the last, I conclude the essay by turning to how Harvey embeds the analogy within a natural theological cosmology. (shrink)

The majority of G protein-coupled receptors (GPCRs) self-assemble in the form dimeric/oligomeric complexes along the plasma membrane. Due to the molecular interactions they participate, GPCRs can potentially provide the framework for discriminating a wide variety of intercellular signals, as based on some kind of combinatorial receptor codes. GPCRs can in fact transduce signals from the external milieu by modifying the activity of such intracellular proteins as adenylyl cyclases, phospholipases and ion channels via interactions with specific G-proteins. However, in spite of (...) the number of cell functions they can actually control, both GPCRs and their associated signal transduction pathways are extremely well conserved, for only a few alleles with null or minor functional alterations have so far been found. This would seem to suggest that, beside a mechanism for DNA repairing, there must be another level of quality control that may help maintaining GPCRs rather stable throughout evolution. We propose here receptor oligomerization to be a basic molecular mechanism controlling GPCRs redundancy in many different cell types, and the plasma membrane as the first hierarchical cell structure at which selective categorical sensing may occur. Categorical sensing can be seen as the cellular capacity for identifying and ordering complex patterns of mixed signals out of a contextual matrix, i.e., the recognition of meaningful patterns out of ubiquitous signals. In this context, redundancy and degeneracy may appear as the required feature to integrate the cell system into functional units of progressively higher hierarchical levels. (shrink)

The claims that “The brain processes information” or “Cognition is information processing” are accepted as truisms in cognitive science. However, it is unclear how to evaluate such claims absent a specification of “information” as it is used by neurocognitive theories. The aim of this article is, thus, to identify the key features of information that information-based neurocognitive theories posit. A systematic identification of these features can reveal the explanatory role that information plays in specific neurocognitive theories, and can, therefore, be (...) both theoretically and practically important. These features can be used, in turn, as desiderata against which candidate theories of information may be evaluated. After discussing some characteristics of explanation in cognitive science and their implications for “information”, three notions are briefly introduced: natural, sensory, and endogenous information. Subsequently, six desiderata are identified and defended based on cognitive scientific practices. The global workspace theory of consciousness is then used as a specific case study that arguably posits either five or six corresponding features of information. (shrink)