Today there are two major theoretical frameworks in biology. One is the ‘chemical paradigm’, the idea that life is an extremely complex form of chemistry. The other is the ‘information paradigm’, the view that life is not just ‘chemistry’ but ‘chemistry-plus-information’. This implies the existence of a fundamental difference between information and chemistry, a conclusion that is strongly supported by the fact that information and information-based-processes like heredity and natural selection simply do not exist in the world of chemistry. Against (...) this conclusion, the supporters of the chemical paradigm have pointed out that information processes are no different from chemical processes because they are both described by the same physical quantities. They may appear different, but this is only because they take place in extremely complex systems. According to the chemical paradigm, in other words, biological information is but a shortcut term that we use to avoid long descriptions of countless chemical reactions. It is intuitively appealing, but it does not represent a new ontological entity. It is merely a derived construct, a linguistic metaphor. The supporters of the information paradigm insist that information is a real and fundamental entity of Nature, but have not been able to prove this point. The result is that the chemical view has not been abandoned and the two paradigms are both coexisting today. Here it is shown that an alternative does exist and is a third theoretical framework that is referred to as the ‘code paradigm’. The key point is that we need to introduce in biology not only the concept of information but also that of meaning because any code is based on meaning and a genetic code does exist in every cell. The third paradigm is the view that organic information and organic meaning exist in every living system because they are the inevitable results of the processes of copying and coding that produce genes and proteins. Their true nature has eluded us for a long time because they are nominable entities, i.e., objective and reproducible observables that can be described only by naming their components in their natural order. They have also eluded us because nominable entities exist only in artifacts and biologists have not yet come to terms with the idea that life is artifact making. This is the idea that life arose from matter and yet it is fundamentally different from it because inanimate matter is made of spontaneous structures whereas life is made of manufactured objects. It will be shown, furthermore, that the existence of information and meaning in living systems is documented by the standard procedures of science. We do not have to abandon the scientific method in order to introduce meaning in biology. All we need is a science that becomes fully aware of the existence of organic codes in Nature. (shrink)

The first use of the term "information" to describe the content of nervous impulse occurs 20 years prior to Shannon`s (1948) work, in Edgar Adrian`s The Basis of Sensation (1928). Although, at least throughout the 1920s and early 30s, the term "information" does not appear in Adrian`s scientific writings to describe the content of nervous impulse, the notion that the structure of nervous impulse constitutes a type of message subject to certain constraints plays an important role in all of his (...) writings throughout the period. The appearance of the concept of information in Adrian`s work raises at least two important questions: (i) what were the relevant factors that motivated Adrian`s use of the concept of information? (ii) What concept of information does Adrian appeal to, and how can it be situated in relation to contemporary philosophical accounts of the notion of information in biology? The first question involves an account of the application of communications technology in neurobiology as well as the historical and scientific background of Adrian`s major scientific achievement, which was the recording of the action potential of a single sensory neuron. The response to the second question involves an explication of Adrian`s concept of information and an evaluation of how it may be situated in relation to more contemporary philosophical explications of a semantic concept of information. I suggest that Adrian`s concept of information places limitations on the sorts of systems that are referred to as information carriers by causal and functional accounts of information. (shrink)

The social, behavioral, and a good chunk of the biological sciences concern the nature of individual agency, where our paradigm for an individual is a human being. Theories of economic behavior, of mental function and dysfunction, and of ontogenetic development, for example, are theories of how such individuals act, and of what internal and external factors are determinative of that action. Such theories construe individuals in distinctive ways.

[[THIS IS THE COMPLETE SECOND ISSUE OF MΕTASCIENCE]] -/- This second issue of the journal Mεtascience continues the char acterization of this new branch of knowledge that is metasci ence. If it is new, it is not in a radical sense since Mario Bunge practiced it in an exemplary way, since logical positivists were accused of practicing only a mere metascience, since scientists have always practiced it implicitly, and since some philosophers no longer practice philosophy but rather metascience, but without (...) characterizing it or theorizing it, that is, without realizing that they have abandoned one general discourse for another. The novelty therefore lies in this aware ness that a general discourse without philosophy is possible: a scien tific general discourse. The twelve contributions gathered in this volume illustrate the metascientific approach to knowledge of the world as well as to knowledge of knowledge of the world, that is, science. And like Bunge’s project, they are neither part of the analytical movement nor the continental movement in philosophy. We will read here studies about the Bungean system, some applications of Bungean thought, some metascientific contributions, and some reflections around meta science. Among metascientific disciplines, ontology occupies a prominent place in this issue of Mεtascience. Metascience differs from philoso phy in its rejection of the fundamental philosophical distinction be tween appearance and reality. Metascientific ontology therefore does not postulate the existence of any metaphysical reality. But metasci entific ontology, no more than philosophical ontology, is a factual sci ence. The first, because it studies scientific constructs and not concrete objects, the second, because it is interested in transcendent or meta physical objects. (shrink)

This dissertation focuses on teleology and functions in biology. More precisely, it focuses on the scientific legitimacy of teleofunctional attributions and explanations in biology. It belongs to a multi-faceted debate that can be traced back to at least the 1970s. One aspect of the debate concerns the naturalization of functions. Most authors try to reduce, translate or explain functions and teleology in terms of efficient causes so that they find their place in the framework of the natural sciences. Our approach (...) here is radically different, as we question the premise that teleological explanations are disguised causal explanations. On the contrary, we defend that they are acceptable in natural sciences and in biology in particular. We challenge the idea that teleological explanations are immature causal explanations, as well as the idea that teleology and functions are some sort of intentional explanations. We therefore reject the accusations of anthropomorphism, vitalism and finalism. On the contrary, we defend that teleology, causality and intentionality correspond to different, autonomous and complementary modes of representation of the outside world. -/- ———[FRANÇAIS]——— -/- Ce travail de thèse porte sur la téléologie et les fonctions en biologie. Plus précisément, il porte sur la légitimité scientifique des attributions et des explications téléofonctionnelles en biologie. Il s’inscrit dans le cadre d’un débat à plusieurs facettes que l’on peut faire remonter au moins jusqu’aux années 1970 et qui est encore très actif aujourd’hui. L’un des aspects du débat porte sur la naturalisation des fonctions, c’est-à-dire sur la manière de les réduire, de les traduire ou de les expliciter en termes de causes efficientes de sorte qu’elles trouvent leur place dans le cadre des sciences de la nature. Notre approche ici est radicalement différente, car nous remettons en question la prémisse selon laquelle les explications téléologiques seraient des explications causales déguisées. Nous défendons au contraire qu’elles sont acceptables en tant que telles aussi bien de façon générale que dans le domaine scientifique et en particulier en biologie. De façon générale, nous remettons en question l’idée selon laquelle la pensée téléologique serait une pensée causale immature, ainsi que sa dépendance présumée vis-à-vis de la psychologie, c’est-à-dire de l’intentionnalité. Nous rejetons donc les accusations d’anthropomorphisme, de vitalisme et de finalisme formulées contre elle. Nous défendons au contraire que la téléologie, la causalité et l’intentionnalité correspondent à des modes différents, autonomes et complémentaires de représentation du monde extérieur. (shrink)

This is a short overview of the biological functions debate in philosophy. While it was fairly comprehensive when it was written, my short book ​A Critical Overview of Biological Functions has largely supplanted it as a definitive and up-to-date overview of the debate, both because the book takes into account new developments since then, and because the length of the book allowed me to go into substantially more detail about existing views.

The idea that only complex brains can possess genuine representations is an important element in mainstream philosophical thinking. An alternative view, which I label ‘liberal representationalism’, holds that we should accept the existence of many more full-blown representations, from activity in retinal ganglion cells to the neural states produced by innate releasing mechanisms in cognitively unsophisticated organisms. A promising way of supporting liberal representationalism is to show it to be a consequence of our best naturalistic theories of representation. However, several (...) philosophers and scientists have recently argued against this strategy. In the paper I counter these objections in defense of liberal representationalism. (shrink)

Exactly how do the sign/symbol/token systems of endo- and exo-biosemiosis differ from those of cognitive semiosis? Do the biological messages that integrate metabolism have conceptual meaning? Semantic information has two subsets: Descriptive and Prescriptive. Prescriptive information instructs or directly produces nontrivial function. In cognitive semiosis, prescriptive information requires anticipation and “choice with intent” at bona fide decision nodes. Prescriptive information either tells us what choices to make, or it is a recordation of wise choices already made. Symbol systems allow recordation (...) of deliberate choices and the transmission of linear digital prescriptive information. Formal symbol selection can be instantiated into physicality using physical symbol vehicles (tokens). Material symbol systems (MSS) formally assign representational meaning to physical objects. Even verbal semiosis instantiates meaning into physical sound waves using an MSS. Formal function can also be incorporated into physicality through the use of dynamically-inert (dynamically-incoherent or -decoupled) configurable switch-settings in conceptual circuits. This paper examines the degree to which biosemiosis conforms to the essential formal criteria of prescriptive semiosis and cybernetic management. (shrink)

In this article, I argue that the use of scientific models that attribute intentional content to complex systems bears a striking similarity to the way in which statistical descriptions are used. To demonstrate this, I compare and contrast an intentional model with a statistical model, and argue that key similarities between the two give us compelling reasons to consider both as a type of phenomenological model. I then demonstrate how intentional descriptions play an important role in scientific methodology as a (...) type of phenomenal model, and argue that this makes them as essential as any other model of this type. (shrink)

Academia is subdivided into separate disciplines, most of which are quite discrete. In this review I trace the interactions between two of these disciplines: biology and philosophy of biology. I concentrate on those topics that have the most extensive biological content: function, species, systematics, selection, reduction and development. In the final section of this paper I touch briefly on those issues that biologists and philosophers have addressed that do not have much in the way of biological content.

Implicit God-like and ghost-in-the-machine metaphors underlie much current thinking about genomes. Although many criticisms of such views exist, none have succeeded in substituting a different, widely accepted view. Viewing the genome with its protein packaging as a brain gets rid of Gods and ghosts while plausibly integrating machine and information-based views. While the ‘wetware’ of brains and genomes are very different, many fundamental principles of how they function are similar. Eukaryotic cells are compound entities in which case the nuclear genome (...) might best be thought of more as a government than simply as a brain. (shrink)

Jacques Monod (1971) argued that certain molecular processes rely critically on the property of chemical arbitrariness, which he claimed allows those processes to “transcend the laws of chemistry”. It seems natural, as some philosophers have done, to interpret this in modal terms: a biological relationship is chemically arbitrary if it is possible, within the constraints of chemical “law”, for that relationship to have been otherwise than it is. But while modality is certainly important for understanding chemical arbitrariness, understanding its biological (...) role also requires an account of the concrete causal-functional features that distinguish arbitrary from non-arbitrary phenomena. In this paper I elaborate on this under-emphasised aspect by offering a general account of these features: arbitrary relations are instantiated by mechanisms that involve molecular adapters, which causally couple two properties or processes which would otherwise be uncorrelated. Additionally, adapters work by acting as intermediate rather than cooperating causes. (shrink)

First the ‘Weismann barrier’ and later on Francis Crick’s ‘central dogma’ of molecular biology nourished the gene-centric paradigm of life, i.e., the conception of the gene/genome as a ‘central source’ from which hereditary specificity unidirectionally flows or radiates into cellular biochemistry and development. Today, due to advances in molecular genetics and epigenetics, such as the discovery of complex post-genomic and epigenetic processes in which genes are causally integrated, many theorists argue that a gene-centric conception of the organism has become problematic. (...) Here, we first explore the causal implications of the following two central dogma-related issues: (1) widespread reverse transcription—arguing for an extension from ‘DNA-genome’ to RNA-encompassing ‘NA-genome’ and, thus, from traditional DNA-centrism to a broader ‘NA-centrism’; and (2) the absence of a mechanism of reverse translation—arguing for the ‘structural primacy’ of NA-sequence over protein in cellular biochemistry. Secondly, we explore whether this latter conclusion can be extended to a ‘functional primacy’ of NA-sequence over protein in cellular biochemistry, which would imply a limited kind of ‘gene/NA-centrism’ confined to the subcellular level of NA/protein-based biochemistry. Finally, we explore the conditions—and their (non)fulfilment—for a more generalised form of gene-centrism extendable to higher levels of biological organisation. We conclude that the higher we go in the biological hierarchy, the more dubious gene-centric claims become. (shrink)

In this paper I use a case study—the discovery of the chaperon function exerted by proteins in the various steps of the hereditary process—to re-discuss the question whether the nucleic acids are the sole repositories of relevant information as assumed in the information theory of heredity. The evidence I here present of a crucial role for molecular chaperones in the folding of nascent proteins, as well as in DNA duplication, RNA folding and gene control, suggests that the family of proteins (...) acting as molecular chaperones provides information that is complementary to that stored in the nucleic acids, and equally important. A re-evaluation of the role of proteins in the hereditary process is in order away from the gene-centric approach of the information theory of heredity, to which neo-Darwinian evolutionists adhere. (shrink)

We examine the idea that there is a sub-discipline in philosophy of science, phi-losophy in science, whose researchers use philosophical tools to advance solu-tions to scientific problems. Rather, we propose that these tools are standard epistemic, cognitive, or intellectual tools at work in all rational activity, and therefore these researchers engage in scientific or metascientific research.

The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of (...) three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal.This semantic framework is applied to two cases from the history of biology: the homology concept as used in 19th and 20th century biology, and the gene concept as used in different parts of the 20th century. The homology case study argues that the advent of Darwinian evolutionary theory, despite introducing a new definition of homology, did not bring about a new homology concept (distinct from the pre-Darwinian concept) in the 19th century. Nowadays, however, distinct homology concepts are used in systematics/evolutionary biology, in evolutionary developmental biology, and in molecular biology. The emergence of these different homology concepts is explained as occurring in a rational fashion. The gene case study argues that conceptual progress occurred with the transition from the classical to the molecular gene concept, despite a change in reference. In the last two decades, change occurred internal to the molecular gene concept, so that nowadays this concept's usage and reference varies from context to context. I argue that this situation emerged rationally and that the current variation in usage and reference is conducive to biological practice.The dissertation uses ideas and methodological tools from the philosophy of mind and language, the philosophy of science, the history of science, and the psychology of concepts. (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)

For a number of years, the debate in evolutionary biology over the ’levels of selection’ has attracted intense interest from philosophers of science. The main question concerns the level of the biological hierarchy at which natural selection occurs. Does selection act on organisms, genes, groups, colonies, demes, species, or some combination of these? According to traditional Darwinian theory the answer is the organism -- it is the differential survival and reproduction of individual organisms that drives the evolutionary process. But there (...) are alternative views too, including pluralist views which say that the choice between different levels of selection is often a matter of perspective, not empirical fact. (shrink)

A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name a few. Based on my experience teaching students from these and similar majors, I argue that the field of environmental ethics has much to teach these students. They come to me with pent-up questions and a feeling that more is needed to fully engage in their subjects, and (...) I believe some exposure to environmental ethics can help focus their interests and goals. I identify three primary areas in which environmental ethics can con- tribute to their education. The first is an examination of who (or what) should be considered to be part of our moral community (i.e., the community to whom we owe direct duties). Is it humans only? Or does it include all sentient life? Or all life? Or ecosystems considered holistically? Often, readings implicitly assume one or more of these answers; the goal is to make the student more sensitive to these implicit claims and to get them to think about the different reasons that support them. The second area, related to the first, is the application of the different answers concerning the extent of the ethical community to real environmental issues and problems. Students need to be aware of how the different answers concerning the moral community can imply conflicting answers for how we should act in certain cases and to think about ways to move toward conflict resolution. The third area in which environmental ethics can contribute is a more conceptual one, focusing on central concepts such as biodiversity, sustainability, species, and ecosystems. Exploring and evaluating various meanings of these terms will make students more reflective and thoughtful citizens and biologists, sensitive to the implications that different conceptual choices make. (shrink)

This paper assesses Sarkar's ([2003]) deflationary account of genetic information. On Sarkar's account, genes carry information about proteins because protein synthesis exemplifies what Sarkar calls a ‘formal information system’. Furthermore, genes are informationally privileged over non-genetic factors of development because only genes enter into arbitrary relations to their products (in virtue of the alleged arbitrariness of the genetic code). I argue that the deflationary theory does not capture four essential features of the ordinary concept of genetic information: intentionality, exclusiveness, asymmetry, (...) and causal relevance. It is therefore further removed from what is customarily meant by genetic information than Sarkar admits. Moreover, I argue that it is questionable whether the account succeeds in demonstrating that information is theoretically useful in molecular genetics. Introduction Sarkar's Information System The Pre-theoretic Features of Genetic Information 3.1 Intentionality 3.2 Exclusiveness 3.3 Asymmetry 3.4 Causal relevance Theoretical Usefulness Conclusion CiteULike Connotea Del.icio.us What's this? (shrink)

Watson and Crick’s discovery of the structure of DNA led to developments that transformed many biological sciences. But what were the relevant developments and how did they transform biology? Much of the philosophical discussion concerning this question can be organized around two opposing views: theoretical reductionism and layer-cake antireductionism. Theoretical reductionist and their anti-reductionist foes hold two assumptions in common. First, both hold that biological knowledge is structured like a layer cake, with some biological sciences, such as molecular biology cast (...) at lower levels of organization, and others, such as classical genetics, cast at higher levels. Second, both assume that scientific knowledge is structured by theory and that the productivity of scientific research depends on whether the underlying theory identifies the fundamentals upon which the phenomena to be explained and investigated depend. In the first part of this paper, I challenge these assumptions. In the second part, I show how recasting the basic theory of classical genetics made it possible to retool the methodologies of genetics. It was the investigative power of these retooled methodologies, and not the explanatory power of a gene-based theory, that transformed biology. (shrink)

This paper explores John Maynard Smith’s conceptual work on animal signals. Maynard Smith defined animal signals as traits that (1) change another organism’s behaviour while benefiting the sender, that (2) are evolved for this function, and that (3) have their effects through the evolved response of the receiver. Like many ethologists, Maynard Smith assumed that animal signals convey semantic information. Yet his definition of animal signals remains silent on the nature of semantic information and on the conditions determining its content. (...) I therefore compare three ways to specify the semantic content of animal signals. The first suggestion models semantic content on Maynard Smith’s theory of genetic information. On the second proposal, semantic content is equated with a condition identified by conventional content ascriptions. The third suggestion is to explain semantic content in terms of consumer-based teleosemantics. I show how these accounts equate semantic content with distinct kinds of conditions and how they differ with respect to the kinds of traits that qualify as carrying semantic information. (shrink)

Recently the terms “codes” and “information” as used in the context of molecular biology have been the subject of much discussion. Here I propose that a variety of structural realism can assist us in rethinking the concepts of DNA codes and information apart from semantic criteria. Using the genetic code as a theoretical backdrop, a necessary distinction is made between codes qua symbolic representations and information qua structure that accords with data. Structural attractors are also shown to be entailed by (...) the mapping relation that any DNA code is a part of (as the domain). In this framework, these attractors are higher-order informational structures that obviate any “DNA-centric” reductionism. In addition to the implications that are discussed, this approach validates the array of coding systems now recognized in molecular biology. (shrink)

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

The genetic code has been regarded as arbitrary in the sense that the codon-amino acid assignments could be different than they actually are. This general idea has been spelled out differently by previous, often rather implicit accounts of arbitrariness. They have drawn on the frozen accident theory, on evolutionary contingency, on alternative causal pathways, and on the absence of direct stereochemical interactions between codons and amino acids. It has also been suggested that the arbitrariness of the genetic code justifies attributing (...) semantic information to macromolecules, notably to DNA. I argue that these accounts of arbitrariness are unsatisfactory. I propose that the code is arbitrary in the sense of Jacques Monod's concept of chemical arbitrariness: the genetic code is arbitrary in that any codon requires certain chemical and structural properties to specify a particular amino acid, but these properties are not required in virtue of a principle of chemistry. This notion of arbitrariness is compatible with several recent hypotheses about code evolution. I maintain that the code's chemical arbitrariness is neither sufficient nor necessary for attributing semantic information to nucleic acids. (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 recognition of species proceeds by two fairly distinct phases: (1) the sorting of individuals into groups or basic taxa (‘discovery’) (2) the checking of those taxa as candidates for species-hood (‘justification’). The target here is a rational reconstruction of phase 1, beginning with a discussion of key terms. The transmission of ‘meaning’ is regarded as bimodal: definition states the intension of the term, and diagnosis provides a disjunction of criteria for recognition of its extension. The two are connected by (...) a spectrum, with purely theoretical definition at one pole and purely ‘operational’ diagnosis at the other, with the more operational elements explained by the more theoretical. The current plethora of species concepts provides a good example. Accepting the Ghiselin–Hull thesis, that a species is an individual, a basic taxon is therefore also an individual with organisms as its parts. In a generalised synchronic individual its parts are conceptually integrated by an integrating principle (IP), which consists of a relation applying within a plan or rule. Fully developed, such an IP ensures the maximisation of the information content of the individual. A diachronic individual is then the set of its component synchronic parts, and its IP is provided by near-identity in an appropriate space-time (not necessarily physical). The integration of parts of an individual is illuminated by Gasking's concept of a proper group (in this case a chain-group), whose members are related by the relation serially fitting together with, the IP completed by an appropriate plan or rule. Gasking also applied the term cluster to a proper group persisting over a substantial period of time, individuated by any member acting as focus. A basic taxon is therefore a cluster of individuals, integrated by the relation significantly taxonomically similar and the rule in character-space-time. The nature of those concepts is discussed and defended. A species will inherit certain of the attributes of the preceding basic taxon (taxa). In at least the synchronic version its parts (individuals) will resemble each other significantly, providing the intuitive applicability of ‘members of’ and ‘instances of’ a species. Also, the notion that a species’ name is given by pure ostension, via a name-bearer (holotype) is empirically incoherent: the name cannot be applied in practice without an appropriate set of diagnostic traits. (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)

Terms loaded with informational connotations are often employed to refer to genes and their dynamics. Indeed, genes are usually perceived by biologists as basically ‘the carriers of hereditary information.’ Nevertheless, a number of researchers consider such talk as inadequate and ‘just metaphorical,’ thus expressing a skepticism about the use of the term ‘information’ and its derivatives in biology as a natural science. First, because the meaning of that term in biology is not as precise as it is, for instance, in (...) the mathematical theory of communication. Second, because it seems to refer to a purported semantic property of genes without theoretically clarifying if any genuinely intrinsic semantics is involved. Biosemiotics, a field that attempts to analyze biological systems as semiotic systems, makes it possible to advance in the understanding of the concept of information in biology. From the perspective of Peircean biosemiotics, we develop here an account of genes as signs, including a detailed analysis of two fundamental processes in the genetic information system (transcription and protein synthesis) that have not been made so far in this field of research. Furthermore, we propose here an account of information based on Peircean semiotics and apply it to our analysis of transcription and protein synthesis. (shrink)

The established definition of replication in terms of the conditions of causality, similarity and information transfer is very broad. We draw inspiration from the literature on self-reproducing automata to strengthen the notion of information transfer in replication processes. To the triple conditions of causality, similarity and information transfer, we add a fourth condition that defines a “generative replicator” as a conditional generative mechanism, which can turn input signals from an environment into developmental instructions. Generative replication must have the potential to (...) enhance complexity, which in turn requires that developmental instructions are part of the information that is transmitted in replication. Demonstrating the usefulness of the generative replicator concept in the social domain, we identify social generative replicators that satisfy all of the four proposed conditions. (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)

‘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)

A recent debate concerning the representational content of DNA in developmental processes has opposed “dynamicists” and “computationalists.” I review the arguments in favor of a representational interpretation of the role of genes, and show that they are inconclusive. There is a very restricted sense in which genes can be said to represent something, and stronger claims about DNA being a program for the construction of an organism are overstatements. I also show that arbitrariness, taken by representationalists to be a central (...) criterion for identifying representational vehicles, is neither a sufficient nor a necessary condition to qualify as a representation. Finally, I propose a relatively new way to define what programs are, which implies that genetic regulatory networks shouldn’t be thought of as being programs. As a consequence, insofar as cognition and development share similar mechanisms, any computational account of cognition should be significantly weakened. (shrink)