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)

Combinatorial behavior involves combining different elements into larger aggregates with meaning. It is generally contrasted with compositionality, which involves the combining of meaningful elements into larger constituents whose meaning is derived from its component parts. Combinatoriality is commonly considered a capacity found in primates and other animals, whereas compositionality often is considered uniquely human. Questioning the validity of this claim, this multidisciplinary special issue of the International Journal of Primatology unites papers that each study aspects of combinatoriality and compositionality found (...) in primate and bird communication systems, tool use, skills, and human language. The majority of authors conclude that compositionality is evolutionarily preceded by combinatoriality and that neither are uniquely human. This introduction briefly introduces readers to the major findings and issues raised by the contributors. -/- . (shrink)

The field of the philosophy of biology is flourishing in its aim to evaluate and rethink the view inherited from the previous century ---the Modern Synthesis. Different research areas and theories have come to the fore in the last decades in order to account for different biological phenomena that, in the first instance, fall beyond the explanatory scope of the Modern Synthesis. This thesis is anchored and motivated by this revolt in the philosophy of biology. -/- The central target in (...) this context is the possibility of naturalizing teleology, a classical nightmare for the history of biology itself. This requires, principally, understanding the causes of teleological explanations without assuming an unfashioned backward causation of sorts. As the riddles of teleological explanations are about their temporal dimension, I analyze different temporal scales of biological processes: evolutionary, developmental, and physiological. -/- The first one is the one defended in the context of the Modern Synthesis. As expected, one of the aims of this thesis is to evaluate the adequacy of an evolutionary account of teleological explanation. The scrutiny is negative. Evolutionary explanations in the context of the Modern Synthesis lack the necessary causal roots to naturalize teleology. Concerning the physiological scale, a long tradition pushed up by Kant and the organicist movement in the 20th century allows us to better understand how teleological explanations can be naturalized in physiological process. The key notions in this temporal scale are self-organization and the recursive, looped character of physiological process. While the physiological scale may be suitably accounted by contemporaries views, such as Autonomous Systems Theory, different central teleological phenomena remain unexplained from a purely physiological perspective. In particular, different issues concerning the (adaptive) construction of organism ---such as plasticity, robustness, variation, novelty, inheritance--- deserve an ontogenetic analysis. -/- The principal aim of this thesis is to provide a theory of teleological development that falls beyond the Modern Synthesis' framework and is prompted by different insights from the history of biology. I call it Agential Teleosemantics. It rests on two central pillars. First, that developmental processes, beyond any gene-centered stance, can be understood in informational terms; i.e. developmental processes are about the interaction of developmental resources conveying biological information. The second ingredient is agentivity, namely the idea that development is regulated by an agentive system according to the adaptiveness of the phenotypic outcomes produced. The role of agency in Agential Teleosemantic is equivalent to the role of genes in the Modern Synthesis: it is responsible for explaining the order and the adaptive complexity in the living realm. -/- The second target of this thesis regards the possibility of naturalizing intentional explanations in cognitive science. The central project involved in such an aim is known as teleosemantics. Classical teleosemantics however is etiological: it explains the teleofunctions of representational systems in terms of evolutionary processes. The different disputes in the contemporary philosophy of biology provide two insights to analyze teleosemantics in cognitive science. First, the challenges against the Modern Synthesis must be extended to the evolutionary approach of etiological teleosemantics. Second, as Agential Teleosemantics suggests an alternative source for teleofunctions ---ontogeny, I offer an attempt to integrate Agential Teleosemantics into cognitive science in order to provide an alternative teleosemantic project to understand intentional explanations in cognitive science. (shrink)

Cultural evolution is normally framed in informational terms. However, it is not clear whether this is an adequate way to model cultural evolutionary phenomena and what, precisely, “information” is supposed to mean in this context. Would cultural evolutionary theory benefit from a well-developed theory of cultural information? The prevailing sentiment is that, in contradistinction to biology, informational language should be used nontechnically in this context for descriptive, but not explanatory, purposes. Against this view, this article makes the case for the (...) need to take a proper biology-based “informational turn” in the cultural evolutionary sciences. I argue that the current vague use of informational language misses out on the potential benefits for advancing understanding of phenomena that information-theoretic reasoning has provided in other sciences, especially genetics. In particular, by emphasizing the informational aspects of cultural evolutionary processes, this approach can clarify some conceptual and methodological problems that have plagued cultural evolutionary theory since its inception, including (1) how to determine the channel conditions of cultural information flow, (2) the nature and scope of cultural information, and (3) how to quantify trends of cultural cumulation. More generally, theories of cultural evolution will be incomplete until the mechanisms underlying cultural processes are better understood and integrated into the explanations. This article explores the adequacy of an information-theoretic framework to accomplish these purposes. (shrink)

New definitions are proposed for communication and language. Communication is defined as the evolution of physical, biochemical, cellular, community, and technological information exchange. Language is defined as community communication whereby the information exchanged comprises evolving individual and group-constructed knowledge and beliefs, that are enacted, narrated, or otherwise conveyed by evolving rule-governed and meaningful symbol systems, that are grounded, interpreted, and used from within evolving embodied, cognitive, ecological, sociocultural, and technological niches. These definitions place emphasis on the evolutionary aspects of communication (...) and language, and they are here differentiated from four older paradigms that instead focus either on the referential or social aspects of language, or the informational or semantic aspects of communication. In contrast with these paradigms, the definitions proposed here for communication and language are in line with a pluralistic evolutionary worldview, one that necessitates the recognition that a multitude of units, levels, mechanisms and processes are involved in bringing forth communication and language. (shrink)

In this talk I present the main results from Anta (2021), namely, that the theoretical division between Boltzmannian and Gibbsian statistical mechanics should be understood as a separation in the epistemic capabilities of this physical discipline. In particular, while from the Boltzmannian framework one can generate powerful explanations of thermal processes by appealing to their microdynamics, from the Gibbsian framework one can predict observable values in a computationally effective way. Finally, I argue that this statistical mechanical schism contradicts the Hempelian (...) (1958) thesis that the predictive power of a scientific theory is directly proportional to its explanatory potential, and vice versa. (shrink)

Evolutionary biologists, evolutionary epistemologists, and biosemioticians have demonstrated that organisms not merely adapt to an external world, but that they actively construct their environmental, sociocultural, and cognitive niches. Denis Noble demonstrates that such is no different for those organisms that engage in science, and he lays bare several crucial assumptions that define the scientific dogmas and practices of evolutionary biology.

Biological and cognitive sciences rely heavily on the idea of information transmitted between natural events or processes. This paper critically assesses some current philosophical views of natural information and defends a view of natural information as Nomic and Factive. Dretske offered a Factive view of information, and recent work on the topic has tended to reject this aspect of his view in favor of a non-Factive, probabilistic approach. This paper argues that the reasoning behind this move to non-Factivity is flawed (...) and mixes up different problems with Dretske’s original view. I show that one of these problems—strictness—has to do with Nomicity rather than Factivity. The other problem—reference class ambiguity—is not solvable just in terms of a theory of natural information. On the Dretske-inspired view I defend, natural information is Factive and Nomic but is insufficient to determine the cognitive or biological content of a natural process. In sum I present an examination what natural information is and what role it can play in our understanding of living and thinking things. (shrink)

There is no denying the Central Dogma’s impact on the biological sciences. Since the Dogma’s formulation by Francis Crick in 1958, however, many have debated the Dogma’s empirical adequacy. My aim is to move beyond these discussions, and instead consider the Central Dogma’s significance to contemporary biological practice. To do this, I consider four distinct approaches for determining the non-descriptive methodological significance of a scientific principle. I argue that these approaches fail to vindicate the Central Dogma, and that, under many (...) of these approaches, the Dogma amounts to a triviality. (shrink)

This paper presents the concept of physical information, and it discusses what physical information is, and how it can be defined. The existence of physical information has been discussed in several studies which recognize that properties of information are characteristic of physical phenomena. That is, information has an objective existence, a lack of meaning, and can be quantified. In addition, these studies recognize how a phenomenon that is denoted as physical information can be expressed as an organization of natural or (...) artificial entities. This paper argues that concepts of (abstract) information that are associated with meaning also depend (to a substantial degree) on physical information. (shrink)

Evolutionary epistemology has experienced a continuous rise over the last decades. Important new theoretical considerations and novel empirical findings have been integrated into the existing framework. In this paper, I would like to suggest three lines of research that I believe will significantly contribute to further advance EE: ontogenetic considerations, key ideas from cognitive biology, and the framework of the Extended Evolutionary Synthesis. EE, in particular the program of the evolution of epistemological mechanisms, seeks to provide a phylogenetic account of (...) the generation of cognitive processes underlying knowledge creation. Traditionally, EE and EEM have been oriented towards an account of evolutionary theory that mainly drew from the tenets of the Modern Synthesis. The Modern Synthesis largely dismisses ontogenetic processes and considers them irrelevant for evolutionary explanations. If anything, the role of development in evolution is believed to be that of a constraint. There is, however, ample evidence for a tight intertwinement of developmental and evolutionary processes. Organisms employ their cognitive apparatus to interact with the environment in order to achieve a fully functioning perceptual and cognitive nervous system. Also, ontogeny provides generative potentials to enable variations that natural selection can act upon. EEM’s agenda may, therefore, strongly benefit from bringing together ontogenetic and phylogenetic approaches. To grapple with this challenge, an alternative vision of the evolutionary theory termed Extended Evolutionary Synthesis could be used. This extended evolutionary theory explores relationships between the processes of individual development and phenotypic change during evolution and can provide a more suitable framework for EEM to draw from. In recent years, cognitive biology has gained momentum as an independent research field. Cognitive biology builds on the concepts of EEM and understands knowledge as a biogenic phenomenon. Its main objective is also the formulation of substantiated interrelations between cognition and evolution but it focuses on cognitive functionality at all levels of biological organization. It thus employs a “vertical” approach that encompasses nested hierarchies which span from single molecules, cells, and tissues to the organismal level, communities, and societies. In contrast to cognitive biology, EEM is here understood to adopt a “horizontal” approach that focuses on phylogenetic explanations of cognition and knowledge acquisition. Linking EEM with the key ideas of cognitive biology could make EEM’s research program stronger as it can more easily accommodate phylogenetic and ontogenetic questions within a hierarchical, multilevel perspective. This is of particular importance for a more comprehensive account of cognition since living systems are subject to context-dependent causal influences from different organizational levels. In addition to EEM, there is a second program of EE. This program has been labeled evolutionary epistemology of theories and understands the increase in human knowledge, such as scientific theories, as naturalistic accounts of evolution. Both, EEM and EET initially drew from the core concepts of the Modern Synthesis. Several scholars have severely criticized the analogies made between EET and the Neo-Darwinian key processes of evolution. In particular processes of random mutation, the rate of variation, natural selection as the unique driving force, and the adaptationist agenda are believed to reveal disanalogies. In contrast to the Modern Synthesis, the Extended Evolutionary Synthesis not only recognizes developmental processes but also ecological interactions and systems dynamics as well as social and cultural evolutionary reciprocity as important evolutionary processes. Concepts of the Extended Evolutionary Synthesis are therefore expected to be more fruitful for re-conceptualizing parallels between scientific theorizing and biological evolution. (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)

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

We describe an approach to measuring biological information where ‘information’ is understood in the sense found in Francis Crick’s foundational contributions to molecular biology. Genes contain information in this sense, but so do epigenetic factors, as many biologists have recognized. The term ‘epigenetic’ is ambiguous, and we introduce a distinction between epigenetic and exogenetic inheritance to clarify one aspect of this ambiguity. These three heredity systems play complementary roles in supplying information for development. -/- We then consider the evolutionary significance (...) of the three inheritance systems. Whilst the genetic inheritance system was the key innovation in the evolution of heredity, in modern organisms the three systems each play important and complementary roles in heredity and evolution. -/- Our focus in the earlier part of the paper is on ‘proximate biology’, where information is a substantial causal factor that causes organisms to develop and causes offspring to resemble their parents. But much philosophical work has focused on information in ‘ultimate biology’. Ultimate information is a way of talking about the evolutionary design of the mechanisms of development and inheritance. We conclude by clarifying the relationship between the two. Ultimate information is not a causal factor that acts in development or heredity, but it can help to explain the evolution of proximate information, which is. (shrink)

Most of us think of memory in terms of the brain's ability to store and retrieve events, facts, and skills. Philosophers and cognitive scientists seek to understand memory in terms of causation and justification. This article steps back from these considerations to reflect broadly on what memory is. Drawing on the paradigm shift underway in mind sciences, I explore the implications of the emerging understanding of cognition as embodied, embedded, extended, and enacted. This new paradigm undermines epistemological dualism and individualism (...) and makes it possible to view memory as an ecological process. (shrink)

The biological sciences have always proven a fertile ground for philosophical analysis, one from which has grown a rich tradition stemming from Aristotle and flowering with Darwin. And although contemporary philosophy is increasingly becoming conceptually entwined with the study of the empirical sciences with the data of the latter now being regularly utilised in the establishment and defence of the frameworks of the former, a practice especially prominent in the philosophy of physics, the development of that tradition hasn’t received the (...) wider attention it so thoroughly deserves. This review will briefly introduce some recent significant topics of debate within the philosophy of biology, focusing on those whose metaphysical themes (in everything from composition to causation) are likely to be of wide-reaching, cross-disciplinary interest. (shrink)

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)

Naturalistic theories of representation seek to specify the conditions that must be met for an entity to represent another entity. Although these approaches have been relatively successful in certain areas, such as communication theory or genetics, many doubt that they can be employed to naturalize complex cognitive representations. In this essay I identify some of the difficulties for developing a teleosemantic theory of cognitive representations and provide a strategy for accommodating them: to look into models of signaling in evolutionary game (...) theory. I show how these models can be used to formulate teleosemantics and expand it in new directions. (shrink)

Theories of epistemology make reference—via the perspective of an observer—to the structure of information transfer, which generates reality, of which the observer himself forms a part. It can be shown that any epistemological approach which implies the participation of tautological structural elements in the information transfer necessarily leads to an antinomy. Nevertheless, since the time of Aristotle the paradigm of mathematics—and thus tautological structure—has always been a hidden ingredient in the various concepts of knowledge acquisition or general theories of information (...) transfer. We hold that Darwin’s Evolutionary Theory is the first scientific theory which consistently presupposes a non-tautological structure for the information transfer and, at the same time, keeps it strictly distinct from the tautological metric of scientific observation. The consequences of this technique—namely the dissociation of information from intentionality—have not yet been fully drawn. (shrink)

According to the proponents of Developmental Systems Theory and the Causal Parity Thesis, the privileging of the genome as “first among equals” with respect to the development of phenotypic traits is more a reflection of our own heuristic prejudice than of ontology - the underlying causal structures responsible for that specified development no more single out the genome as primary than they do other broadly “environmental” factors. Parting with the methodology of the popular responses to the Thesis, this paper offers (...) a novel criterion for ‘causal primacy’, one that is grounded in the ontology of the unique causal role of dispositional properties. This paper argues that, if the genome is conceptualised as realising dispositional properties that are “directed toward” phenotypic traits, the parity of ‘causal roles’ between genetic and extra-genetic factors is no longer apparent, and further, that the causal primacy of the genome is both plausible and defensible. (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)

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)

A central idea of developmental systems theory is ‘parity’ or ‘symmetry’ between genes and non-genetic factors of development. The precise content of this idea remains controversial, with different authors stressing different aspects and little explicit comparisons among the various interpretations. Here I characterise and assess several influential versions of parity.

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)

Genes are thought to have evolved from long-lived and multiply-interactive molecules in the early stages of the origins of life. However, at that stage there were no replicators, and the distinction between interactors and replicators did not yet apply. Nevertheless, the process of evolution that proceeded from initial autocatalytic hypercycles to full organisms was a Darwinian process of selection of favourable variants. We distinguish therefore between Neo-Darwinian evolution and the related Weismannian and Central Dogma divisions, on the one hand, and (...) the more generic category of Darwinian evolution on the other. We argue that Hull’s and Dawkins’ replicator/interactor distinction of entities is a sufficient, but not necessary, condition for Darwinian evolution to take place. We conceive the origin of genes as a separation between different types of molecules in a thermodynamic state space, and employ a notion of reproducers. (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)

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)

This book is conceived as an introductory text into the theory of syntactic and semantic information, and information flow.

The phenomenon of species extinction raises more and more concern among ecologists facing the actual crisis of biodiversity. Scientific investigations of the causes and effects of extinction must be completed by a philosophical analysis of the concept of extinction that aims to clarify the meanings of the term ‘extinction’ and to analyse modalities, criteria and degrees of extinction. We will focus our attention on the apparent paradox of the possible ‘resurrection’ of species in the near future with the help of (...) genetic biotechnology and cloning techniques. The ontological background of the extinction concept is analysed in relation to the idea of species as classes. We will also show that there is no simple analogy between death and species extinction, and develop a conceptualist and dualistic system of supra-individual entities , supported by an instrumentalist approach to genetic manipulations which transform species into interactive kinds, which can go extinct and be recreated. (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)

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)

According to the received view of evolution, only genes are inherited. From this view it follows that only genetically-caused phenotypic variation is selectable and, thereby, that all selection is at bottom genetic selection. This paper argues that the received view is wrong. In many species, there are intergenerationally-stable phenotypic differences due to environmental differences. Natural selection can act on these nongenetically-caused phenotypic differences in the same way it acts on genetically-caused phenotypic differences. Some selection is at bottom nongenetic selection. The (...) argument against the received view involves a reformulation of the concepts of inheritance and heritability. Inherited factors are all those developmental factors responsible for parent–offspring similarity; some inherited factors are genetic and some are not. Heritable variation is intergenerationally-stable phenotypic variation; some such variation is genetically-caused and some is not. The received view and its critics The possibility of nongenetic selection (the lucky butterfly) The reality of nongenetic selection 3.1 Imprinting mechanisms 3.2 Other learning mechanisms 3.3 Other nongenetic mechanisms Genetic and nongenetic inheritance mechanisms Genetic and nongenetic inherited factors Genetic and nongenetic heritability Conclusions + Current address: Dr Matteo Mameli, Research Fellow, King's College, Cambridge, CB2 1ST, United Kingdom, matteo.mameli{at}kings.cam.ac.uk' + u + '@' + d + ''//-->. (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)

‘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)

We reconstruct genetic determinism as a reductionist thesis to the effect that the molecular properties of cells can be accounted for to a great extent by their genetic outfit. The non-reductionist arguments offered at this molecular level often use the relationship between structure and function as their point of departure. By contrast, we develop a non-reductionist argument that is confined to the structural characteristics of biomolecules; no appeal to functions is made. We raise two kinds of objections against the reducibility (...) claim underlying genetic determinism. First, some conceptual distinctions at the protein level cannot be captured on a genetic basis. A one-to-many relationship between DNA sequences and proteins emerges from them. Second, the relationship between genes and proteins is characterized by explanatory loops or reciprocal explanatory dependence. The presence of proteins is explained by the transcription from corresponding DNA sequences, and the latter is in turn accounted for by the action of proteins. By contrast, a reductive account requires a unidirectional explanatory dependence. (shrink)

. Evolutionary psychology and behavioural genomics are both approaches to explain human behaviour from a genetic point of view. Nonetheless, thus far the development of these disciplines is anything but interdependent. This paper examines the question whether evolutionary psychology can contribute to behavioural genomics. Firstly, a possible inconsistency between the two approaches is reviewed, viz. that evolutionary psychology focuses on the universal human nature and disregards the genetic variation studied by behavioural genomics. Secondly, we will discuss the structure of biological (...) explanations. Some philosophers rightly acknowledge that explanations do not involve laws which are exceptionless and universal. Instead, generalisations that are invariant suffice for successful explanation as long as two other stipulations are recognised: the domain within which the generalisation has no exceptions as well as the distribution of the mechanism described by the generalisation should both be specified. It is argued that evolutionary psychology can contribute to behavioural genomic explanations by accounting for these two specifications. (shrink)

In this article, I consider the term “environment” in various claims and models by evolutionists and ecologists. I ask whether “environment” is amenable to a philosophical explication, in the same way some key terms of evolutionary theorizing such as “fitness,” “species,” or more recently “population” have been. I will claim that it cannot. In the first section, I propose a typology of theoretical terms, according to whether they are univocal or equivocal, and whether they have been the object of formal (...) or conceptual attempts of clarification. “Environment” will appear to be in a position similar to “population,” yet almost no extant attempt has been made to make sense of its meaning and reference. In the second section, I will present several theoretical claims or issues that refer to “environment” in apparently very diverse ways, but always supposing a contrastive term, which is not always the same. The third section directly considers models in evolution and in ecology, and asks “where” in them is the environment term. The fourth section proposes that “environment” refers to a distinction between a varying and an invariant term, but shows that this does not exhaust its meaning, which requires making more conceptual differences. Then, I take on the suggestion that there might be two “environment” terms, one in ecology and one in evolution, but show that is not the case. Finally I center on the specific notion of “complex environment,” which is the object of several research programs, and propose a typology of “complex environments” across theories. (shrink)

We demonstrate how different normalization techniques in GC‐MS analysis impart unique properties to the data, influencing any biological inference. Using simulations, and empirical data, we compare the most commonly used techniques (Total Sum Normalization ‘TSN’; Median Normalization ‘MN’; Probabilistic Quotient Normalization ‘PQN’; Internal Standard Normalization ‘ISN’; External Standard Normalization ‘ESN’; and a compositional data approach ‘CODA’). When differences between biological classes are pronounced, ESN and ISN provides good results, but are less reliable for more subtly differentiated groups. MN, TSN, and (...) CODA approaches produced variable results dependent on the structure of the data, and are prone to false positive biomarker identification. In contrast, PQN exhibits the lowest false positive rate, though with occasionally poor model performance. Because ESN requires extensive pre‐planning, and offers only mixed reliability, and ISN, TSN, MN, and CODA approaches are prone to introducing artefactual differences, we recommend the use of PQN in GC–MS research. (shrink)

The question of whether the modern evolutionary synthesis requires an extension has recently become a topic of discussion, and a source of controversy. We suggest that this debate is, for the most part, not about the modern synthesis at all. Rather, it is about the extent to which genetic mechanisms can be regarded as the primary determinants of phenotypic characters. The modern synthesis has been associated with the idea that phenotypes are the result of gene products, while supporters of the (...) extended synthesis have suggested that environmental factors, along with processes such as epigenetic inheritance, and niche construction play an important role in character formation. We argue that the methodology of the modern evolutionary synthesis has been enormously successful, but does not provide an accurate characterization of the origin of phenotypes. For its part, the extended synthesis has yet to be transformed into a testable theory, and accordingly, has yielded few results. We conclude by suggesting that the origin of phenotypes can only be understood by integrating findings from all levels of the organismal hierarchy. In most cases, parts and processes from a single level fail to accurately explain the presence of a given phenotypic trait. The debate between the proponents of the modern and extended syntheses is somewhat reminiscent of the duck-rabbit illusion. The two sides are probably talking about the same thing, but from different perspectives. If not, then we argue that the challenge is to do an experiment that rules out the alternative view. (shrink)

This article reconsiders the theoretical role of the genetic code. By drawing on published and unpublished sources from the 1950s, I analyse how the code metaphor was actually employed by the scientists who first promoted its use. The analysis shows that the term ‘code’ picked out mechanism sketches, consisting of more or less detailed descriptions of ordinary molecular components, processes, and structural properties of the mechanism of protein synthesis. The sketches provided how-possibly explanations for the ordering of amino acids by (...) nucleic acids. I argue that employing the code metaphor was justified in virtue of its descriptive-denotational and explanatory roles, and because it highlighted a similarity with conventional codes that was particularly salient at the time. 1 Introduction2 Coding Schemes in the 1950s2.1 The research problem: Determining amino acid sequences2.2 The solution: Mapping schemes or ‘codes’3 The Code Metaphor Played Descriptive and Explanatory Roles4 Theness of Codes and the Expendability of the Code Metaphor5 The Role of Arbitrariness6 Conclusions. (shrink)

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Information plays an important role not only in evolution—genetics can be seen as a mechanism to transfer information from one generation to the next—but also in ecology: virtually all organisms use information about their environment to adjust their behavior and life histories. Indeed, being adapted to something can be defined as having the right information to solve the life-history problems that this creates. It then becomes irrelevant precisely where this information came from (genetics, experience, culture, etc.) but rather becomes an (...) issue of how to assess the fitness value of this information. Here I will explore in some detail the conceptual consequences of the information-based view of evolution. In particular, I will focus on how individuals are actually associations of smaller units that depend on each other’s genetic information and on information from multiple external sources. An important and fundamental problem arises when these different sources of information do not suggest the same adaptations. Conflicting information may thus give new insight into the causes of stress. (shrink)

Recent work on the evolution of signaling systems provides a novel way of thinking about genetic information, where information is passed between genes in a regulatory network. I use examples from evolutionary developmental biology to show how information can be created in these networks and how it can be reused to produce rapid phenotypic change.

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)

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 theory of niche construction adds a second general inheritance system, ecological inheritance, to evolution . Ecological inheritance is the inheritance, via an external environment, of one or more natural selection pressures previously modified by niche-constructing organisms. This addition means descendant organisms inherit genes, and biotically transformed selection pressures in their environments, from their ancestors. The combined inheritance is called niche inheritance. Niche inheritance is used as a basis for classifying the multiple genetic and non-genetic, inheritance systems currently being proposed (...) as possibly significant in evolution . Implications of niche inheritance for the relationship between evolution and development are discussed. (shrink)