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)

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)

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

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)

Arbitrariness is a distinctive feature of human language, and a growing body of comparative work is investigating its presence in animal communication. But what is arbitrariness, exactly? We propose to distinguish four notions of semiotic arbitrariness: a notion of opaque association between sign forms and semiotic functions, one of sign-function mapping optionality, one of acquisition-dependent sign-function coupling, and one of lack of motivatedness. We characterize these notions, illustrate the benefits of keeping them apart, and describe two reactions to our proposal: (...) abandoning arbitrariness-talk in favor of the newly introduced conceptual vocabulary, or feeding the distinctions back into the parent concept. (shrink)

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

Recent research on bacteria and other microorganisms has provided interesting insights into the nature of life, cooperation, evolution, individuality or species. In this paper, I focus on the capacity of bacteria to produce molecules that are usually classified as ’signals’ and I defend two claims. First, I argue that certain interactions between bacteria should actually qualify as genuine forms of communication. Second, I use this case study to revise our general theories of signaling. Among other things, I argue that a (...) plausible requirement for a state to qualify as a signal is that it is a minimal cause. (shrink)

Although the definition of ‘signal’ has been controversial for some time within the life sciences, current approaches seem to be converging toward a common analysis. This powerful framework can satisfactorily accommodate many cases of signaling and captures some of its main features. This paper argues, however, that there is a central feature of signals that so far has been largely overlooked: its special causal role. More precisely, I argue that a distinctive feature of signals is that they are minimal causes. (...) I explain this notion, suggest some strategies for identifying its instances and defend its relevance by means of conceptual and empirical considerations. (shrink)

Binding specificity is a centrally important concept in molecular biology, yet it has received little philosophical attention. Here I aim to remedy this by analyzing binding specificity as a causal property. I focus on the concept’s role in drug design, where it is highly prized and hence directly studied. From a causal perspective, understanding why binding specificity is a valuable property of drugs contributes to an understanding of causal selection—of how and why scientists distinguish between causes, not just causes from (...) noncauses. In particular, the specificity of drugs is precisely what underwrites their value as experimental interventions on biological processes. (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)

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)

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)

Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a (...) shallow notion of correlation, the so-called causal sense of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a semantic sense, whereas semantics are deliberately omitted from Shannon’s theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon’s theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence. (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)

Arbitrariness is a distinctive feature of human language, and a growing body of comparative work is investigating its presence in animal communication. But what is arbitrariness, exactly? We propose to distinguish four notions of semiotic arbitrariness: a notion of opaque association between sign forms and semiotic functions, one of sign‐function mapping optionality, one of acquisition‐dependent sign‐function coupling, and one of lack of motivatedness. We characterize these notions, illustrate the benefits of keeping them apart, and describe two reactions to our proposal: (...) abandoning arbitrariness‐talk in favor of the newly introduced conceptual vocabulary, or feeding the distinctions back into the parent concept. (shrink)

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

Intentionality is a central feature of our understanding of the world. We daily attribute intentional states (like beliefs, desires or perceptual states) to explain the behavior of other agents, and many theories appeal to them to understand more complex notions. Nonetheless, intentional states are puzzling entities. This article explains what intentionality is and why it is so important and problematic at the same time. Secondly, it examines various naturalistic theories, which seek to show that intentionality is compatible with a scientific (...) worldview. Finally, given that all extant proposals face significant difficulties, it explores the available options in case no naturalistic theory can succeed. (shrink)

The arbitrariness of a signal has long been seen as a theoretically important but difficult to pin down notion. In this article, we suggest there are at least two different notions of arbitrariness at play in philosophical and scientific debates concerning the use of arbitrary signals, and work towards improved analyses of both. We then consider how these different types of arbitrariness can co-occur and come apart. Finally, we examine the connections between these two types of arbitrariness and the cognitive (...) complexity of signal users with an eye towards better evaluating one possible form of human-nonhuman communicative continuity. We show that each type of arbitrariness bears its own nuanced relationship to cognitive complexity, demonstrating the theoretical importance of keeping these two notions separate. (shrink)

Progress in molecular biology has revealed profound relations between linguistic and genomic sciences, mainly through advances in bioinformatics. The structural symmetries between biochemical and verbal syntaxes raise the question of their origins: did they emerge independently, or did one arise from the other? Does the genetic code contain the traces of a protolanguage, a universal grammar whose gradual evolution and successive mutations progressively led to the polymorphism of natural languages? To explore this question, we review the isomorphism of the genetic (...) code and verbal codes from lexical, syntactic, semantic and pragmatic standpoints. We discuss the limits of these symmetries and their anthropomorphic connotations. We observe the gradual evolution of species and languages according to parallel mechanisms, and the genetic roots of the physiology of language. In conclusion, we hypothesize that human observers may not be projecting linguistic frameworks onto genomic structures. Rather, it could be their linguistic faculties that reflect the grammatical structure of genetic code. (shrink)

Biological modalities (e.g., biological possibility, necessity and counterfactuality) play an important explanatory role in biological practice. However, biological modalities lack truth conditions and the inferential relationship between biological and other modalities is unclear. This thesis addresses these problems, first, by improving upon Daniel Dennett's Library of Mendel. Second, a family of modal logics is introduced. In the simplest model, states are interpreted as codons, the binary relation is interpreted as single substitution mutation and the valuation induces a partition of blocks (...) of codons that code for some amino acid. In addition, the proposed framework allows for a grading of biological possibility and captures various competing notions of biological possibility. Applications include a model checker and a lawless Lewis-style semantics for biological counterfactuals. In short, this thesis lays the groundwork for a theory of biological modalities. (shrink)