An oft-repeated claim is that there is information in some biological entity or process, most especially in genes. Some of these claims derive from the Central Dogma, population genetics, and the neo-Darwinian program. Others derive from attacks upon evolution, in an attempt to show that “information cannot be created” by natural selection. In this paper I will try to show that the term “information” is a homonym for a range of distinct notions, and that these notions are (...) either of concrete properties, in which case they are little more than a periphrasis for correlation and causation, or of abstract properties, in which case they are observer-dependent. In short, if information is in the concrete world, it is causality. If it is abstract, it is in the head. (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)

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

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

In this paper, I adopt the view that the form which is embodied in matter gives it its essence and converts it into substance (Aristotle). I furthermore understand information as the transmissible state of the form. Living beings as substances can create order in their environment adapted to their needs. The environment in turn has the potential to change the form and other causes such as matter, efficiency/functionality, and goal/intention. Living beings can internalize these changes, propagate them through replication, (...) or share them as information with others. Living beings have progressively acquired through this process advanced form- and information-processing and generation abilities. This positive feedback loop with enhancement in form and information has become one of the main drivers of biological evolution. Based on these considerations, I will address the nature of form and information and the changes that they have undergone during biological evolution. (shrink)

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

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

Whether “information” exists in biology, and in what sense, has been a topic of much recent discussion. I explore Shannon, Dretskean, and teleosemantic theories, and analyze whether or not they are able to give a successful naturalistic account of information—specifically accounts of meaning and error—in biological systems. I argue that the Shannon and Dretskean theories are unable to account for either, but that the teleosemantic theory is able to account for meaning. However, I argue that it is (...) unable to account for error. Thus I conclude that while talk of informational meaning is justifiable within a naturalistic framework, talk of informational error is not, and must be used in a metaphorical sense only. (shrink)

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

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

In 1958, Francis Crick distinguished the flow of information from the flow of matter and the flow of energy in the mechanism of protein synthesis. Crick’s claims about information flow and coding in molecular biology are viewed from the perspective of a new characterization of mechanisms and from the perspective of information as holding a key to distinguishing work in molecular biology from that of biochemistry in the 1950s–1970s . Flow of matter from beginning to (...) end does not occur in the protein synthesis mechanism; flow of information does. The flow of information and coding in molecular biological mechanisms are distinguished, on the one hand, from formal information theory, and, on the other, from information as used in cognitive neuroscience, where information and representation are often coupled. (shrink)

The taxa that appear in biological classifications are commonly seen as representing information about the traits of their member organisms. This paper examines in what way taxa feature in the storage and retrieval of such information. I will argue that taxa do not actually store much information about the traits of their member organisms. Rather, I want to suggest, taxa should be understood as functioning to localize organisms in the genealogical network of life on Earth. Taxa store (...) information about where organisms are localized in the network, which is important background information when it comes to establishing knowledge about organismal traits, but it is not itself information about these traits. The view of species and higher taxa that is proposed here follows from examining three problems that occur in contemporary biological systematics and are discussed here: the problem of generalization over taxa, the problem of phylogenetic inference, and the problematic nature of the Tree of Life. (shrink)

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

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

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

Open peer commentary on the article “Info-computational Constructivism and Cognition” by Gordana Dodig-Crnkovic. Upshot: Info-computational constructivism calls attention to some of the open questions about the origins of information and computation in the living realm. It remains unclear whether both were developed and shaped by evolution by natural selection or if they appeared in living systems independently of it. If the former, it is possible to sketch a scenario with a certain degree of reasonableness and postulate some of the (...) conditions that triggered the emergence of these biological properties. (shrink)

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

Every cell, tissue, organ and organism is competent to use signs to exchange information reaching common coordinations and organisations of both single cell and group behavior. These sign-mediated interactions we term biological communication. The regulatory system that works in development, morphology, cell fate and identity, physiology, genetic instructions, immunity, memory/learning, physical and mental disease depends on epigenetic marks. The communication of cells, persistent viruses and their defectives such as mobile genetic elements and RNA networks ensures both the transport of (...) regulatory instructions and the reprogramming of these instructions. But how are the different states of the epigenome orchestrated? The epigenetic pathways respond to various signaling cues such as DNA methylation, histone variants, histone modifications, chromatin structure, nucleosome remodeling, and epigenetic interactions. Epigenetic signals are responsible for the establishment, maintenance and reversal of transcriptional states that are fundamental for the cell's ability to memorize past events, such as changes in the external environment, socio-sphere or developmental cues. External signals trigger changes in the epigenome, allowing cells to respond dynamically. Internal signals direct activities that are necessary for body maintenance, and repairing damaged tissues and organs. With the emergence of epigenetic memory, organisms can fix historical and context dependent impressive experiences. Evolution from now on learnt to learn. Learning means organisms can avoid reproduction of always the same. This is key to adaptation. However, inheritance of acquired characteristics is only one of the many examples of the explanatory power of epigenetics. Behavioral epigenetics demonstrates the way in which environmental and social experiences produce individual differences in behaviour, cognition, personality, and mental health. This book assembles experts to outline the various motifs of all kinds of epigenetic regulation of cells throughout their lives. (shrink)

Biosemiotics contains at its core fundamental issues of naturalism: are normative properties, such as meaning, referent, and others, part of the natural world, or are they part of a second, intentional and normative, metaphysical realm — one that might be analogically applied to natural phenomena, such as within biological cells — but a realm that nevertheless remains metaphysically distinct? Such issues are manifestations of a fundamental metaphysical split between a “natural” realm and a realm of normativity and intentionality. This problematic (...) metaphysical split derives from conceptual problems originating with the Pre-Socratics; transcending that split requires correcting those problems. In particular, transcending that split requires a model of metaphysical emergence, and, in particular, normative emergence. This paper will limn that argument regarding metaphysical emergence, but focus most strongly on an overview of a model of normative, representational emergence that overcomes that metaphysical diremption. (shrink)

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

We analyze von Weizsäcker’s view regarding the concept of information in physics. In his view, information arises from the reduction of properties of a physical object to their logical descriptive propositions. The smallest element of a lattice of propositions is an atom of information which is considered as the essence of every physical identity including position space. von Weizsäcker calls this element, “ur”. Moreover, Biological evolution is described in terms of enhancement of the variety of forms. Form (...) could be also reduced to descriptive logical propositions, thus to atoms of information. Therefore, information is the fundamental basis in von Weizsäcker’s plan for unifying all branches of Physics including Chemistry and Biology. Yet, there are inadequacies in his lines of reasoning, critically assessed in this paper. (shrink)

Biological systems are typically hierarchically organized, open, nonlinear systems, and inherit all of the characteristics of such systems that are found in the purely physical and chemical domains, to which all biological systems belong. In addition, biological systems exhibit functional properties, and they contain information in a form that is used internally to make required functional distinctions. The existence of these additional biological properties is widely granted, but their exact nature is controversial. I will address first the issue of (...) biological function, and then turn to the issue of information in biosystems. (shrink)

The partner choice approach to understanding the evolution of cooperation builds on approaches that focus on partner control by considering processes that occur prior to pair or group formation. Proponents of the partner choice approach rightly note that competition to be chosen as a partner can help solve the puzzle of cooperation. I aim to build on the partner choice approach by considering the role of signalling in partner choice. Partnership formation often requires reliable information. Signalling is thus important (...) in the context of partner choice. However, the issue of signal reliability has been understudied in the partner choice literature. The issue deserves attention because – despite what proponents of the partner choice approach sometimes claim – that approach does face a cheater problem, which we might call the problem of false advertising in biological markets. Both theoretical and empirical work is needed to address this problem. I will draw on signalling theory to provide a theoretical framework within which to organise the scattered discussions of the false advertising problem extant in the partner choice literature. I will end by discussing some empirical work on cooperation, partner choice, and punishment among humans. (shrink)

Essentialism in philosophy is the position that things, especially kinds of things, have essences, or sets of properties, that all members of the kind must have, and the combination of which only members of the kind do, in fact, have. It is usually thought to derive from classical Greek philosophy and in particular from Aristotle’s notion of “what it is to be” something. In biology, it has been claimed that pre-evolutionary views of living kinds, or as they are sometimes (...) called, “natu-ral kinds”, are essentialist. This static view of living things presumes that no tran-sition is possible in time or form between kinds, and that variation is regarded as accidental or inessential noise rather than important information about taxa. In contrast it is held that Darwinian, and post-Darwinian, biology relies upon varia-tion as important and inevitable properties of taxa, and that taxa are not, therefore, kinds but historical individuals. Recent attempts have been made to undercut this account, and to reinstitute essentialism in biological kind terms. Others argue that essentialism has not ever been a historical reality in biology and its predecessors. In this chapter, I shall outline the many meanings of the notion of essentialism in psychology and social science as well as science, and discuss pro- and anti-essentialist views, and some recent historical revisionism. It turns out that nobody was essentialist to speak of in the sense that is antievolutionary in biology, and that much confusion rests on treating the one word, “essence” as meaning a single notion when in fact there are many. I shall also discuss the philosophical implica-tions of essentialism, and what that means one way or the other for evolutionary biology. Teaching about evolution relies upon narratives of change in the ways the living world is conceived by biologists. This is a core narrative issue. (shrink)

Two decades ago, Rolf Landauer (1991) argued that “information is physical” and ought to have a role in the scientific analysis of reality comparable to that of matter, energy, space and time. This would also help to bridge the gap between biology and mathematics and physics. Although it can be argued that we are living in the ‘golden age’ of biology, both because of the great challenges posed by medicine and the environment and the significant advances that (...) have been made—especially in genetics and molecular and cell biology—we feel that information as an essential aspect of life has been neglected, or at least misunderstood. We therefore summon Maxwell’s Demon and its distant relative the ratchet, and apply these to biology. (shrink)

Frank E. Zachos offers a comprehensive review of one of today's most important and contentious issues in biology: the species problem. After setting the stage with key background information on the topic, the book provides a brief history of species concepts from antiquity to the Modern Synthesis, followed by a discussion of the ontological status of species with a focus on the individuality thesis and potential means of reconciling it with other philosophical approaches. More than 30 different species (...) concepts found in the literature are presented in an annotated list, and the most important ones, including the Biological, Genetic, Evolutionary and different versions of the Phylogenetic Species Concept, are discussed in more detail. Specific questions addressed include the problem of asexual and prokaryotic species, intraspecific categories like subspecies and Evolutionarily Significant Units, and a potential solution to the species problem based on a hierarchical approach that distinguishes between ontological and operational species concepts. A full chapter is dedicated to the challenge of delimiting species by means of a discrete taxonomy in a continuous world of inherently fuzzy boundaries. Further, the book outlines the practical ramifications for ecology and evolutionary biology of how we define the species category, highlighting the danger of an apples and oranges problem if what we subsume under the same name ("species") is in actuality a variety of different entities. A succinct summary chapter, glossary and annotated list of references round out the coverage, making the book essential reading for all biologists looking for an accessible introduction to the historical, philosophical and practical dimensions of the species problem. (shrink)

The main purpose of the paper is to justify the thesis that the presence of biological information is conditional for existence and persistence of life. We will begin with the notion of biological information. In this proposition information is identified with impact, and it is shown the dependence of its location and functioning on the level of organization of animate matter. In accordance with a suggestion of Thomas Aquinas, it seems that precisely information is the reason (...) for the appearance of socalled immanent activities where new life appears. (shrink)

The development of form in living organisms continues to challenge biological research. The concept of biological information encoded in the genetic program that controls development forms a major part of the semiotic metaphor in biology. Development is here seen in analogy to an execution of a program, written in a formal language in the computer. Other versions of the semiotic or "nature-as-language" metaphor use other formal or informal aspects of language to comprehend the specific structural relations in nature (...) as explored by molecular and evolutionary biology. This intuitively appealing complex of related ideas, which has a long history in the philosophy of nature and biology, is critically reviewed. The general nature of metaphor in science is considered, and different levels of metaphorical transfer of signification is distinguished. It is argued, that the metaphors may be of considerable value, not only heuristically, but in order to comprehend the irreducible nature of living organisms. In arguing for a semiotic perspective on living nature, it makes a marked difference whether the departure is made from the tradition of F. de Saussure´s structural linguistics or from the tradition of general semiotics of C. S. Peirce. An agenda is made for a Peircean perspective on the semiotics of nature. (shrink)

With the purpose to understand better the role of information not only in communication systems, but actually in our environmental reality, this paper presented the model of Universal Triangle of Reality, composed by Matter, Energy and Information, as fundamental constitutive components of this reality. Arguments coming from the field of physics, both at the cosmic and microparticles scale are presented, showing undoubtable conclusions that information is a fundamental component of reality in our material world. At the cosmic (...) level, where the unusual high concentration of mass in the black holes constitutes a special state of matter, suitable for analysis of their special properties, the problem of the conservation principle of information is discussed. At the quantum level, the special unusual characteristics derived from the non-localization principle are also highlighted, together with information-involved problems and solutions. The Universal Triangle of Reality in the living systems reveals the high role of the involved information, both as the informational common organization on the entire evolution scale, and as the info-dynamics processes inside of own structure and resulted from interaction with the environment. The relevant advances in the approaching and understanding of the functionality of the living systems from informational point of view are highlighted, showing the high contribution of information concepts in understanding/solving of various older/recent problems in philosophy, neuroscience/neurology/psychiatry, neuro-physics/neuropsychology/behavior sciences, geriatrics/gerontology, biology and life sciences. Keywords: information-matter-energy, universal triangle of reality in non-living and living systems, informational system of human body and living structures, neurosciences and life sciences. (shrink)

This paper sets out to analyze how causation works by focusing on biology, as represented by epidemiology and by scientific information on how the body works (“physiology”). It starts by exploring the specificity of evolved physiological systems, in which evolutionary, developmental and proximal causes all fit together, and the concept of function is meaningful; in contrast, this structure does not apply in epidemiology (or outside biology). Using these two contrasting branches of biology, I examine the role (...) both of mechanism and of difference making in causation. I find that causation necessarily involves both mechanism and difference making, and that they play complementary roles. Both are seen as ontologically necessary, even if the evidence is not always available for both. Influential monist accounts that focus on one of these, at the expense of ignoring the other, are found to be inadequate on these and on other grounds. Recent attempts to combine them are reviewed, notably that of Russo and Williamson (Int Stud Philos Sci 21:157–170, 2007), and it is argued that their epistemic view requires there to be a source of the different types of evidence that a rational agent would consider, and that this source must be ontic. I then analyze how causal relationships work in evolved physiological systems and in those studied by epidemiology, with a particular focus on how mechanism interacts with input. Finally, I consider this concept of causation from the perspective of everyday language, and of its possible generalisability outside biology. (shrink)

The idea that development is the expression of information accumulated during evolution and that heredity is the transmission of this information is surprisingly hard to cash out in strict, scientific terms. This paper seeks to do so using the sense of information introduced by Francis Crick in his sequence hypothesis and central dogma of molecular biology. It focuses on Crick's idea of precise determination. This is analysed using an information-theoretic measure of causal specificity. This allows (...) us to reconstruct some of Crick's claims about information in transcription and translation. Crick's approach to information has natural extensions to non-coding regions of DNA, to epigenetic marks, and to the genetic or environmental upstream causes of those epigenetic marks. Epigenetic information cannot be reduced to genetic information. The existence of biological information in epigenetic and exogenetic factors is relevant to evolution as well as to development. (shrink)

Beginning with this issue, the "Review Essays" section of the journal has been renamed "Critical Assessments." The new name more accurately describes not only the content of the section but also the journal's methods of assessment. Submissions to the section are peer reviewed; published essays are catalogued and indexed like the rest of the content of Perspectives in Biology and Medicine.Where many journals publish reviews on the assets and liabilities of newly published books, the Critical Assessments section of Perspectives (...) in Biology and Medicine aims for robust, engaging essays, written in an informal style about important new books, and also about important new articles. Books are a typical means of publishing... (shrink)

Modern biology gives many casuistic descriptions of mutual informational interconnections between organisms. Semiotic and hermeneutic processes in biosphere require a set of “sentient” community of players who optimize their living strategies to be able to stay in game. Perceptible surfaces of the animals, semantic organs, represent a special communicative interface that serves as an organ of self-representation of organic inwardness. This means that theinnermost dimensions and potentialities of an organism may enter the senses of other living being when effectively (...) expressed on the outermost surfaces of theformer and meaningfully interpreted by the later. Moreover, semantic organs do not exist as objectively describable entities. They are always born via interpretative act and their actual form depends on both the potentialities of body plan of a bearer and the species-specific interpretation of a receiver. As such the semantic organs represent an important part of biological reality and thus deserve to be contextualized within existing comparative vocabulary. Here we argue that the study of the organic self-representation has a key importance for deeper insight into the evolution of communicative coupling among living beings. (shrink)

Metaphor influences the construction of biological models and theories and the analysis of its use can reveal important tools of thought. Some aspects of biological organisation are investigated through the analysis of metaphors associated with treating biosystems as a kind of text. In particular, the use of glue and verbs is considered. Some of the reasons why glue is important in the construction of hierarchies are pursued in the light of specific examples, and some of the conceptual links between glue (...) in biology and other domains is discussed. Verbs are shown to be important in the construction of networks. Some of the relations between glue, verb and text are considered and the text metaphor is placed within a much broader context of ideas associated with form, relation and system. The paper concludes with comments on the nature of biological information and the need for extending or better understanding the verbal vocabulary. (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 discuss foundational issues of quantum information biology —one of the most successful applications of the quantum formalism outside of physics. QIB provides a multi-scale model of information processing in bio-systems: from proteins and cells to cognitive and social systems. This theory has to be sharply distinguished from “traditional quantum biophysics”. The latter is about quantum bio-physical processes, e.g., in cells or brains. QIB models the dynamics of information states of bio-systems. We argue that the (...) class='Hi'>information interpretation of quantum mechanics is the most natural interpretation of QIB. Biologically QIB is based on two principles: adaptivity; openness. These principles are mathematically represented in the framework of a novel formalism— quantum adaptive dynamics which, in particular, contains the standard theory of open quantum systems. (shrink)

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

Molecular Weismannism is the claim that: “In the development of an individual, DNA causes the production both of DNA (genetic material) and of protein (somatic material). The reverse process never occurs. Protein is never a cause of DNA”. This principle underpins both the idea that genes are the objects upon which natural selection operates and the idea that traits can be divided into those that are genetic and those that are not. Recent work in developmental biology and in philosophy (...) of biology argues that an acceptance of Molecular Weismannism requires the tacit assumption that genetic causes are different in kind from other developmental causes. They argue that if this assumption proves to be unwarranted then we should abandon, not just gene selectionism and gene centred functional solutions to the units of selection problem, but also the very notion that there is any such thing as a “genetic trait”. A group of possible causal distinctions (proximity, ultimacy and specificity) are explored and found wanting. It is argued that an extended version of information theory, while not strong enough to support Molecular Weismannism, will support both the claim that traits can be divided into those that are genetic and those that are not as well as the claim that there is good reason to privilege genetic causes within evolutionary and developmental explanations. The outcome of this for the units of selection debate is explored. (shrink)

Book Information Nature's Purposes: Analyses of Function and Design in Biology. Edited by Allen Colin, Bekoff Mark and Lauder George. MIT Press. Cambridge. 1998. Pp. vi + 597. Paperback, US$31.50.

Causal selection is the task of picking out, from a field of known causally relevant factors, some factors as elements of an explanation. The Causal Parity Thesis in the philosophy of biology challenges the usual ways of making such selections among different causes operating in a developing organism. The main target of this thesis is usually gene centrism, the doctrine that genes play some special role in ontogeny, which is often described in terms of information-bearing or programming. This (...) paper is concerned with the attempt of confronting the challenge coming from the Causal Parity Thesis by offering principles of causal selection that are spelled out in terms of an explicit philosophical account of causation, namely an interventionist account. I show that two such accounts that have been developed, although they contain important insights about causation in biology, nonetheless fail to provide an adequate reply to the Causal Parity challenge: Ken Waters's account of actual-difference making and Jim Woodward's account of causal specificity. A combination of the two also doesn't do the trick, nor does Laura Franklin-Hall's account of explanation (in this volume). We need additional conceptual resources. I argue that the resources we need consist in a special class of counterfactual conditionals, namely counterfactuals the antecedents of which describe biologically normal interventions. (shrink)

Increasingly, biologists are using computers to model and to create biological representations. However, the exponential growth in available biological dataposes a challenge for experimental and theoretical researchers in both Biology and in Computer Science. In short, when even the simple retrieval of relevant biological information for a researcher becomes a complex task — its analysis and synthesis with other biological information will become even more daunting and unlikely. In this context, specially organized ‘structures of representation’ are needed (...) for the efficient interpretation of experimentally generated data. The “semantic Web” is a recent trend in networking techniques that we will examine here as a possible strategy for the computation of biological data — one that may allow us to take into account both the semiotic dimensions of biological processes, as well as their dynamic organization into stable and systemic levels. Thereupon, we propose that a semantic network for biology could benefit from principles rooted in such previous representation efforts as computer-generated ‘landscapes’ and ‘physical attractors’ — and that such principles could, in turn, then be better integrated into biological research through the development of a more semiotically informed user / computer interface design. (shrink)

Based on a conference on the nature and origin of biological information held at Cornell University in 2011, this edited volume presents new research by experts in information theory, computer science, numerical simulation, thermodynamics, evolutionary theory, whole organism biology, developmental biology, molecular biology, genetics, physics, biophysics, mathematics, and linguistics.