Biological Information, Causality and Specificity - an Intimate Relationship

In this chapter we examine the relationship between biological information, the key biological concept of specificity, and recent philosophical work on causation. We begin by showing how talk of information in the molecular biosciences grew out of efforts to understand the sources of biological specificity. We then introduce the idea of ‘causal specificity’ from recent work on causation in philosophy, and our own, information theoretic measure of causal specificity. Biological specificity, we argue, is simple the causal specificity of certain biological processes. This, we suggest, means that causal relationships in biology are ‘informational’ relationships simply when they are highly specific relationships. Biological information can be identified with the storage, transmission and exercise of biological specificity. It has been argued that causal relationships should not be regarded as informational relationship unless they are ‘arbitrary’. We argue that, whilst arbitrariness is an important feature of many causal relationships in living systems, it should not be used in this way to delimit biological information. Finally, we argue that biological specificity, and hence biological information, is not confined to nucleic acids but distributed among a wide range of entities and processes

Gene

The historian Raphael Falk has described the gene as a ‘concept in tension’ (Falk 2000) – an idea pulled this way and that by the differing demands of different kinds of biological work. Several authors have suggested that in the light of contemporary molecular biology ‘gene’ is no more than a handy term which acquires a specific meaning only in a specific scientific context in which it occurs. Hence the best way to answer the question ‘what is a gene’, and the only way to provide a truly philosophical answer to that question is to outline the diversity of conceptions of the gene and the reasons for this diversity. In this essay we draw on the extensive literature in the history of biology to explain how the concept has changed over time in response to the changing demands of the biosciences . Finally, we outline some of the conceptions of the gene current today. The seeds of change are implicit in many of those current conceptions and the future of the gene concept looks set to be at as turbulent as the past

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Signals that make a Difference

Recent work by Brian Skyrms offers a very general way to think about how information flows and evolves in biological networks—from the way monkeys in a troop communicate, to the way cells in a body coordinate their actions. A central feature of his account is a way to formally measure the quantity of information contained in the signals in these networks. In this paper, we argue there is a tension between how Skyrms talks of signaling networks and his formal measure of information. Although Skyrms refers to both how information flows through networks and that signals carry information, we show that his formal measure only captures the latter. We then suggest that to capture the notion of flow in signalling networks, we need to treat them as causal networks. This provides the formal tools to define a measure that does capture flow, and we do so by drawing on recent work defining causal specificity. Finally, we suggest that this new measure is crucial if we wish to explain how evolution creates information. For signals to play a role in explaining their own origins and stability, they can’t just carry information about acts; they must be difference-makers for acts

What are biological sexes?

Biological sexes (male, female, hermaphrodite) are defined by different gametic strategies for reproduction. Sexes are regions of phenotypic space which implement those gametic reproductive strategies. Individual organisms pass in and out of these regions – sexes - one or more times during their lives. Importantly, sexes are life-history stages rather than applying to organisms over their entire lifespan. This fact has been obscured by concentrating on humans, and ignoring species which regularly change sex, as well as those with non-genetic or facultatively genetic sex determination systems. But the general point applies equally to humans. Assigning sexes to pre-reproductive life history stages involves ‘prospective narration’ – classifying the present in terms of its anticipated future. Assigning sexes to adult stages of non-reproductive castes or non-reproductive individuals is a complex matter whose biological meaning differs from case to case. The chromosomal and phenotypic ‘definitions’ of biological sex that are contested in philosophical discussions of sex are actually operational definitions which track gametic sex more or less effectively in some species or group of species. Neither ‘definition’ can be stated for species in general except by defining them in terms of gametic sex. The gametic definition of sex also features in widely accepted models which explain why two biological sexes – either in separate individuals or combined in hermaphroditic individuals - are almost universal in multicellular species. Finally, the fact that a species has only two biological sexes does not imply that every member of the species is either male, female or hermaphroditic, or that the sex of every individual organism is clear and determinate. The idea of biological sex is critical for understanding the diversity of life, but ill-suited to the job of determining the social or legal status of human beings as men or women

Two-electron atoms, ions and molecules

The quantum mechanics of two-electron systems is reviewed, starting with the ground state of the helium atom and helium-like ions, with central charge $Z\ge 2$. For Z=1, demonstrating the stability of the negative hydrogen ion, H$^-$, cannot be achieved using a mere product of individual electron wave functions, and requires instead an explicit account for the anticorrelation among the two electrons. The wave function proposed by Chandrasekhar is revisited, where the permutation symmetry is first broken and then restored by a counter-term. More delicate problems can be studied using the same strategy: the stability of hydrogen-like ions $(M^+,m^-,m^-)$ for any value of the proton-to-electron mass ratio $M/m$; the energy of the lowest spin-triplet state of helium and helium-like ions; the stability of the doubly-excited hydrogen ion with unnatural parity. The positronium molecule $(e^+,e^+,e^-,e^-)$, which has been predicted years ago and discovered recently, can also be shown to be stable against spontaneous dissociation, though the calculation is a little more involved. Emphasis is put on symmetry breaking which can either spoil or improve the stability of systems.Comment: 16 pages, 2 figure

The idea of mismatch in evolutionary medicine

Mismatch is a prominent concept in evolutionary medicine and a number of philosophers have published analyses of this concept. The word ‘mismatch’ has been used in a diversity of ways across a range of sciences, leading these authors to regard it as a vague concept in need of philosophical clarification. Here, in contrast, we concentrate on the use of mismatch in modelling and experimentation in evolutionary medicine. This reveals a rigorous theory of mismatch within which the term ‘mismatch’ is indeed used in several ways, not because it is ill-defined but because different forms of mismatch are.distinguished within the theory. Contemporary evolutionary medicine has unified the idea of ‘evolutionary mismatch’, derived from the older idea of ‘adaptive lag’ in evolution, with ideas about mismatch in development and physiology derived from the Developmental Origins of Health and Disease (DOHaD) paradigm. A number of publications in evolutionary medicine have tried to make this theoretical framework explicit. We build on these to present the theory in as simple and general a form as possible. We introduce terminology, largely drawn from the existing literature, to distinguish the different forms of mismatch. This integrative theory of mismatch captures how organisms track environments across space and time on multiple scales in order to maintain an adaptive match to the environment, and how failures of adaptive tracking lead to disease. Mismatch is a productive organising concept within this theory which helps researchers articulate how physiology, development and evolution interact with one another and with environmental change to explain health outcomes

Effect of short range order on electronic and magnetic properties of disordered Co based alloys

We here study electronic structure and magnetic properties of disordered CoPd and CoPt alloys using Augmented Space Recursion technique coupled with the tight-binding linearized muffin tin orbital (TB-LMTO) method. Effect of short range ordering present in disordered phase of alloys on electronic and magnetic properties has been discussed. We present results for magnetic moments, Curie temperatures and electronic band energies with varying degrees of short range order for different concentrations of Co and try to understand and compare the magnetic properties and ordering phenomena in these systems.Comment: 15 pages,17 postscript figures,uses own style file