John Collier

INFORMATION IN BIOLOGICAL SYSTEMS

Introduction The notion of information has developed in a number of different ways (as discussed in this volume), and many of them have been applied to biology, both usefully and gratuitously, and even misleadingly. These multiple notions of information have not surprisingly led to apparently contradictory claims by authors who have really been talking past each other, although there are also substantive issues at stake. The aim of this chapter is to review some of the ways that notions of information have been used in biology, to disentangle them, and to evaluate their implications and aptness, as well as to point out some of the more widespread confusions. In particular, I will compare the use of information as a technology of measurement, which does not imply that there is anything present that might be called „information‟, with a stronger usage of information in biology that attributes information to biological systems in a non-instrumental way. This distinction between instrumental and substantive uses of information in biological studies often turns on the notion of information used, so it is important in each case to be clear what is at stake. Where there is a choice, I will focus on the substantive use of information in biology. Roughly, substantive use of information uses information in an explanatory way in addition to any representational instruments. 1 I will not discuss what falls under the general heading of

Anticipatory Functions, Digital-Analog Forms and Biosemiotics: Integrating the Tools to Model Information and Normativity in Autonomous Biological Agents

We argue that living systems process information such that functionality emerges in them on a continuous basis. We then provide a framework that can explain and model the normativity of biological functionality. In addition we offer an explanation of the anticipatory nature of functionality within our overall approach. We adopt a Peircean approach to Biosemiotics, and a dynamical approach to Digital-Analog relations and to the interplay between different levels of functionality in autonomous systems, taking an integrative approach. We then apply the underlying biosemiotic logic to a particular biological system, giving a model of the B-Cell Receptor signaling system, in order to demonstrate how biosemiotic concepts can be used to build an account of biological information and functionality. Next we show how this framework can be used to explain and model more complex aspects of biological normativity, for example, how cross-talk between different signaling pathways can be avoided. Overall, we describe an integrated theoretical framework for the emergence of normative functions and, consequently, for the way information is transduced across several interconnected organizational levels in an autonomous system, and we demonstrate how this can be applied in real biological phenomena. Our aim is to open the way towards realistic tools for the modeling of information and normativity in autonomous biological agents.

A Dynamical Approach to Identity and Diversity in Complex Systems

The subject of this chapter is the identity of individual dynamical objects and properties. Two problems have dominated the literature: trans-temporal identity and the relation between composition and identity. Most traditional approaches to identity rely on some version of classification via essential or typical properties, whether nominal or real. Nominal properties have the disadvantage of producing unnatural classifications, and have several other problems. Real properties, however, are often inaccessible or hard to define (strict definition would make them nominal). I suggest that classification should be in terms of dynamical properties of systems, starting with individual systems rather than classes, and working up by abstractions that fit causal generalities. The advantage of this approach is that individuality is testable and revisable as we come to know more about systems. Another advantage is that if anything is real, then it is the dynamical. Once I have presented this approach in general, I will show that the central concept of dynamical cohesion (the “dividing glue”) is amenable to giving a principled account of individuation as a process, at the same time explaining the origin of diversity. Some other advantages of this approach are presented, including how it can be used as a basis for testable classifications. This last has moral implications, since cohesion at the individual and the social levels, and their interactions, can impinge on proper moral decisions.

Signs Without Minds

In a number of places, such as CP 2.274 (1897), Peirce argues that anything with the necessary triadic structure of sign, object and interpretant can be a proper sign, even if there is no mental representation involved, though he says in the same passage that signs usually, if not always, have a mental interpretant (Peirce, The philosophy of Peirce, selected writings, 1940, p. 100). He notes that the notion of interpretant does not logically require consciousness, but since we have no clear cases that do not, so we must at least fix our understanding of semiosis with these clear cases (Peirce, The philosophy of Peirce, selected writings, 1940, p. 282). The advent of biosemiotics has extended the notion of semiosis well into the non-mental sphere. In some cases in biosemiotics the signs are similar to human cognitive signs by involving perceptions and possibly even deliberate action, but many proposed cases within biosemiotics do not involve anything that might be considered to be mental, especially within endobiosemiotics, which involves at its lowest level chemical processes. If these extensions of Peircean semiotics are sound we need a clear idea of what it is to be a sign when minds are not involved. Peirce gives us some hints about how the notion of semiosis might be extended, and what the limits of its extension might be. These come from both his paradigmatically mental signs as well as what he says about non-mental signs, including signs in biological systems.

Holism and Emergence: Dynamical Complexity Defeats Laplace’s Demon

Abstract The paradigm of Laplacean determinism combines three regulative principles: determinism, predictability, and the explanatory adequacy of universal laws together with purely local conditions. Historically, it applied to celestial mechanics, but it has been expanded into an ideal for scientific theories whose cogency is often not questioned. Laplace’s demon is an idealization of mechanistic scientific method. Its principles together imply reducibility, and rule out holism and emergence. I will argue that Laplacean determinism fails even in the realm of planetary dynamics, and that it does not give suitable criteria for explanatory success except within very well defined and rather exceptional domains. Ironically, the very successes of Laplacean method in the Solar System were made possible only by processes that are not themselves tractable to Laplacean methodology. The results of some of these processes were first observed in 1964, and violate the Lapacean requirements of locality and predictability, opening the door to holism and nonreducibility, i.e., emergence. Despite the falsification of Laplacean methodology, the explanatory resources of holism and emergence remain in scientific limbo, though emergence has been used somewhat indiscriminately in recent scientific literature. I make some remarks at the end about the proper use of emergence in its traditional sense going back to C.D. Broad.

Explaining Biological Functionality: Is Control Theory Enough?

Abstract It is generally agreed that organisms are Complex Adaptive Systems. Since the rise of Cybernetics in the middle of the last century ideas from information theory and control theory have been applied to the adaptations of biological organisms in order to explain how they work. This does not, however, explain functionality, which is widely but not universally attributed to biological systems. There are two approaches to functionality, one based on etiology (what a trait was selected for), and the other based in autonomy. I argue that the etiological approach, as understood in terms of control theory, suffers from a problem of symmetry, by which function can equally well be placed in the environment as in the organism. Focusing on the autonomy view, I note that it can be understood to some degree in terms of control theory in its version called second order cybernetics. I present an approach to second order cybernetics that seems plausible for organisms with limited computational power, due to Hooker, Penfold and Evans. They hold that this approach gives something like concepts, certainly abstractions from specific situations, a trait required for functionality in its system adaptive form (i.e., control of the system by itself). Using this cue, I argue that biosemiotics provides the methodology to incorporate these quasi concepts into an account of functionality.

Informal pragmatics and linguistic creativity

Examples of successful linguistic communication give rise to two important insights: (1) it should be understood most fundamentally in terms of the pragmatic success of each individual utterance, and (2) linguistic conventions need to be understood as on a par with the non-linguistic regularities that competent language users rely upon to refer. Syntax and semantics are part of what Barwise and Perry call the context of the utterance, contributing to the pragmatics of the utterance. This full and distributed multichannel context determines meaning if anything does. On the standard account of context, context disambiguates the meaning of language, but it is at least as apt in many situations to say that language disambiguates context. In practice, the two work together, sometimes with more emphasis on one than the other. Reference should be understood in pragmatic terms (it is an act) and, since success is often achieved in non-standard, creative ways, any formalisation of pragmatics can only be partial. The need for such an inventive approach to referring traces back to the need for language to be highly efficient, with expressions underdetermining their interpretation. Next, the shared semantic and syntactic regularities, which might seem to be independent of the context of an utterance, should be understood as also being part of that context. Past usage underdetermines how terms can be used since it allows for multiple projections. Successful reference with novel uses that are disambiguated by context can become the ground for new conventions.

Prospects for Reconciling Sellars’ World Images

Abstract Almost fifty years ago Wilfrid Sellars described two competing ways of imagining the world, the Manifest Image and the Scientific Image. The Manifest Image is an idealization of common sense aided by critical philosophy, whereas the Scientific Image is the product of our best science. The methodologies of the two images are very different: the Manifest Image deals with experience and looks only at relations among bits of experience and analysis of experience into the relations that must lie behind it, whereas the Scientific Image is grounded in explanations of experience, typically causal explanations. This need not be a problem if the two images are compatible. Sellars argued, however, that the Manifest Image implies continuity, but the best science of the time told us (or appeared to tell us) that the world is made up of discrete subatomic particles and discrete transitions between quantum states, making the two incompatible. Although Sellars noted that future science might show that the world is continuous, he did not follow this up. Science in the last fifty years has given much more evidence for continuity in the world from complexity studies and Quantum Mechanics, so perhaps the two images can be reconciled after all.

After the fall: Religious capacities and the error theory of morality

The target article proposes an error theory for religious belief. In contrast, moral beliefs are typically not counterintuitive, and some moral cognition and motivation is functional. Error theories for moral belief try to reduce morality to nonmoral psychological capacities because objective moral beliefs seem too fragile in a competitive environment. An error theory for religious belief makes this unnecessary.

Evolutionary Moral Realism

Evolutionary moral realism is the view that there are moral values with roots in evolution that are both specifically moral and exist independently of human belief systems. In beginning to sketch the outlines of such a view, we examine moral goods like fairness and empathetic caring as valuable and real aspects of the environments of species that are intelligent and social, or at least developing along an evolutionary trajectory that could lead to a level of intelligence that would enable individual members of the species to recognize and respond to such things as the moral goods they in fact are. We suggest that what is most morally interesting and important from a biological perspective is the existence and development of such trajectories, rather than the position of one particular species, such as our own, on one particular trajectory.