The biomedical literature makes extensive use of the concept of a genetic program. So far, however, the nature of genetic programs has received no satisfactory elucidation from the standpoint of computer science. This unsettling omission has led to doubts about the very existence of genetic programs, on the grounds that gene regulatory networks lack a predetermined schedule of execution, which may seem to contradict the very idea of a program. I show, however, that we can make perfect sense of genetic (...) programs, if only we abandon the preconception that all computers have a von Neumann architecture. Instead, genetic programs instantiate the computational architecture of Post–Newell Production Systems. That is, genetic programs are unordered sets of conditional instructions, instructions that fire independently when their conditions are matched. For illustration I present a paradigm Production System that regulates the functioning of the well-known lac operon of E. coli. On close reflection it turns out that not only genes, but also proteins encode instructions. I propose, therefore, to rename genetic programs to biomolecular programs. Biomolecular and/or genetic programs, and the cellular computers than run them, are to be understood not as von Neumann computers, but as Post–Newell production systems. (shrink)

In this paper, I plan to show that the use of a specific population concept—Millstein’s Causal Interactionist Population Concept (CIPC)—has interesting and counter-intuitive ramifications for discussions of the reality of biological race in human beings. These peculiar ramifications apply to human beings writ large and to individuals. While this in and of itself may not be problematic, I plan to show that the ramifications that follow from applying Millstein’s CIPC to human beings complicates specific biological racial realist accounts—naïve or otherwise. (...) I conclude with the notion that even if biological races do exist—by fulfilling all of the criteria needed for Millstein’s population concept (which, given particular worries raised by Gannett (Synthese 177:363–385, 2010), and Winther and Kaplan (Theoria 60:54–80, 2013) may not)—the lower-bound limit for the scope of biological racial realism is at the level of populations, and as such they cannot say anything about whether or not individual organisms themselves have races. (shrink)

Justin Garson has recently argued that proper functions are proximal activities of traits selected by phylogenetic or ontogenetic selection processes, and that traits are dysfunctional only if they cannot perform their proper functions for constitutional reasons. We partially agree with Garson, but reject the view that functions are proximal activities, as well as his account of dysfunctions. Instead, we propose our own theory that biological functions are selected dispositions and that a trait is dysfunctional in virtue of not having the (...) dispositions for which it was selected. This account can explain both defects (or dysfunctions in Garson’s sense) and dysfunctions due to environmental factors. Moreover, it offers a neat way to explain the graduality of dysfunction. (shrink)

The environment is a continuous source of matter and energy, which dynamizes the adaptive processes of biological systems, so that these systems emerge, persist or are extinguished as a consequence of their reactions to the environment. This perspective, forged from classical physics, gives way to multiple ecological theories, with evolution being the most prominent one. In all these cases, information would be both dependent and subsequent to matter and energy. Thus, the emergence and dynamics of genetic material or ecological attributes (...) such as abundance, richness or diversity depend mainly on the interaction of these two fundamental states. However, recent approaches from quantum physics and complexity views put forward the notion that information can be independent and prior to matter and energy, which allows us to see ecological processes from another perspective, i.e., as including complex biological systems as capable of showing emergent properties such as cognition. We proposed here a set of postulates and ideas that suggests how the ability to manipulate (internalize, integrate, store and generate) information can be developed by those systems, which would directly and non-randomly influence ecological attributes and their dynamics; i.e., how this property can possibly help replacing the notion of the environment as the ultimate cause of changes. Besides fully detailing the sources of knowledge and our rationale in this sense, we have also discussed how these thoughts and possibilities can be employed in devising better and more comprehensive approaches for biological conservation strategies. (shrink)

In this paper, I aim to explore whether fitness, understood as a causal disposition, can be characterized as an emergent property of organisms, or if it is reducible to the anatomical, physiological, and environmentally relative properties that characterize them. In doing so, I refer to Jessica Wilson’s characterization of ontological emergence and examine if fitness meets her criteria for ontological emergent properties (dependence and autonomy); and, if so, to what degree (weak or strong).

Foraging is a central competence of all mobile organisms. Models and concepts from foraging theory have been applied widely throughout biology to the search for many kinds of external resources, including food, sexual encounters, minerals, water, and the like. In cognitive science and neuroscience, the tools of foraging theory are increasingly applied to a wide range of other types of search, including for abstract resources like information or for internal resources like memories, concepts, and strategies for problem solving. Despite its (...) importance in ecology and increasing relevance for the study of cognition, the concept of foraging is rarely analyzed. Here, I aim to rectify this situation. I outline three desiderata: first, an analysis should differentiate foraging from search and decision making more generally; second, an analysis should unify different types of foraging; and third, an analysis should help ground predictions. I present an analysis of foraging as the serial search for general resources in accept-or-reject, exclusive, persistent decision contexts. Not all search is serial and not all decision making is exclusive, differentiating foraging from search and decision making generally. With the aid of Markov decision processes and directed cyclical models, I show how the analysis implies a cyclical graph. This cyclical graph is embedded in the description of many types of foraging, unifying the different instances. Finally, I argue that the cyclical graph is also embedded in representations of novel task contexts that have not previously been viewed as foraging. I illustrate this novel application of the concept of foraging by arguing that reasoning is a type of foraging. (shrink)

Humans are extremely prosocial and there are many possible explanations for how we came to be this way. Some have suggested that commitments explain the evolution of human prosociality. Commitments can serve to secure mutually beneficial interaction in the face of short-term incentives to cheat. In this paper, I have two aims. First, I argue that commitment not only applies to familiar practices such as promising but also explains small-scale collaboration among humans as early as two million years ago. In (...) particular, it explains the stability of group hunting. In doing so, I provide a precisification of the concept of commitment. Second, I argue that earlier, non-linguistic forms of commitment can act as an evolutionary scaffold for more complex forms. As such, I will demonstrate how commitment can be understood to have coevolved with human cooperation. The coevolution of commitment and cooperation over our evolutionary history is, I suggest, a crucial part of the explanation of modern human prosociality. (shrink)

Ecological neutral theory has been controversial as an alternative to niche theory for explaining community structure. Neutral theory, which explains community structure in terms of ecological drift, is frequently charged with being unrealistic, but commentators have usually not provided an account of theory or model realism. In this paper, I propose a framework for comparing the “realism” or accuracy of alternative theories within a domain with respect to the extent to which the theories abstract and idealize. Using this framework I (...) argue, contrary to most previous commentators, that neutral and niche theories are similarly realistic. Realism cannot provide a basis for accepting or rejecting either type of theory; instead, community ecologists should continue working with a plurality of models. While theoretical unification may become possible, we should treat a plurality of complementary, partial models as the expected situation within community ecology. (shrink)