Cerebrospinal fluid (CSF) is a fluidic part of the brain’s microenvironment that isolates the brain from the rest of the body. CSF dilutes metabolites from neuronal activities and removes them from the brain. Its production and resorption are regulated dynamically and are central to maintaining brain homeostasis. We discovered that the major CSF source, the choroid plexus (CP), harbors the brain’s strongest circadian clock. Here, we consider some implications of the CP circadian clock for metabolite clearance in the brain. If (...) the circadian clock contributes to timed production of the CSF, its synchronization with sleep timing can maximize clearance efficiency and help prevent neurodegenerative diseases such as Alzheimer’s disease. (shrink)

This paper proposes an abstract mathematical frame for describing some features of biological time. The key point is that usual physical (linear) representation of time is insufficient, in our view, for the understanding key phenomena of life, such as rhythms, both physical (circadian, seasonal …) and properly biological (heart beating, respiration, metabolic …). In particular, the role of biological rhythms do not seem to have any counterpart in mathematical formalization of physical clocks, which are based on frequencies along the usual (...) (possibly thermodynamical, thus oriented) time. We then suggest a functional representation of biological time by a 2-dimensional manifold as a mathematical frame for accommodating autonomous biological rhythms. The “visual” representation of rhythms so obtained, in particular heart beatings, will provide, by a few examples, hints towards possible applications of our approach to the understanding of interspecific differences or intraspecific pathologies. The 3- dimensional embedding space, needed for purely mathematical reasons, allows to introduce a suitable extra-dimension for “representation time”, with a cognitive significance. (shrink)

A methodical synopsis of photomedicine is given, for a deeper understanding of dis-ease, from the viewpoint of humanistic systems medicine; the physical anthropology of medical photo-physics is elaborated, with special reference to psychophysical circadianity.

Recently, Bechtel and Abrahamsen have argued that mathematical models study the dynamics of mechanisms by recomposing the components and their operations into an appropriately organized system. We will study this claim through the practice of combinational modeling in circadian clock research. In combinational modeling, experiments on model organisms and mathematical/computational models are combined with a new type of model—a synthetic model. We argue that the strategy of recomposition is more complicated than what Bechtel and Abrahamsen indicate. Moreover, synthetic modeling as (...) a kind of material recomposition strategy also points beyond the mechanistic paradigm. (shrink)

I examine to what extent accounts of mechanisms based on formal interventionist theories of causality can adequately represent biological mechanisms with complex dynamics. Using a differential equation model for a circadian clock mechanism as an example, I first show that there exists an iterative solution that can be interpreted as a structural causal model. Thus, in principle, it is possible to integrate causal difference-making information with dynamical information. However, the differential equation model itself lacks the right modularity properties for a (...) full integration. A formal mechanistic model will therefore have to leave out either noncausal or causal explanatory relations. (shrink)

It’s often claimed in the philosophical and scientific literature on temporal representation that there is no such thing as a genuine sensory system for time. In this paper, I argue for the opposite—many animals, including all mammals, possess a genuine sensory system for time based in the circadian system. In arguing for this conclusion, I develop a semantics and meta-semantics for explaining how the endogenous rhythms of the circadian system provide organisms with a direct information link to the temporal structure (...) of their environment. In doing so, I highlight the role of sensory systems in an information processing architecture. (shrink)

Various writers have attempted to use the sender-receiver formalism to account for the representational capacities of biological systems. This paper has two goals. First, I argue that the sender-receiver approach to representation cannot be complete. The mammalian circadian system represents the time of day, yet it does not control circadian behaviours by producing signals with time of day content. Informative signalling need not be the basis of our most basic representational capacities. Second, I argue that representational capacities are primarily about (...) control, and only when specific conditions obtain does this control require informative signalling. (shrink)

Many philosophers and psychologists have attempted to elucidate the nature of mental representation by appealing to notions like isomorphism or abstract structural resemblance. The ‘structural representations’ that these theorists champion are said to count as representations by virtue of functioning as internal models of distal systems. In his 2007 book, Representation Reconsidered, William Ramsey endorses the structural conception of mental representation, but uses it to develop a novel argument against representationalism, the widespread view that cognition essentially involves the manipulation of (...) mental representations. Ramsey argues that although theories within the ‘classical’ tradition of cognitive science once posited structural representations, these theories are being superseded by newer theories, within the tradition of connectionism and cognitive neuroscience, which rarely if ever appeal to structural representations. Instead, these theories seem to be explaining cognition by invoking so-called ‘receptor representations’, which, Ramsey claims, aren’t genuine representations at all—despite being called representations, these mechanisms function more as triggers or causal relays than as genuine stand-ins for distal systems. I argue that when the notions of structural and receptor representation are properly explicated, there turns out to be no distinction between them. There only appears to be a distinction between receptor and structural representations because the latter are tacitly conflated with the ‘mental models’ ostensibly involved in offline cognitive processes such as episodic memory and mental imagery. While structural representations might count as genuine representations, they aren’t distinctively mental representations, for they can be found in all sorts of non-intentional systems such as plants. Thus to explain the kinds of offline cognitive capacities that have motivated talk of mental models, we must develop richer conceptions of mental representation than those provided by the notions of structural and receptor representation. (shrink)

We advance an account that grounds cognition, specifically decision-making, in an activity all organisms as autonomous systems must perform to keep themselves viable—controlling their production mechanisms. Production mechanisms, as we characterize them, perform activities such as procuring resources from their environment, putting these resources to use to construct and repair the organism's body and moving through the environment. Given the variable nature of the environment and the continual degradation of the organism, these production mechanisms must be regulated by control mechanisms (...) that select when a production is required and how it should be carried out. To operate on production mechanisms, control mechanisms need to procure information through measurement processes and evaluate possible actions. They are making decisions. In all organisms, these decisions are made by multiple different control mechanisms that are organized not hierarchically but heterarchically. In many cases, they employ internal models of features of the environment with which the organism must deal. Cognition, in the form of decision-making, is thus fundamental to living systems which must control their production mechanisms. (shrink)

Western science claims to provide unique, objective information about the world. This is supported by the observation that peoples across cultures will agree upon a common description of the physical world. Further, the use of scientific instruments and mathematics is claimed to enable the objectification of science. In this work, carried out by reviewing the scientific literature, the above claims are disputed systematically by evaluating the definition of physical reality and the scientific method, showing that empiricism relies ultimately upon the (...) human senses for the evaluation of scientific theories and that measuring instruments cannot replace the human sensory system. Nativist and constructivist theories of human sensory development are reviewed, and it is shown that nativist claims of core conceptual knowledge cannot be supported by the findings in the literature, which shows that perception does not simply arise from a process of maturation. Instead, sensory function requires a long process of learning through interactions with the environment. To more rigorously define physical reality and systematically evaluate the stability of perception, and thus the basis of empiricism, the development of the method of dimension analysis is reviewed. It is shown that this methodology, relied upon for the mathematical analysis of physical quantities, is itself based upon empiricism, and that all of physical reality can be described in terms of the three fundamental dimensions of mass, length and time. Hereafter the sensory modalities that inform us about these three dimensions are systematically evaluated. The following careful analysis of neuronal plasticity in these modalities shows that all the relevant senses acquire from the environment the capacity to apprehend physical reality. It is concluded that physical reality is acquired rather than given innately, and leads to the position that science cannot provide unique results. Rather, those it can provide are sufficient for a particular environmental setting. (shrink)