Biological pattern generation: the cellular and computational logic of networks in motion

In 1900, Ramón y Cajal advanced the neuron doctrine, defining the neuron as the fundamental signaling unit of the nervous system. Over a century later, neurobiologists address the circuit doctrine: the logic of the core units of neuronal circuitry that control animal behavior. These are circuits that can be called into action for perceptual, conceptual, and motor tasks, and we now need to understand whether there are coherent and overriding principles that govern the design and function of these modules. The discovery of central motor programs has provided crucial insight into the logic of one prototypic set of neural circuits: those that generate motor patterns. In this review, I discuss the mode of operation of these pattern generator networks and consider the neural mechanisms through which they are selected and activated. In addition, I will outline the utility of computational models in analysis of the dynamic actions of these motor networks.     

Thérapies cognitives et philosophile stoïcienne

Stoicism comprises three parts: physics, logic, and ethics, coherently organized and based on the principle of logos or universal reason. The doctrine of assent and the great importance attached to the domination of “passions” by reason have obvious similarities to the principles of modern cognitive therapies.     

The sanctity of life as a sacred value

The doctrine of the sanctity of life has traditionally been characterised as a Judeo-Christian doctrine that has it that bodily human life is an intrinsic good and that it is always impermissible to kill an innocent human. Abortion and euthanasia are often assumed to violate the doctrine. The doctrine is usually understood as being derived from religious dogma and, as such, not amenable to debate. I show that this characterisation of the doctrine is problematic in a number of ways, and I go on to rethink the doctrine. In doing so I follow in the footsteps of Ronald Dworkin, who offered a characterisation of the doctrine in his 1993 Life's Dominion, drawing on a conceptualisation of sacredness that is radically different from standard ones and not dependent on religious dogma. I'll argue that although Dworkin's efforts have much to recommend, his conceptualisation of sacredness is inadequate. Dworkin attempted to reconceptualise sacredness ‘from the armchair’. Here I explain how sacred values are thought of in anthropology and psychology and argue that the sanctity of human life should be understood in the same way. I'll explain how doing so allows us to resolve a number of conceptual problems that bedevil standard characterisations of the doctrine of the sanctity of life. I'll also consider the possibility of a compromise over the sanctity of human life, and as a consequence, compromise over the permissibility of abortion and euthanasia. I'll argue that such compromise is possible, albeit difficult to achieve.     

Optimal Information Representation and Criticality in an Adaptive Sensory Recurrent Neuronal Network

Recurrent connections play an important role in cortical function, yet their exact contribution to the network computation remains unknown. The principles guiding the long-term evolution of these connections are poorly understood as well. Therefore, gaining insight into their computational role and into the mechanism shaping their pattern would be of great importance. To that end, we studied the learning dynamics and emergent recurrent connectivity in a sensory network model based on a first-principle information theoretic approach. As a test case, we applied this framework to a model of a hypercolumn in the visual cortex and found that the evolved connections between orientation columns have a "Mexican hat" profile, consistent with empirical data and previous modeling work. Furthermore, we found that optimal information representation is achieved when the network operates near a critical point in its dynamics. Neuronal networks working near such a phase transition are most sensitive to their inputs and are thus optimal in terms of information representation. Nevertheless, a mild change in the pattern of interactions may cause such networks to undergo a transition into a different regime of behavior in which the network activity is dominated by its internal recurrent dynamics and does not reflect the objective input. We discuss several mechanisms by which the pattern of interactions can be driven into this supercritical regime and relate them to various neurological and neuropsychiatric phenomena.     

Observations of synaptic structures: origins of the neuron doctrine and its current status

The neuron doctrine represents nerve cells as polarized structures that contact each other at specialized (synaptic) junctions and form the developmental, functional, structural and trophic units of nervous systems. The doctrine provided a powerful analytical tool in the past, but is now seldom used in educating neuroscientists. Early observations of, and speculations about, sites of neuronal communication, which were made in the early 1860s, almost 30 years before the neuron doctrine was developed, are presented in relation to later accounts, particularly those made in support of, or opposition to, the neuron doctrine. These markedly differing accounts are considered in relation to limitations imposed by preparative and microscopical methods, and are discussed briefly as representing a post-Darwinian, reductionist view, on the one hand, opposed to a holistic view of mankind as a special part of creation, on the other. The widely misunderstood relationship of the neuron doctrine to the cell theory is discussed, as is the degree to which the neuron doctrine is still strictly applicable to an analysis of nervous systems. Current research represents a 'post-neuronist' era. The neuron doctrine provided a strong analytical approach in the past, but can no longer be seen as central to contemporary advances in neuroscience.     

Patient autonomy, assessment of competence and surrogate decision-making: a call for reasonableness in deciding for others

In this paper, I address some of the shortcomings of established clinical ethics centring on personal autonomy and consent and what I label the Doctrine of Respecting Personal Autonomy in Healthcare. I discuss two implications of this doctrine: 1) the practice for treating patients who are considered to have borderline decision-making competence and 2) the practice of surrogate decision-making in general. I argue that none of these practices are currently aligned with respectful treatment of vulnerable individuals. Because of 'structural arbitrariness' in the whole process of how we assess decision-making competence, this area is open to disrespectful treatment of people. The practice of surrogate decision- making on the basis of a single person's judgment is arguably not consistent with ethical and political requirements derived from the doctrine itself. In response to the inadequacies of the doctrine, I suggest a framework for reasonableness in surrogate decision-making which might allow practice to avoid the problems above. I conclude by suggesting an extended concept of Patient Autonomy which integrates both personal autonomy and the regulative idea of morality that is required by reasonableness in deciding for non-competent others.     

Extremal principles and goal functions of biocenotic systems

This review considers two alternative principles known in ecology, maximizing or minimizing the diversity-entropy of biological systems, and shows the inadequacy of both extremal principles as applied to natural biocenotic assemblages. A necessary condition for existence of multispecies systems is not extremization of any parameters thereof but optimization of the relations of these parameters (including those that uniquely determine the extent of species diversity). Thus, the goal function that any biocenotic system tends to minimize in the course of succession and evolution proves to be the deviation from this optimal ratio.     

Trichromacy, opponent colours coding and optimum colour information transmission in the retina

This paper presents a systematic analysis of the role of opponent type processing in colour vision and the relation between opponent type colour transformations and the initial three colour mechanisms. It is shown that efficient information transmission is achieved by a transformation of the initial three colour mechanisms into an achromatic and two opponent chromatic channels. The derivation of the transformation is dependent solely on criteria from information theory. Thus it provides a logical rationale reconciling opponent type processing as an optimal necessary step after the initial three colour mechanisms, unifying respectively the Hering and Young-Helmholtz approaches to colour vision. The effects of chromatic adaptation on the spectral response of the achromatic and two chromatic channels are discussed from the point of view of information theory. It is argued that adaptation serves as a dynamic readjustment of these responses, necessary to meet criteria of efficient colour information transmission. The results are confronted with empirical observations to test the principles of the theory and the relation to other theories is discussed. Within the same framework the issue of trichromacy is discussed. It is argued that a broad class of typical colour spectra can effectively be represented by three significant degrees of freedom that make up a trichromatic system.     

Design principles and operating principles: the yin and yang of optimal functioning

Metabolic engineering has as a goal the improvement of yield of desired products from microorganisms and cell lines. This goal has traditionally been approached with experimental biotechnological methods, but it is becoming increasingly popular to precede the experimental phase by a mathematical modeling step that allows objective pre-screening of possible improvement strategies. The models are either linear and represent the stoichiometry and flux distribution in pathways or they are non-linear and account for the full kinetic behavior of the pathway, which is often significantly effected by regulatory signals. Linear flux analysis is simpler and requires less input information than a full kinetic analysis, and the question arises whether the consideration of non-linearities is really necessary for devising optimal strategies for yield improvements. The article analyzes this question with a generic, representative pathway. It shows that flux split ratios, which are the key criterion for linear flux analysis, are essentially sufficient for unregulated, but not for regulated branch points. The interrelationships between regulatory design on one hand and optimal patterns of operation on the other suggest the investigation of operating principles that complement design principles, like a user's manual complements the hardwiring of electronic equipment.     

Size Control in Plants—Lessons from Leaves and Flowers

To achieve optimal functionality, plant organs like leaves and petals have to grow to a certain size. Beginning with a limited number of undifferentiated cells, the final size of an organ is attained by a complex interplay of cell proliferation and subsequent cell expansion. Regulatory mechanisms that integrate intrinsic growth signals and environmental cues are required to enable optimal leaf and flower development. This review focuses on plant-specific principles of growth reaching from the cellular to the organ level. The currently known genetic pathways underlying these principles are summarized and network connections are highlighted. Putative non–cell autonomously acting mechanisms that might coordinate plant-cell growth are discussed.Over millions of years, plant leaves and flowers evolved into an enormous range of shapes and sizes. Likely reflecting adaptations to changing environmental conditions, even closely related species often differ dramatically in their organ sizes (Mizukami 2001). Although interspecies diversity is remarkably high, species-specific leaf and petal characteristics are often highly uniform between individuals grown under constant conditions. This suggests that tight genetic control is used to integrate intrinsic growth signals and environmental cues to enable organ growth to a defined size. This review summarizes the current knowledge of the regulatory networks of plant size control at the cellular and at the organ level. We will focus on the regulation of determinate growth of lateral plant organs, such as simple leaves and petals.     

Extremal principles and goal functions of biocoenotic systems

A review considers known in the ecology two alternative principles of maximizing or minimizing the diversity-entropy of biological systems, and shows the inadequacy of both extremal principles in application to natural biocoenotic assemblages. A necessary condition for the multispecific system's existence is not extremization any of their parameters, but optimization of the relations of their parameters (including those that uniquely determine the value of species diversity). Thus, the goal function, which tends to minimize any biocoenotic system in the course of succession and evolution, is a deviation from this optimal ratio.     

Compelled organ donation

Along with ethical considerations, compelling an individual to donate organs, tissues, or bodily fluids brings several legal doctrines into conflict. The privacy of one's body is generally considered sacrosanct by American courts, which have upheld a competent adult's right to refuse medical procedures, even in cases when they are necessary to save the life of another. Although medical and legal communities stress “respect for the individual” as being paramount under American jurisprudential principles, the doctrine of “substituted judgment” permits a court to act (for example, by consenting to organ donation) on behalf of an incompetent individual or child. Parents also have the right to cause a child to “donate” an organ, and although a means exists by which the child can refuse, this may not be realistically feasible for young children. The revised Uniform Anatomical Gift Act of 2006, while clarifying issues of who may make organ donation decisions, does not resolve all the practical issues of compelled organ donation for minors.     

For the law, neuroscience changes nothing and everything

The rapidly growing field of cognitive neuroscience holds the promise of explaining the operations of the mind in terms of the physical operations of the brain. Some suggest that our emerging understanding of the physical causes of human (mis)behaviour will have a transformative effect on the law. Others argue that new neuroscience will provide only new details and that existing legal doctrine can accommodate whatever new information neuroscience will provide. We argue that neuroscience will probably have a transformative effect on the law, despite the fact that existing legal doctrine can, in principle, accommodate whatever neuroscience will tell us. New neuroscience will change the law, not by undermining its current assumptions, but by transforming people's moral intuitions about free will and responsibility. This change in moral outlook will result not from the discovery of crucial new facts or clever new arguments, but from a new appreciation of old arguments, bolstered by vivid new illustrations provided by cognitive neuroscience. We foresee, and recommend, a shift away from punishment aimed at retribution in favour of a more progressive, consequentialist approach to the criminal law.     

Analysis and simulation of hollow-fiber bioreactor dynamics

A flexible and economical computer simulation model for the process analysis, parameter prediction, and optimal design of hollow-fiber biochemical reactors (HFBRs) has been developed. The validity and predictive capability of the HFBR simulator was successfully tested with two independent laboratory case studies. Of particular interest are the transient transport and bioconversion mechanisms including the effect of radial mass convection on the substrate uptake in the lumen. The portable computer code is an efficient tool to aid in theoretical and experimental investigations. The underlying principles used for the model development are applicable to a broad family of (membrane) bioreactors.     

Animal learning and intelligence

The ability to learn is common to most animal species: the need to exploit past experience being obviously extremely important for survival, many animals have evolved ways of coping with it. Although the complexity of learning needed for optimal survival may be different in different species, the basic mechanisms appear to be fairly constant even in phylogenetically distant ones. This homogeneity across species in learning mechanisms is in some ways surprising in view of the large phylogenetic differences and of the considerable variability not only in the general plan of their bodily structures, but also, more specifically, in their neural organization and in their behavioral adaptations. One possible explanation is that animals have acquired learning very precociously, and that the original and basic mechanisms have proved so efficient and faultproof as to be preserved from then on without any significant modification. Most researchers of the subject seem to accept the equation «intelligence=learning capability», operationally very useful because it leads to a variety of formal tests. Some researchers, stressing that behavior is subject to the same evolutionary principles as any other character of the organism and acknowledging some problems in the accepted laws of learning, have tried to find a satisfactory answer to the question of animal intelligence by attempting a synthesis between the concepts of animal learning psychology and those of ethology. To some extent, dissatisfaction with established learning theories originated within the theories themselves: the study of phenomena such as autoshaping, selective attention, preferential learning of some responses amongst the many possible, conditioned learning of taste aversions, etc. Further difficulties for conditioning theories arose from the discovery of ethological phenomena. Other researchers have attempted to check the hypothesis that animals possess cognition. A number of complex experimental situtations have been devised to this purpose, but the results still are far from conclusive.     

A model for seed size variation among plants

Summary I developed a model for seed size variation among plants assuming that the pollen captured per flower depends on both the allocation to pollen capture mechanisms per flower and the number of flowers on each plant. I showed that the optimal seed size increases with (1) the total resource allocation to reproduction, (2) decreasing outcross pollen availability, (3) decreasing probability of seedling establishment and (4) decreasing selfing rate. However, optimal seed size does not depend on the total resource allocation if the total number of pollen grains captured by a plant increases linearly with its flower number. In addition, the optimal seed size is not always positively correlated with the optimal resource allocation to pollen capture mechanisms per flower. I discussed implications of the results for seasonal decline in seed size and seed size variations among populations, such as alutitudinal variation.     

The co-evolution of host cationic antimicrobial peptides and microbial resistance

Endogenous cationic antimicrobial peptides (CAMPs) are among the most ancient and efficient components of host defence. It is somewhat of an enigma that bacteria have not developed highly effective CAMP-resistance mechanisms, such as those that inhibit many therapeutic antibiotics. Here, we propose that CAMPs and CAMP-resistance mechanisms have co-evolved, leading to a transient host-pathogen balance that has shaped the existing CAMP repertoire. Elucidating the underlying principles of this process could help in the development of more sustainable antibiotics.     

Joint evolution of predator body size and prey-size preference

We studied the joint evolution of predator body size and prey-size preference based on dynamic energy budget theory. The predators’ demography and their functional response are based on general eco-physiological principles involving the size of both predator and prey. While our model can account for qualitatively different predator types by adjusting parameter values, we mainly focused on ‘true’ predators that kill their prey. The resulting model explains various empirical observations, such as the triangular distribution of predator–prey size combinations, the island rule, and the difference in predator–prey size ratios between filter feeders and raptorial feeders. The model also reveals key factors for the evolution of predator–prey size ratios. Capture mechanisms turned out to have a large effect on this ratio, while prey-size availability and competition for resources only help explain variation in predator size, not variation in predator–prey size ratio. Predation among predators is identified as an important factor for deviations from the optimal predator–prey size ratio.     

Secrets of caveolae- and lipid raft-mediated endocytosis revealed by mammalian viruses

In recent years, it has been unambiguously shown that caveolae and lipid rafts can internalize cargo upon stimulation by multivalent ligands, demonstrated by the infectious entry routes of certain non-enveloped viruses that bind integrins or glycosphingolipids. We currently understand little about the membrane trafficking principles of this endocytic route, but it is clear that we cannot use paradigms from classical membrane traffic. Recent evidence indicates that caveolae- and lipid raft-mediated endocytosis plays important roles in cell adhesion and anchorage-dependent cell growth, but the underlying mechanisms are not known. In this review, I will introduce new models based on current research that aims at identifying the core machinery, regulatory components and design principles of this endocytic route in order to understand its role in cellular physiology. Again, viruses are proving to be excellent tools to reach that goal.