Architecture, constraints, and behavior

The ecology of collective behavior

Networks of local interactions regulate biological systems. Ecological constraints set by resource distribution, operating costs, and the threat of rupture produce similar collective behavior in ants, cells, and gene transcription.

Similar patterns of interaction, such as network motifs and feedback loops, are used in many natural collective processes, probably because they have evolved independently under similar pressures. Here I consider how three environmental constraints may shape the evolution of collective behavior: the patchiness of resources, the operating costs of maintaining the interaction network that produces collective behavior, and the threat of rupture of the network. The ants are a large and successful taxon that have evolved in very diverse environments. Examples from ants provide a starting point for examining more generally the fit between the particular pattern of interaction that regulates activity, and the environment in which it functions.

Of plasticity and specificity: dialectics of the microenvironment and macroenvironment and the organ phenotype

The study of biological form and how it arises is the domain of the developmental biologists; but once the form is achieved, the organ poses a fascinating conundrum for all the life scientists: how are form and function maintained in adult organs throughout most of the life of the organism? That they do appears to contradict the inherently plastic nature of organogenesis during development. How do cells with the same genetic information arrive at, and maintain such different architectures and functions, and how do they keep remembering that they are different from each other? It is now clear that narratives based solely on genes and an irreversible regulatory dynamics cannot answer these questions satisfactorily, and the concept of microenvironmental signaling needs to be added to the equation. During development, cells rearrange and differentiate in response to diffusive morphogens, juxtacrine signals, and the extracellular matrix (ECM). These components, which constitute the modular microenvironment, are sensitive to cues from other tissues and organs of the developing embryo as well as from the external macroenvironment. On the other hand, once the organ is formed, these modular constituents integrate and constrain the organ architecture, which ensures structural and functional homeostasis and therefore, organ specificity. We argue here that a corollary of the above is that once the organ architecture is compromised in adults by mutations or by changes in the microenvironment such as aging or inflammation, that organ becomes subjected to the developmental and embryonic circuits in search of a new identity. But since the microenvironment is no longer embryonic, the confusion leads to cancer: hence as we have argued, tumors become new evolutionary organs perhaps in search of an elusive homeostasis.

Cortical high-density counterstream architectures

Small-world networks provide an appealing description of cortical architecture owing to their capacity for integration and segregation combined with an economy of connectivity. Previous reports of low-density interareal graphs and apparent small-world properties are challenged by data that reveal high-density cortical graphs in which economy of connections is achieved by weight heterogeneity and distance-weight correlations. These properties define a model that predicts many binary and weighted features of the cortical network including a core-periphery, a typical feature of self-organizing information processing systems. Feedback and feedforward pathways between areas exhibit a dual counterstream organization, and their integration into local circuits constrains cortical computation. Here, we propose a bow-tie representation of interareal architecture derived from the hierarchical laminar weights of pathways between the high-efficiency dense core and periphery.

In Darwinian evolution, feedback from natural selection leads to biased mutations

Natural selection provides feedback through which information about the environment and its recurring challenges is captured, inherited, and accumulated within genomes in the form of variations that contribute to survival. The variation upon which natural selection acts is generally described as "random." Yet evidence has been mounting for decades, from such phenomena as mutation hotspots, horizontal gene transfer, and highly mutable repetitive sequences, that variation is far from the simplifying idealization of random processes as white (uniform in space and time and independent of the environment or context).  This paper focuses on what is known about the generation and control of mutational variation, emphasizing that it is not uniform across the genome or in time, not unstructured with respect to survival, and is neither memoryless nor independent of the (also far from white) environment. We suggest that, as opposed to frequentist methods, Bayesian analysis could capture the evolution of nonuniform probabilities of distinct classes of mutation, and argue not only that the locations, styles, and timing of real mutations are not correctly modeled as generated by a white noise random process, but that such a process would be inconsistent with evolutionary theory.

A Systems Engineering Perspective on Homeostasis and Disease

Engineered systems are coupled networks of interacting sub-systems, whose dynamics are constrained to requirements of robustness and flexibility. They have evolved by design to optimize function in a changing environment and maintain responses within ranges. Analysis, synthesis, and design of complex supply chains aim to identify and explore the laws governing optimally integrated systems. Optimality expresses balance between conflicting objectives while resiliency results from dynamic interactions among elements. Our increasing understanding of life’s multi-scale architecture suggests that living systems share similar characteristics with much to be learned about biological complexity from engineered systems. If health reflects a dynamically stable integration of molecules, cell, tissues, and organs; disease indicates displacement compensated for and corrected by activation and combination of feedback mechanisms through interconnected networks. In this article, we draw analogies between concepts in systems engineering and conceptual models of health and disease; establish connections between these concepts and physiologic modeling; and describe how these mirror onto the physiological counterparts of engineered systems.

Design of silicon brains in the nano-CMOS era: spiking neurons, learning synapses and neural architecture optimization

We present a design framework for neuromorphic architectures in the nano-CMOS era. Our approach to the design of spiking neurons and STDP learning circuits relies on parallel computational structures where neurons are abstracted as digital arithmetic logic units and communication processors. Using this approach, we have developed arrays of silicon neurons that scale to millions of neurons in a single state-of-the-art Field Programmable Gate Array (FPGA). We demonstrate the validity of the design methodology through the implementation of cortical development in a circuit of spiking neurons, STDP synapses, and neural architecture optimization.

Systems biology: the role of engineering in the reverse engineering of biological signaling

One of the principle tasks of systems biology has been the reverse engineering of signaling networks. Because of the striking similarities to engineering systems, a number of analysis and design tools from engineering disciplines have been used in this process. This review looks at several examples including the analysis of homeostasis using control theory, the attenuation of noise using signal processing, statistical inference and the use of information theory to understand both binary decision systems and the response of eukaryotic chemotactic cells.

Hypoxia-induced phrenic long-term facilitation: emergent properties

As in other neural systems, plasticity is a hallmark of the neural system controlling breathing. One spinal mechanism of respiratory plasticity is phrenic long-term facilitation (pLTF) following acute intermittent hypoxia. Although cellular mechanisms giving rise to pLTF occur within the phrenic motor nucleus, different signaling cascades elicit pLTF under different conditions. These cascades, referred to as Q and S pathways to phrenic motor facilitation (pMF), interact via cross-talk inhibition. Whereas the Q pathway dominates pLTF after mild to moderate hypoxic episodes, the S pathway dominates after severe hypoxic episodes. The biological significance of multiple pathways to pMF is unknown. This review will discuss the possibility that interactions between pathways confer emergent properties to pLTF, including pattern sensitivity and metaplasticity. Understanding these mechanisms and their interactions may enable us to optimize intermittent hypoxia-induced plasticity as a treatment for patients that suffer from ventilatory impairment or other motor deficits.

Hubs of brain functional networks are radically reorganized in comatose patients

Human brain networks have topological properties in common with many other complex systems, prompting the following question: what aspects of brain network organization are critical for distinctive functional properties of the brain, such as consciousness? To address this question, we used graph theoretical methods to explore brain network topology in resting state functional MRI data acquired from 17 patients with severely impaired consciousness and 20 healthy volunteers. We found that many global network properties were conserved in comatose patients. Specifically, there was no significant abnormality of global efficiency, clustering, small-worldness, modularity, or degree distribution in the patient group. However, in every patient, we found evidence for a radical reorganization of high degree or highly efficient "hub" nodes. Cortical regions that were hubs of healthy brain networks had typically become nonhubs of comatose brain networks and vice versa. These results indicate that global topological properties of complex brain networks may be homeostatically conserved under extremely different clinical conditions and that consciousness likely depends on the anatomical location of hub nodes in human brain networks.

Systematic and systemic immunology: on the future of research and its applications

This paper is a shortened English transcription of a lecture given on 13 February 2012 at the College de France. The lecture concluded a series of talks delivered the same year on the theme: "Immunity: the game of chance and specificity". The article comprises four parts: I. The game of chance and specificity. II. About the future of research in immunology. III. On the future of the applications of research in immunology. IV. The social conditions of the evolution of research and its applications.

Shifting gears: seeking new approaches for mind/brain mechanisms

Using an autobiographical approach, I review several animal and human split-brain studies that have led me to change my long-term view on how best to understand mind/brain interactions. Overall, the view is consistent with the idea that complex neural systems, like other complex information processing systems, are highly modular. At the same time, how the modules come to interact and produce unitary goals is unknown. Here, I review the importance of self-cueing in that process of producing unitary goals from disparate functions. The role of self-cueing is demonstrably evident in the human neurologic patient and especially in patients with hemispheric disconnection. When viewed in the context of modularity, it may provide insights into how a highly parallel and distributed brain locally coordinates its activities to produce an apparent unitary output. Capturing and understanding how this is achieved will require shifting gears away from standard linear models and adopting a more dynamical systems view of brain function.

Selfish cellular networks and the evolution of complex organisms

Human gametogenesis takes years and involves many cellular divisions, particularly in males. Consequently, gametogenesis provides the opportunity to acquire multiple de novo mutations. A significant portion of these is likely to impact the cellular networks linking genes, proteins, RNA and metabolites, which constitute the functional units of cells. A wealth of literature shows that these individual cellular networks are complex, robust and evolvable. To some extent, they are able to monitor their own performance, and display sufficient autonomy to be termed "selfish". Their robustness is linked to quality control mechanisms which are embedded in and act upon the individual networks, thereby providing a basis for selection during gametogenesis. These selective processes are equally likely to affect cellular functions that are not gamete-specific, and the evolution of the most complex organisms, including man, is therefore likely to occur via two pathways: essential housekeeping functions would be regulated and evolve during gametogenesis within the parents before being transmitted to their progeny, while classical selection would operate on other traits of the organisms that shape their fitness with respect to the environment.