Affective disorders arise in stressful situations from aberrant sensory information integration that affects energetic nutrient (i.e., glucose) utilization to the cognitive centers of the brain. Because energy flow is mediated by molecular signals and receptors that evolved before the first complex brains, the phylogenetically oldest signaling systems are essential in the etiology of affective disorders. The corticotropin‐releasing factor (CRF) peptide subfamily is a phylogenetically old metazoan peptide family and is pivotal for regulating organismal energy response associated with stress. Highly (...) conserved, both the CRF peptide family and its receptors possess a structural relationship to the teneurins, and their receptors, latrophilins, respectively. The CRF homologous region of teneurin is defined as the “teneurin C‐terminal associated peptide” (TCAP) and antagonizes CRF action, regulates mitochondrial energy production, and is anxiolytic in vivo. Here, it is postulated that TCAP represents an ancient peptide that mediates intercellular information transfer of stressful and noxious events by regulating energy utilization among neurons. (shrink)

Friedrich Nietzsche’s Zarathustra, the protagonist of his most famous book, can be regarded as a philosopher who works towards becoming a sage—something that, towards the end of the narrative, ultimately seems to happen. Over the course of the account, he travels between his lonely cave and human society several times, walking up and down a mountain. In this article, I focus on how Nietzsche describes those walks using language that breaks with Cartesian dualism through its employment of such expressions as (...) “lead-drop thoughts.” As a systematic frame of reference intended to support the analysis of these descriptions, I make use of Antoni Kempinski’s concept of energetic-informational metabolism. Then, motivated by the preceding observations, I outline the philosophico-therapeutic hypothesis of a human transformation taking place as a two-phase procedure: (1) replacing the view of Cartesian dualism with what I call the “theatre of forces,” and (2) “de-selfing” the stage, or regarding this theatre as impersonal. Finally, reaching out to a Buddhist philosophical conception of the impersonal, I consider the possibility of a metaphysics entirely derived from sensations. (shrink)

There are three main kinds of causal connections between two events: the transfer of energy, the transfer of information and the triggering of the transfer of one of them or both. There are also other kinds of causal connections.

In this paper I present the explanatory potential of Antoni Kępiński’s model of information metabolism in the question of data smog (data glut, information overload). Kępiński’s model is not well known and the bibliography concerning the model of information metabolism is still rather poor. In the article I present the model as a good heuristics for explaining information exchange between the system and the environment. The particular aim of my deliberations is to use the model of information (...) class='Hi'>metabolism to discuss the pathological, although common phenomenon of data smog. This allows for a holistic view of the problem and allows for new statements on data smog, ethical consequences and counteracting the negative consequences of information overload. (shrink)

Developing models of biological mechanisms, such as those involved in respiration in cells, often requires collaborative effort drawing upon techniques developed and information generated in different disciplines. Biochemists in the early decades of the 20th century uncovered all but the most elusive chemical operations involved in cellular respiration, but were unable to align the reaction pathways with particular structures in the cell. During the period 1940-1965 cell biology was emerging as a new discipline and made distinctive contributions to understanding the (...) role of the mitochondrion and its component parts in cellular respiration. In particular, by developing techniques for localizing enzymes or enzyme systems in specific cellular components, cell biologists provided crucial information about the organized structures in which the biochemical reactions occurred. Although the idea that biochemical operations are intimately related to and depend on cell structures was at odds with the then-dominant emphasis on systems of soluble enzymes in biochemistry, a reconceptualization of energetic processes in the 1960s and 1970s made it clear why cell structure was critical to the biochemical account. This paper examines how numerous excursions between biochemistry and cell biology contributed a new understanding of the mechanism of cellular respiration. (shrink)

To explain consciousness as a physical process we must acknowledge the role of energy in the brain. Energetic activity is fundamental to all physical processes and causally drives biological behavior. Recent neuroscientific evidence can be interpreted in a way that suggests consciousness is a product of the organization of energetic activity in the brain. The nature of energy itself, though, remains largely mysterious, and we do not fully understand how it contributes to brain function or consciousness. According to (...) the principle outlined here, energy, along with forces and work, can be described as actualized differences of motion and tension. By observing physical systems, we can infer there is something it is like to undergo actualized difference from the intrinsic perspective of the system. Consciousness occurs because there is something it is like, intrinsically, to undergo a certain organization of actualized differences in the brain. (shrink)

The emerging field of synthetic biology aims to engineer novel biological entities. The envisioned future bio-based economy builds largely on “cell factories”: organisms that have been metabolically engineered to sustainably produce substances for human ends. In this paper, we argue that synthetic biology’s goal of creating efficient production vessels for industrial applications implies a set of ontological assumptions according to which living organisms are machines. Traditionally, a machine is understood as a technological, isolated and controllable production unit consisting of parts. (...) But modified organisms, or hybrids, require us to think beyond the machine paradigm and its associated dichotomies between artificial and natural, organisms and artefacts. We ask: How may we conceptualise hybrids beyond limiting ontological categories? Our main claim is that the hybrids created by synthetic biology should be considered not as machines but as metabolic systems. We shall show how the philosophical account of metabolism can inform an ontology of hybrids that moves beyond what we call the “machine ontology”, considering that metabolism enables thinking beyond the dominant dichotomies and allows us to understand and design lifeforms in a bio-based economy. Thus, the aim of this paper is twofold: first, to develop the philosophical ontology of hybrids, and second, to move synthetic biology beyond the problematically limiting view of hybrids. (shrink)

Understanding terrestrial carbon metabolism is critical because terrestrial ecosystems play a major role in the global carbon cycle. Furthermore, humans have severely disrupted the carbon cycle in ways that will alter the climate system and directly affect terrestrial metabolism. Changes in terrestrial metabolism may well be as important an indicator of global change as the changing temperature signal. Improving our understanding of the carbon cycle at various spatial and temporal scales will require the integration of multiple, complementary (...) and independent methods that are used by different research communities. Tools such as air sampling networks, inverse numerical methods, and satellite data allow us to study the strength and location of the global- and continental-scale carbon sources and sinks. Bottom-up studies provide estimates of carbon fluxes at finer spatial scales and examine the mechanisms that control fluxes at the ecosystem, landscape, and regional scales. Bottom-up approaches include comparative and process studies that provide the necessary mechanistic information to develop and validate terrestrial biospheric models. An iteration and reiteration of top-down and bottom-up approaches will be necessary to help constrain measurements at various scales. We propose a major international effort to coordinate and lead research programs of global scope of the carbon cycle. (shrink)

Information was a frequently used concept in many fields of investigation. However, this concept is still not really understood, when it is referred for instance to consciousness and its informational structure. In this paper it is followed the concept of information from philosophical to physics perspective, showing especially how this concept could be extended to matter in general and to the living in particular, as a result of the intimate interaction between matter and information, the human body appearing as (...) a bipolar informed-matter structure. It is detailed on this way how this concept could be referred to consciousness, and an informational modeling of consciousness as an informational system of the human body is presented. Based on the anatomic architecture of the organism and on the inference of the specific information concepts, it is shown that the informational system of the human body could be described by seven informational subsystems, which are reflected in consciousness as corresponding cognitive centers. These results are able to explain the main properties of consciousness, both the cognitive and extra-cognitive properties of the mind, like that observed during the near-death experiences and other similar phenomena. Moreover, the results of such a modeling are compared with the existing empirical concepts and models on the energetic architecture of the organism, showing their relevance for the understanding of consciousness. (shrink)

Over the past several years, discoveries from mouse genetics have had direct impact on our understanding of vitamin A metabolism. Although the metabolism of vitamin A in the mouse does have some special features (for example very large stores of liver and pulmonary retinyl esters), the ability to construct knockout and transgenic mouse models has yielded an impressive amount of information directly relevant to understanding the general principles of vitamin A transport, storage and degradation. We discuss below the (...) metabolism of vitamin A through a number of genetically engineered mouse strains with alterations in genes that affect this metabolism. The novelty of this experimental approach is evidenced by the fact that the oldest of these strains was first reported only eight years ago.1) BioEssays 23:409–419, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

The ‘managed-metabolism’ hypothesis suggests that a ‘cooperation barrier’ must be overcome if self-producing chemical organizations are to undergo the transition from non-life to life. This dynamical barrier prevents un-managed autocatalytic networks of molecular species from individuating into complex, cooperative organizations. The barrier arises because molecular species that could otherwise make significant cooperative contributions to the success of an organization will often not be supported within the organization, and because side reactions and other ‘free-riding’ processes will undermine cooperation. As a (...) result, the barrier seriously impedes the emergence of individuality, complex functionality and the transition to life. This barrier is analogous to the cooperation barrier that also impedes the emergence of complex cooperation at all levels of living organization. As has been shown at other levels of organization, the barrier can be overcome comprehensively by appropriate ‘management’. Management implements a system of evolvable constraints that can overcome the cooperation barrier by ensuring that beneficial co-operators are supported within the organization and by suppressing free-riders. In this way, management can control and manipulate the chemical processes of a collectively autocatalytic organization, producing novel processes that serve the interests of the organization as a whole and that could not arise and persist in an un-managed chemical organization. Management self-organizes because it is able to capture some of the benefits that are produced when its interventions promote cooperation, thereby enhancing productivity. Selection will therefore favour the emergence of managers that take over and manage chemical organizations so as to overcome the cooperation barrier. The managed-metabolism hypothesis demonstrates that if management is to overcome the cooperation barrier comprehensively, its interventions must be digitally coded. In this way, the hypothesis accounts for the two-tiered structure of all living cells in which a digitally-coded genetic apparatus manages an analogically-informed metabolism.GraphicalOpen image in new window. (shrink)

The standard representation of the Central Dogma (CD) of Molecular Biology conspicuously ignores metabolism. However, both the metabolites and the biochemical fluxes behind any biological phenomenon are encrypted in the DNA sequence. Metabolism constrains and even changes the information flow when the DNA‐encoded instructions conflict with the homeostasis of the biochemical network. Inspection of adaptive virulence programs and emergence of xenobiotic‐biodegradation pathways in environmental bacteria suggest that their main evolutionary drive is the expansion of their metabolic networks towards (...) new chemical landscapes rather than perpetuation and spreading of their DNA sequences. Faulty enzymatic reactions on suboptimal substrates often produce reactive oxygen species (ROS), a process that fosters DNA diversification and ultimately couples catabolism of the new chemicals to growth. All this calls for a revision of the CD in which metabolism (rather than DNA) has the leading role. (shrink)

The information-hierarchical approach is used to analyze the evolutionary developed organization of mankind. This organization is shown to be hierarchical, from molecular hierarchical levels to the religious ones. Time cycles of each level operation are included in the greater cycle of the next level according to the specific schemes defined by the common information principle of natural system development. Time cycles of levels have duration of 1 second, 6 seconds, 42 seconds, 24 hours, 11 days, 1 years, 33 year, 1,000 (...) years, 3,000 years or 6,000 years and all together make up the mankind clock that is similar to the formerly ascertained biosphere clock. The cycles of duration from 1 second to 33 years form the human biological clock, so the information-hierarchical organization of cell metabolism manifests itself as the key mechanism of the clock. The new scientific field has been characterized. It is the management of sustainable development of the states as evolutionary developed systems with the use of information relationships of their functioning. In the case of Christianity adoption by any large ethnos the next 1,000-year cycle of the Christianity-Judaism system will start. (shrink)

Metabolomics, including lipidomics, is emerging as a quantitative biology approach for the assessment of energy flow through metabolism and information flow through metabolic signaling; thus, providing novel insights into metabolism and its regulation, in health, healthy ageing and disease. In this forward‐looking review we provide an overview on the origins of metabolomics, on its role in this postgenomic era of biochemistry and its application to investigate metabolite role and (bio)activity, from model systems to human population studies. We present (...) the challenges inherent to this analytical science, and approaches and modes of analysis that are used to resolve, characterize and measure the infinite chemical diversity contained in the metabolome (including lipidome) of complex biological matrices. In the current outbreak of metabolic diseases such as cardiometabolic disorders, cancer and neurodegenerative diseases, metabolomics appears to be ideally situated for the investigation of disease pathophysiology from a metabolite perspective. (shrink)

The article aims to provide a new perspective on the role played by Maksim Gorky in the creation of Soviet culture. From multiple documentary sources, it reconstructs the private Naturphilosophie that Gorky began developing in the early years of the twentieth century and which continued to inform his views after he took the helm of the Stalinist cultural establishment. At its center was the monistic concept of energy, which Gorky, under the influence of Aleksandr Bogdanov, came to regard as the (...) principle uniting objective processes and subjective phenomena, nature and human history. Insofar as Gorky’s energetics comprises both a doctrine of culture-building and a theory of subjectivity, it allows us to see in a new light the writer’s return to the Soviet Union in the late 1920s. His project for a new socialist culture was, at the same time, a project of subjectivity, as he sought to fashion himself into what he thought a socialist individual should be. (shrink)

Non‐invasive microanalytical methods have been devised to study the energy metabolism of single human preimplantation embryos. Psyruvate, which is added routinely to all media used to culture human embryos, is consumed throughout the preimplantation period, with glucose assuming an increasing role at embryo compaction and blastocyst formation. All of the glucose consumed may be accounted for by the appearance of lactate in the incubation medium. The enzyme hexokinase my be involved in regulating this aerobic glycolysis. There is cosiderable indirect (...) evidence for the utilisation of endogenous as opposed to exogenous energy substrates, the most likely candidate being protein. Information on early human embryo metabolismis likely to find application in a number of areas: these include the improvement of techniques for assisted human conception, notably in the selection of embryos for transfer following In Vitro Fertilisation; the diagnosis of gentic defects at the preimplantation stage; increased undersding of the causes of implantation failure and miscarriage, and the development of novel post‐coital contraceptives. (shrink)

Young traces the evolution of the term information from its general linguistic use into the mainstream of modern science, proposing an entirely new definition of information as a mass-energy phenomenon. He demonstrates that: information is in all cases a form phenomenon; both form and information are mass-energy rather than abstract phenomena; mind can be viewed as a mass-energy rather form-manipulating process; form constitutes a mechanism immanent in the physical universe via which mass-energy systems can communicate informationally and control their own (...) energetic activities. (shrink)

Psychological studies (Proffitt, 2006) have demonstrated that what one sees is influenced by one's goals, physiological state, and emotions. These studies demonstrate that there is a positive correlation between the physical demands (energetic cost) and perceived valence (emotional cost) of a task and the appearance of slant and egocentric distance in the environment. The studies are compelling. However, one can question whether their results are due to changes in the way participants perceived the orientation and extent of their environment (...) or are instead artifacts of the way they judged the difficulty of expected tasks in particular contexts. We asked participants to sketch the rough spatial layout of several paintings as accurately as possible. In this type of task participants continuously compare what they have drawn against what they perceive. Therefore, participants performance can be interpreted as a means to directly measure of the spatial metric of perception. We chose two paintings by Andrew Wyeth as target images: “Christina's World” and “Winter, 1946.” Participants were asked to draw the spatial arrangement of the key features of the scene depicted in the target painting twice: prior to being presented with biographical information about the subject of the painting condition; and then again after being told the biographical information that altered the perceived task demands or emotional valence of the events they depicted. We predicted that participants' drawings would differ in the two conditions indicating that: change in the energetic or emotional costs of the depicted action would cause them to perceive the depicted orientation of hills as steeper and distance between key landmarks as longer. Results from the energetic cost condition support this prediction. We will discuss our results and the suggestion that these types of effects reflect a role for motor simulation in perception (Witt, 2005). (shrink)

Ovarian cancer is the most lethal gynecological malignancy and is often associated with both DNA repair deficiency and extensive metabolic reprogramming. While still emerging, the interplay between these pathways can affect ovarian cancer phenotypes, including therapeutic resistance to the DNA damaging agents that are standard‐of‐care for this tumor type. In this review, we will discuss what is currently known about cellular metabolic rewiring in ovarian cancer that may impact DNA damage and repair in addition to highlighting how specific DNA repair (...) proteins also promote metabolic changes. We will also discuss relevant data from other cancers that could be used to inform ovarian cancer therapeutic strategies. Changes in the choice of DNA repair mechanism adopted by ovarian cancer are a major factor in promoting therapeutic resistance. Therefore, the impact of metabolic reprogramming on DNA repair mechanisms in ovarian cancer has major clinical implications for targeted combination therapies for the treatment of this devastating disease. (shrink)

Control of DNA supercoiling by the free-energy of hydrolysis of ATP that involves gene expression is analyzed in terms of three levels of unconnected metabolic pathways. These are synthesis and breakdown of topoisomerase mRNAs, synthesis and breakdown of topoisomerase proteins and supercoiling and relaxation of DNA. The so-called square-matrix method previously developed for the control of metabolic pathways, is extended to deal with this hierarchical control system. It turns out that also in this case, the matrix of control coefficients is (...) equal to the inverse of the so-called elasticity matrix, which contains all relevant elasticity coefficients as well as information about the structure and connectedness of the pathways involved. For a simpler case of a hierarchy of two systems, we demonstrate that the explicit matrix inversion method may be replaced by an implicit method in which the regulatory effects that run through the other level are described by an additional elasticy coefficient which may then be treated as if local. (shrink)

After more than a century of research on glycolysis, we have detailed descriptions of its molecular organization, but despite this wealth of knowledge, linking the enzyme properties to metabolic pathway behavior remains challenging. These challenges arise from multi‐layered regulation and the context and time dependence of component functions. However, when viewed as a system that functions according to the principles of supply and demand, a simplifying theoretical framework can be applied to study its regulation logic and to assess the coherence (...) of experimental interpretations. These principles are universally applicable, as they emphasize the common metabolic tasks of glycolysis: the provision of free‐energy carriers, and precursors for biosynthesis and stress‐related compounds. Here we will review the regulation of multi‐tasking by glycolysis and consider how an understanding of this central metabolic pathway can be pursued using general principles, rather than focusing on the biochemical details of constituent components. (shrink)

A central problem in the cognitive sciences is identifying the link between consciousness and neural computation. The key features of consciousness—including the emergence of representative information content and the initiation of volitional action—are correlated with neural activity in the cerebral cortex, but not computational processes in spinal reflex circuits or classical computing architecture. To take a new approach toward considering the problem of consciousness, it may be worth re‐examining some outstanding puzzles in neuroscience, focusing on differences between the cerebral cortex (...) and spinal reflex circuits. First, the mammalian cerebral cortex exhibits exascale computational power, a feature that is not strictly correlated with the number of binary computational units; second, individual computational units engage in noisy coding, allowing random electrical events to gate signaling outcomes; third, this noisy coding results in the synchronous firing of statistically random populations of cells across the neural network, at a range of nested frequencies; fourth, the system grows into a more ordered state over time, as it encodes the predictive value gained through observation; and finally, the cerebral cortex is extraordinarily energy efficient, with very little free energy lost to entropy during the work of information processing. Here, I argue that each of these five key features suggest the mammalian brain engages in probabilistic computation. Indeed, by modeling the physical mechanisms of probabilistic computation, we may find a better way to explain the unique emergent features arising from cortical neural networks. (shrink)

Integrating concepts of maintenance and of origins is essential to explaining biological diversity. The unified theory of evolution attempts to find a common theme linking production rules inherent in biological systems, explaining the origin of biological order as a manifestation of the flow of energy and the flow of information on various spatial and temporal scales, with the recognition that natural selection is an evolutionarily relevant process. Biological systems persist in space and time by transfor ming energy from one state (...) to another in a manner that generates structures which allows the system to continue to persist. Two classes of energetic transformations allow this; heat-generating transformations, resulting in a net loss of energy from the system, and conservative transformations, changing unusable energy into states that can be stored and used subsequently. All conservative transformations in biological systems are coupled with heat-generating transformations; hence, inherent biological production, or genealogical proesses, is positively entropic. There is a self-organizing phenomenology common to genealogical phenomena, which imparts an arrow of time to biological systems. Natural selection, which by itself is time-reversible, contributes to the organization of the self-organized genealogical trajectories. The interplay of genealogical (diversity-promoting) and selective (diversity-limiting) processes produces biological order to which the primary contribution is genealogical history. Dynamic changes occuring on times scales shorter than speciation rates are microevolutionary; those occuring on time scales longer than speciation rates are macroevolutionary. Macroevolutionary processes are neither redicible to, nor autonomous from, microevolutionary processes. (shrink)

In this paper the life phenomenon is analysed from cybernetic point of view. The Korzeniewski’s approach is discussed and complemented. The analysis is based on autonomous systems theory and information metabolism theory. Philosophical aspects of the problem are taken into consideration as well.

Every manifestation of information, semiosis and meaning we have been able to study experimentally has a physical form. Neglect of their dynamical (energetic) ground tends towards dualism or idealism, leaving the causal basis of semiosis and the causal powers of representations mysterious. Consideration of the necessary physical requirements for the embodiment of semiotic categories imposes a discipline on semiotics required for its integration into the rest of science, especially for the emerging field of biosemiotics, as well as any future (...) extensions to chemistry physics or other realms that might constitute a general, primal semiotics. Without this discipline, or something equally strong, there is a risk of projection of anthropomorphic semiotic terminology onto unsuitable hosts, leading, if unchecked, to the sort of animism that biology in particular has only recently escaped. The problem is suspect whenever teleological notions are used outside of mental or social contexts.1 Although our animistic ancestors may have had a closer rapport with Nature than modern scientists, contemporary scientific explanation requires an understanding of causal structure (Salmon 1984). On the other hand, unless the causal rendition of semiosis can capture full blown cognitive semiosis, it is likely to be too restrictive for the evaluation of primal semiosis in general. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:To Be or Not to Be:Waiving Informed Consent in Emergency ResearchCharles R. McCarthy (bio)The requirements for prior, legally authorized informed consent constitute a necessary condition for recruiting subjects into biomedical or behavioral research. However, informed consent requirements pose a serious problem for most research conducted in emergency care settings. For this reason, the Food and Drug Administration's (FDA) regulations governing investigational devices and the Department of Health and Human (...) Services' (HHS) regulations for the protection of human subjects allow narrow exceptions to the general requirements of informed consent. In a joint effort to clarify the applicability of the current FDA regulations and to better understand the intent of the HHS regulations as they apply to emergency research, the FDA and the National Institutes of Health (NIH) cosponsored a public forum on the ethical conduct of emergency research in January 1995.Although the forum was not designed as a consensus conference and participants vigorously disagreed on some of the details, a broad consensus emerged on several major points: (1) both HHS and FDA regulations should, in the immediate future, be interpreted to allow for randomized clinical trials in emergency situations so long as the subjects are carefully protected; and (2) consideration should be given to producing new, closely harmonized regulations from both agencies that will provide greater clarity concerning what kinds of emergency research may be allowed without obtaining prior informed consent.The FDA-NIH forum in January was occasioned primarily by controversy about the hypothermia research protocol described below, but it is obvious that many other kinds of emergency research also await the outcome of deliberations concerning waiver of informed consent in emergency situations. These include research into the care and treatment of: occlusive stroke; subarachnoid hemorrhage due to intracranial aneurysm; metabolic coma; status epilepticus; cardiac arrest; myocardial infarction; cardiac arrhythmia; hemorrhagic shock; pulmonary embolism; acute asthmatic attack; and poisoning. All of these conditions [End Page 155] are encountered in emergency settings where obtaining informed consent from the patient-subjects to participate in research is seldom possible, and obtaining consent from legally authorized representatives of the subjects is either not feasible, or, if obtained, is of doubtful validity.The Hypothermia Research Case and HHS RegulationsA $7.2 million grant for research on the use of hypothermia in the treatment of severe head trauma, the largest award ever made to the University of Texas Health Sciences Center at Houston, is in danger of expiring before the study is completed. The protocol, which involves the use of cooling blankets to induce hypothermia in patients suffering from severe head injuries, is designed to test the hypothesis that: "Early lowering of the body temperature of patients suffering from severe head trauma to approximately 91 degrees Fahrenheit will slow patients' metabolism and will/will not, as a consequence, reduce the rates of both morbidity and mortality in these patients." The protocol was approved by seven Institutional Review Boards (IRBs), each of which waived the requirement to obtain informed consent from research subjects in accordance with Sec. 46. 116(d) of the HHS Regulations for the Protection of Human Subjects.1However, NIH's Office for Protection from Research Risks (OPRR), which is responsible for assuring compliance with the HHS regulations, has taken a controversial regulatory position by requiring informed consent from a legally authorized representative of each subject to be entered in the hypothermia trial. Because the obtaining of surrogate consent has proved to be very difficult, OPRR's position has slowed the research to a point where it may have to be terminated.At issue in the controversy is a fundamental question of ethics and public policy. Is it ever permissible to involve incompetent subjects in research without either their consent, or the consent of their legally authorized representatives? Pertinent HHS regulations for the protection of human subjects seem to answer the question affirmatively by allowing local IRBs to waive some or all of the elements of informed consent under carefully limited circumstances (45 CFR 46 116(d)). Nevertheless, OPRR has signalled the research community that use of the informed consent waiver provision for the Houston hypothermia study is not permitted under the regulations. OPRR judged that the risks... (shrink)

This article contains the results of a theoretical analysis of the phenomenon of natural language understanding (NLU), as a methodological problem. The combination of structural-ontological and informational-psychological approaches provided an opportunity to describe the subject matter field of NLU, as a composite function of the mind, which systemically combines the verbal and discursive structural layers. In particular, the idea of NLU is presented, on the one hand, as the relation between the discourse of a specific speech message and the (...) meta-discourse of a language, in turn, activated by the need-motivational factors. On the other hand, it is conceptualized as a process with a specific structure of information metabolism, the study of which implies the necessity to differentiate the affective (emotional) and need-motivational influences on the NLU, as well as to take into account their interaction. At the same time, the hypothesis about the influence of needs on NLU under the scenario similar to the pattern of Yerkes-Dodson is argued. And the theoretical conclusion that emotions fulfill the function of the operator of the structural features of the information metabolism of NLU is substantiated. Thus, depending on the modality of emotions in the process of NLU, it was proposed to distinguish two scenarios for the implementation of information metabolism - reduction and synthetic. The argument in favor of the conclusion about the productive and constitutive role of emotions in the process of NLU is also given. (shrink)

Every action, specifically the therapeutic act, is determined by our mental state: love and compassion. Positive thinking, which must lead us in our research and our acts, is based on the fact that therapeutic results are determined by a treatment of the entire human being: “Body–Mind–Spirit,” which is outstretched, according to tradition, on the four levels of consciousness: Plan 7: Body; Plan 6: Metabolism; Plan 5: Mental; Plan 4: Information. Within the context of a chronic condition, homeopathy practice and (...) the use of differentiations factors have been an example of the possible patient's transformation and of the dialogue between science and spirituality. (shrink)

In this paper the life phenomenon is analysed from cybernetic point of view. The Korzeniewski’s approach is discussed and complemented. The analysis is based on autonomous systems theory and information metabolism theory. Philosophical aspects of the problem are taken into consideration as well.

With 500+ papers and 20+ books spanning many scientific disciplines, Mark Burgin has left an indelible mark and legacy for future explorers of human thought and information technology professionals. In this paper, I discuss his contribution to the evolution of machine intelligence using his general theory of information (GTI) based on my discussions with him and various papers I co-authored during the past eight years. His construction of a new class of digital automata to overcome the barrier posed by the (...) Church–Turing Thesis, and his contribution to super-symbolic computing with knowledge structures, cognizing oracles, and structural machines are leading to practical applications changing the future landscape of information systems. GTI provides a model for the operational knowledge of biological systems to build, operate, and manage life processes using 30+ trillion cells capable of replication and metabolism. The schema and associated operations derived from GTI are also used to model a digital genome specifying the operational knowledge of algorithms executing the software life processes with specific purposes using replication and metabolism. The result is a digital software system with a super-symbolic computing structure exhibiting autopoietic and cognitive behaviors that biological systems also exhibit. We discuss here one of these applications. (shrink)

Use of symbols, the key to the biosemiotics field as to many others, required bigger brains which implied a promissory note for greater energy consumption; symbols are obviously expensive. A score years before the current estimate of 18–20% for the human brain’s metabolic demand on the organism, it was known that neural tissue is metabolically dear. This paper first discusses two evolutionary responses to this demand, on both of which there is some consensus. The first, assigning care of altricial infants (...) with burgeoning brains (and in human infants the metabolic demand peaks at 65% of the total) to “allomothers” is not unique to humans. The second, using relatively small neurons as primates do, risks misfires past a certain minimal value. Moreover, in apparent paradox, there is an increasing consensus that large “Von Economo” neurons are critical for communication. This paper’s main contribution is the discussion of two further evolutionary tricks. The first is the use of self-similarity in the cortex, both in structure and process, to allow the cortex readily—and in energetic terms, parsimoniously—to shift between states in a high-dimensional space. This leads to discussion of the kind of formalism appropriate to model these shifts, a formalism which—it is tentatively suggested—may do double duty for the modeling of symbolic thought. The second trick is the superimposition on the background “white noise” of neural firing of EEG-detected waves like gamma. The paper describes a method, using the Hilbert transform, of calculating the dips in energy consumption as the brain is transitioned by gamma waves. It is hypothesized that consciousness may be a spandrel, the incidental result of a neurodynamic imperative that the brain enter a maximally sensitive (in sensory terms) “zero power” state a few times a second. If that is the case, then there are obvious benefits for health in meditation, which can be viewed as a state of consciousness extended over time by limiting afferent stimuli. (shrink)

One of the most striking developments in recent biology has been the proliferation of concepts such as coding, information, representation and programming, especially applied to genes. The idea that genes can be described as having semantic properties, as well as ordinary causal properties, has become so uncontroversial in many quarters that it now appears prominently in biology textbooks. Scott Gilbert's widely used developmental biology text, to pick just one example, tell us that "the inherited information needed for development and (...) class='Hi'>metabolism is encoded in the DNA sequences of the chromosomes" (Gilbert 1997 p. 5). (shrink)

Exactly how do the sign/symbol/token systems of endo- and exo-biosemiosis differ from those of cognitive semiosis? Do the biological messages that integrate metabolism have conceptual meaning? Semantic information has two subsets: Descriptive and Prescriptive. Prescriptive information instructs or directly produces nontrivial function. In cognitive semiosis, prescriptive information requires anticipation and “choice with intent” at bona fide decision nodes. Prescriptive information either tells us what choices to make, or it is a recordation of wise choices already made. Symbol systems allow (...) recordation of deliberate choices and the transmission of linear digital prescriptive information. Formal symbol selection can be instantiated into physicality using physical symbol vehicles (tokens). Material symbol systems (MSS) formally assign representational meaning to physical objects. Even verbal semiosis instantiates meaning into physical sound waves using an MSS. Formal function can also be incorporated into physicality through the use of dynamically-inert (dynamically-incoherent or -decoupled) configurable switch-settings in conceptual circuits. This paper examines the degree to which biosemiosis conforms to the essential formal criteria of prescriptive semiosis and cybernetic management. (shrink)

Constructivist biosemiotics foundations imply the first-person basis of cognition. CBF are developed by the biology of cognition, relational biology, enactive approach, ecology of mind, second order cybernetics, genetic epistemology, gestalt, ecological perception and affordances, and active inference by minimization of free energy. CBF reject the idea of an objective independent reality to be represented by information processing in order to be the fittest. CBF assumes that perception is the behavioral configuration of an object and objects are tokens for eigen-behaviors. Cognition (...) takes place in the organism-environment structural coupling during the ontogeny and phylogeny of all biological unities including unicellular organisms. Therefore, if exogenous DNA particles are just tokens for the cell signalling eigen-behaviors, if there is no ‘information’ in the DNA sequence, how can we explain that the same virus or trans- sequence is associated with a similar phenotype? We call this ‘exogenomic problem’. With this basic example, but sufficiently generic to the whole biological world, we agree respectively with Autopoiesis, -system, and Gaia theory: i) ‘Information, code and meaning’ in the DNA sequence belong to the domain of the observer’s description. ii) Genetic ‘information’ is not a program or algorithmic software in DNA sequence. Rather it is a microphysical observable mode of eigen-behaviors in biological unities. iii) The transfer and acquisition of DNA particles is a biospheric phenomenon that maintains its homeorhesis, symbiotic and biosemiotic entailment. Based on the theoretical and experimental results of these theories, it is concluded that genetic ‘information’ is not a genomic sequence, nor any kind of information, but for the cell DNA must embody physical forcing. Genetic characters are the effects and not the cause of phenotype and DNA particles do not ‘use or manipulate’ cellular metabolism. Rather, any cellular configuration change that occurred before or during DNA perturbation is determined on the basis of the cellular standpoint. (shrink)

This paper presents a historical examination of the influence of the Darwinian metaphor 'the struggle for existence' on a variety of scientific theories which inform our current understanding of the prospects for sustainable development. The first part of the paper traces the use of the metaphor of struggle through two distinct avenues of thought relevant to the search for sustainable development. One of these avenues leads to the biophysical critique of conventional development popularised by 'ecological economists' such as Georgescu-Roegen and (...) Daly. This critique suggests that modern economic systems have gone astray by failing to respect the biological and physical limits to development and that they should be adapted to make them more like ecological systems. The other avenue leads to the modern insights of evolutionary psychology. These latter insights suggest that in certain key respects, the economic system (and actors within it) are already behaving more or less like an ecological system, driven as they are by evolutionary imperatives. Consequently, this second avenue appears to offer far bleaker prospects for achieving sustainable development than the first. However, the final part of the paper re-examines the historical roots of the metaphor itself, and suggests a number of ways in which a critical response to those historical roots might influence our understanding of the prospects for sustainable development. (shrink)

Life can be defined as combining two entities that rest on completely different physico-chemical properties and on a particular way of handling information. The cell, first, is a « machine », that combines elements which are quite similar (although in a fairly fuzzy way) to those involved in a man-made factory. The machine combines two processes. First, it requires explicit compartmentalisation, including scaffolding structures similar to that of the châssis of engineered machines. In addition, cells define clearly an inside, the (...) cytoplasm, and an outside. The cell envelope is more or less complicated in bacteria, and it is much more complicated in organisms made of cells with a nucleus (eukaryotes). Second, the machine also requires dynamic chemical processes, collectively named metabolism, that can be split into intermediary metabolism, managing chemical transformations and transport of small building blocks and management of energy (often with a rotating nanomachine, ATP synthase), and the macromolecule synthesis, salvage and turnover machinery which uses a variety of nanomachines, the ribosome being the most prominent one. The second entity which needs to be associated to life is the genetic program, in the form of the genome, composed of one or several chromosomes made of DNA. This is the entity which associates most clearly to information. -/- Natural selection uses information in a particular way: it is a process that uses energy to prevent degradation of any functional entity. This process keeps building up novel information within organisms. (shrink)

Bacteria adapt to changes in their environment by altering their metabolism, turning on and off genes, and moving toward favorable conditions. Recent results indicate that a common molecular logic may underlie the decision‐making processes by which these simple cells adjust to their surroundings.

In “How Molecules Became Signs”, Prof. Deacon outlines a plausible mechanism whereby biochemical systems could be understood to fulfill the conditions of being “alive” in the context of the two broad families of requirements, namely the energetics of metabolism and the informatics of coding. In so doing, he addresses head-on how to account for the origin and the action of coding in physical systems, and thereby the necessary and sufficient conditions for life. I review some of the relevant issues (...) around the interlocking potential necessary and sufficient conditions whereby these two phenomena are included within systems of interpretation in organisms. (shrink)

It seems obvious that signs in visual art and musical notation are static carriers of visual and acoustic information. Both types of sign, however, represent dynamic processes. In real space-time, there exists no static visible thing or static audible sound. The sources of visible or audible information are dynamic – i.e. complementary substantialenergetic-informational – entities extending in space-time. The same is true of an artificial or organic receiver and processor of visual or audible information. Reality and semiosis – to (...) be, to be perceived, and to be understood or to communicate – are dynamic processes. From a semiotic point of view, thus, pictures, photographic or artistic sign structures can’t be icons – in any case, if icons in a Peirceian manner are understood as signs representing objects for an interpretant by similarity . Similarity between icon and object is not a static precondition but a dynamic result of visual semiosis, i.e. of categorizing. Seeing something or hearing something is, as a consequence, not an “intuitive” or instantaneous Gestalt shift between representamen and object ongoing in an interpretant. And so, according to Fernande SaintMartin 1990: “visual semiotics … has to adopt an epistemology which is more in agreement with the dynamics of observed phenomena. It will recognize that matter is not inertness, but energy.” If the material carrier of semiosis, the representamen, already is to be understood as energy or dynamic process, all the more the whole complementary triadic sign-relation – object-representamen-interpretant – has to be understood as energetic information flow. This is being recognized in the transition from naturalistic, i.e. reproducing or mapping art, to modern, i.e. processing or interpreting/transducing art. Paul Klee 1990 for example says about the semiotic function of visual art: “Art doesn’t reproduce the visible but makes visible” . And he correlates the artistic activity of visualizing with the primordial, cosmogonic process of formation: “Reduced to the primordial process of formation, to creation, the process of cell division emerges” . Visual artistic semiosis is, thus, obviously to be understood as the process of emerging dynamic sign structures. It is the skill of the painter that makes the static results of dynamic semiosis “readable” for the viewer as signs – lines and surfaces - of the dynamic visual meaning of the picture. (shrink)

Features of gait are determined at multiple levels, from the selection of the gait itself (e.g. walk or run) through the specific parameters utilized (stride length, frequency, etc.) to the pattern of muscular excitation. The ultimate choices are neurally determined, but what is involved with that decision process? Human locomotion appears stereotyped not so much because the pattern is predetermined, but because these movement patterns are good solutions for providing movement utilizing the machinery available to the individual (the legs and (...) their requisite components). Under different circumstances the appropriate solution may differ broadly (different gait) or subtly (different parameters). Interpretation of the neural decision making process would benefit from understanding the influences that determine the selection of the appropriate solution in any set of circumstances, including that of normal conditions. In this review we survey an array of studies that point to energetic cost as a key input to the gait coordination system, and not just an outcome of the gait pattern implemented. We then use that information to rigorously define the construct proposed by Sparrow and Newell (1998) where the effects of environment, organism and task act as constraints determining the solution set available, and the coordination pattern is then implemented under a pressure for energetic economy. Environment is defined in terms of affordances based on the ecological psychology definition of the concept and organism is defined as classic morphology and physiology based capabilities. We rely on a novel conceptualization of task that recognizes that the task goal needs to be separated from the mechanisms that achieve the goal if the motivation behind the selection of the mechanism strategy is to be exposed and understood. This reformulation of the Sparrow and Newell construct is then linked to the proposed pressure for economy by considering it as an optimization problem, where the most readily selected gait strategy will be that which achieves the task goal at (or near) the energetic minimum. (shrink)

B cell activation is accompanied by metabolic adaptations to meet the increased energetic demands of proliferation. The metabolic composition of the microenvironment is known to change during a germinal center response, in inflamed tissue and to vary significantly between different organs. To sustain cellular homeostasis B cells need to be able to dynamically adapt to changes in their environment. An inability to take up and process available nutrients can result in impaired B cell growth and a diminished humoral immune (...) response. Furthermore, the metabolic microenvironment can affect B cell signaling and provide a means to avoid aberrant proliferation or modulate B cell function. Thus, a better understanding of the intricate interplay between cell signaling and metabolism could provide novel insight into how B cell function is regulated and have implications for the development of vaccines or treatment of autoimmune disorders and B cell derived malignancies. Throughout their lifespan, B cells are exposed to different metabolic environments. Signaling pathways regulating cellular responses to metabolic stress not only help to maintain B cell viability and to facilitate cellular functions but may also play an important role in preventing excessive proliferation and malignant transformation. (shrink)

Starting from the paradigm of the material continuum we discuss the possibility to transcend the space-time reality (Here-and-Now) in the aim of investigating the energetic and informational reality, support of the continuous present. The altered states of consciousness, obtained by means of "psyche"-type techniques, allow the transformation of a future temporal nexus in an element of the present time. Through this "psyche anticipation" process, a sliding of the time reference takes place, since the future becomes present and the (...) present an element of the past. In this way the initial anticipatory potential is enhanced and allows one more energetic and informational step. By such a step-by-step progression segments of the future could be investigated, thus building an anticipatory model. The "psyche anticipation" techniques can be successfully used in the healing process of some diseases. (shrink)

Spontaneous brain activity has received increasing attention as demonstrated by the exponential rise in the number of published papers on this topic over the last thirty years. Such “intrinsic” brain activity, generated in the absence of an explicit task, is frequently associated with resting-state or default-mode networks. The focus on characterizing spontaneous brain activity promises to shed new light on questions concerning the structural and functional architecture of the brain and how they are related to “mind”. However, many critical questions (...) have yet to be addressed. In this review, we focus on a scarcely explored area, specifically the energetic requirements and constraints of spontaneous activity, taking into account both thermodynamical and informational perspectives. We argue that the “classical” definitions of spontaneous activity do not take into account an important feature, that is, the critical thermodynamic energetic differences between spontaneous and evoked brain activity. Spontaneous brain activity is associated with slower oscillations compared with evoked, task-related activity, hence it exhibits lower levels of enthalpy and “free-energy” (i.e. the energy that can be converted to do work), thus supporting noteworthy thermodynamic energetic differences between spontaneous and evoked brain activity. Increased spike frequency during evoked activity has a significant metabolic cost, consequently, brain functions traditionally associated with spontaneous activity, such as mind wandering, require less energy that other nervous activities. We also review recent empirical observations in neuroscience, in order to capture how spontaneous brain dynamics and mental function can be embedded in a non-linear dynamical framework, which considers nervous activity in terms of phase spaces, particle trajectories, random walks, attractors and/or paths at the edge of the chaos. This takes us from the thermodynamic free-energy, to the realm of “variational free-energy”, a theoretical construct pertaining to probability and information theory which allows explanation of unexplored features of spontaneous brain activity. (shrink)

The brain's reliance on glucose as a primary fuel source is well established, but psychological models of cognitive processing that take energy supply into account remain uncommon. One exception is research on self-control depletion, where debate continues over a limited-resource model of self-control depletion. This model argues that transient reduction in self-control after exertion of prior self-control is caused by the depletion of brain glucose, and that self-control processes are special, perhaps unique, in this regard. This model has been argued (...) to be physiologically implausible in several recent reviews. This paper attempts to correct some inaccuracies that have occurred during debate over the physiological plausibility of this model. We contend that not only is such limitation of cognition by constraints on glucose supply plausible, it is well established in the neuroscience literature across several cognitive domains. Conversely, we argue that there is no evidence that self-control is special in regard to its metabolic cost. Mental processes require physical energy, and the body is limited in its ability to supply the brain with sufficient energy to fuel mental processes. This article reviews current findings in brain metabolism and seeks to resolve the current conflict in the field regarding the physiological plausibility of the self-control glucose-depletion hypothesis. (shrink)

Adequate reprogramming of cellular metabolism in response to stresses or suboptimal growth conditions involves a myriad of coordinated changes that serve to promote cell survival. As protein synthesis is an energetically expensive process, its regulation under stress is of critical importance. Reprogramming of messenger RNA (mRNA) translation involves well‐understood stress‐activated kinases that target components of translation initiation machinery, resulting in the robust inhibition of general translation and promotion of the translation of stress‐responsive proteins. Translational arrest of mRNAs also results (...) in the accumulation of transcripts in cytoplasmic foci called stress granules. Recent studies focus on the key roles of transfer RNA (tRNA) in stress‐induced translational reprogramming. These include stress‐specific regulation of tRNA pools, codon‐biased translation influenced by tRNA modifications, tRNA miscoding, and tRNA cleavage. In combination, signal transduction pathways and tRNA metabolism changes regulate translation during stress, resulting in adaptation and cell survival. This review examines molecular mechanisms that regulate protein synthesis in response to stress. (shrink)

To construct a synthetic cell we need to understand the rules that permit life. A central idea in modern biology is that in addition to the four entities making reality, matter, energy, space and time, a fifth one, information, plays a central role. As a consequence of this central importance of the management of information, the bacterial cell is organised as a Turing machine, where the machine, with its compartments defining an inside and an outside and its metabolism, reads (...) and expresses the genetic program carried by the genome. This highly abstract organisation is implemented using concrete objects and dynamics, and this is at the cost of repeated incompatibilities (frustration), which need to be sorted out by appropriate «patches». After describing the organisation of the genome into the paleome (sustaining and propagating life) and the cenome (permitting life in context), we describe some chemical hurdles that the cell as to cope with, ending with the specific case of the methionine salvage pathway. (shrink)

Cartesian mind body dualism and modern versions of this viewpoint posit a mind thermodynamically unrelated to the body but informationally interactive. The relation between information and entropy developed by Leon Brillouin demonstrates that any information about the state of a system has entropic consequences. It is therefore impossible to dissociate the mind's information from the body's entropy. Knowledge of that state of the system without an energetically significant measurement would lead to a violation of the second law of thermodynamics.

Most philosophers appear to have ignored the distinction between the broad concept of Virtual Machine Functionalism (VMF) described in Sloman&Chrisley (2003) and the better known version of functionalism referred to there as Atomic State Functionalism (ASF), which is often given as an explanation of what Functionalism is, e.g. in Block (1995). -/- One of the main differences is that ASF encourages talk of supervenience of states and properties, whereas VMF requires supervenience of machines that are arbitrarily complex networks of causally (...) interacting (virtual, but real) processes, possibly operating on different time-scales, examples of which include many different procesess usually running concurrently on a modern computer performing various tasks concerned with handling interfaces to physical devices, managing the file system, dealing with security, providing tools, entertainments, and games, and possibly processing research data. Another example of VMF would be the kind of functionalism involved in a large collection of possibly changing socio-economic structures and processes interacting in a complex community, and yet another is illustrated by the kind of virtual machinery involved in the many levels of visual processing of information about spatial structures, processes, and relationships (including percepts of moving shadows, reflections, highlights, optical-flow patterns and changing affordances) as you walk through a crowded car-park on a sunny day: generating a whole zoo of interacting qualia. (Forget solitary red patches, or experiences thereof.) -/- Perhaps VMF should be re-labelled "Virtual MachinERY Functionalism" because the word 'machinery' more readily suggests something complex with interacting parts. VMF is concerned with virtual machines that are made up of interacting concurrently active (but not necessarily synchronised) chunks of virtual machinery which not only interact with one another and with their physical substrates (which may be partly shared, and also frequently modified by garbage collection, metabolism, or whatever) but can also concurrently interact with and refer to various things in the immediate and remote environment (via sensory/motor channels, and possible future technologies also). I.e. virtual machinery can include mechanisms that create and manipulate semantic content, not only syntactic structures or bit patterns as digital virtual machines do. -/- Please note: Click on the title above or the link below to read the paper. I prefer to keep all my papers freely accessible on my web site so that I can correct mistakes and add improvements. -/- http://www.cs.bham.ac.uk/research/projects/cogaff/misc/vm-functionalism.html -/- This is now part of the Meta-Morphogenesis project: http://www.cs.bham.ac.uk/research/projects/cogaff/misc/meta-morphogenesis.html. (shrink)