The structuralist reconstruction of the metabolic biochemistry here presented is a more complete and revised version than the one presented in Donolo, Federico & Lorenzano (2006). This version, as the previous one, continues with the reconstructive task initiated by César Lorenzano (2002), but advances further on those elements which remained pendent of reconstruction: applications subsequent to the paradigmatic one, for being these “too diversified and numerous” (p. 210).In line with which is said before, the objective of this new (...) reconstruction is to make the theoretical network of the biochemistry wider, in order to be able to capture the many successful applications (paradigmatic examples or exemplars) which appear in modern university textbooks. In order to accomplish this, major conceptual precisions are being introduced which will have repercussions in a modification and increased complexity of the fundamental law implicit in the text books, but still conserving the previous basic idea. Because of all this we can say that the present article goes further into the reconstruction task of the metabolic biochemistry theory. (shrink)

Basant (Spring) is a time of dawning light, new life, new birth, and new hope — a time of warmth, vitality, dancing, and blossoming. Every year she comes out of the cold darkness and captivatingly dances around us. She embraces us with her warmth, intoxicates us with her aroma. Like a potent elixir, spring revitalizes our hope. She breathes life into the dead and teaches us the lessons of renewal and rebirth [1]. The dawn of Basant has well appreciated in (...) Gurbani as; "Among the months, blessed is the month when spring always comes."[Mehl First, SGGS: 1168]; "The delightful season of spring has come." [Mehl First, SGGS: 1168] Every year, the vernal equinox occurs on the 21st of March. It indicates the starting of long, brighter days. The birds trill, bees buzz, and the buds of plants and trees burst forth. Humans stroll with a bit more spring in their step and sparkle in their eyes. Gurbani appreciates the blooming of Spring as; "The season of spring has come. It blossoms forth luxuriantly." [Mehl Fifth, SGGS: 1185] Feeling good in spring is more than psychological. The more extended light period of spring days has the power to change our biochemistry in positive ways. The increased sunlight exposure affects hormonal and metabolic functions. We feel more optimistic and resilient; even our reproductive patterns are affected by the light of spring. (shrink)

Whipple disease is a rare, infectious, disease first described from a single case by Whipple in 1907. As well as characterising the clinical and pathological features of the condition, Whipple made two suggestions regarding its aetiology. These were either than the disease was caused by an infectious agent, or that it was of metabolic origin. As the disease is now thought to be caused by infection with the bacterium Tropheryma whipplei, historical reviews of the history of the disease typically (...) mention only the first of these suggestions. In this paper, we therefore revisit Whipple’s other theory. We argue that a diverse and often successful research programme was developed around this mechanism of disease causation which gave rise to many useful findings on the condition. In the later parts of this article, we then turn to discuss the surprising neglect of this period of Whipple disease research in the current literature, and conclude by offering a brief reconstruction of this early history suitable for use in a technical context. (shrink)

Neural activity varies continually from moment to moment. Such temporal variability (TV) has been highlighted as a functionally specific brain property playing a fundamental role in cognition. We sought to investigate the mechanisms involved in TV changes between two basic behavioral states, namely having the eyes open (EO) or eyes closed (EC) in vivo in humans. To these ends we acquired BOLD fMRI, ASL, and [18F]-fluoro-deoxyglucose PET in a group of healthy participants (n = 15), along with BOLD fMRI and (...) [18F]-flumazenil PET in a separate group (n = 19). Focusing on an EO- vs EC-sensitive region in the occipital cortex (identified in an independent sample), we show that TV is constrained in the EO condition compared to EC. This reduction is correlated with an increase in energy consumption and with regional GABAA receptor density. This suggests that the modulation of TV by behavioral state involves an increase in overall neural activity that is related to an increased effect from GABAergic inhibition in addition to any excitatory changes. These findings contribute to our understanding of the mechanisms underlying activity variability in the human brain and its control. (shrink)

Schröedinger’s question “what is life?” was a real challenge for the scientific community and this still remains as an opened question, because in spite of the important advances in various scientific branches like philosophy, biology, chemistry and physics,, each of them assesses life from its particular point of view to explain the life’ characteristic features, so not a coherent and well structured general model of life was reported. In this paper life is approached from informational perspective, starting from earlier Draganeacu's (...) philosophic concepts, showing that actually life is structured by matter and information. Therefore, it is analyzed carbon-matter properties on the basis of which the living structures are composed, giving rise not only of a considerable number of carbon-based compounds, but serving now beside silicon, as an useful material for micro/nanostructure applications. Such specific properties refers to the high ability of carbon to associate/dissociate in chemical reactions regulated/facilitated by informational (Bit unit) YES/NO bistable mechanisms to form macro/small molecules with complementary properties, reactive info-functional pathways of transduction, relaying, amplification, integration, spreading, modulation, activation and positive/negative feedback reactions, like in the informational microelectronic/microsystems circuits. It is argued that the negentropy invoked earlier in Schrödinger's analysis is a consequence of informational-assisted structuration/organization of the cell and human organism. From the analysis of inter/intra-communication mechanisms in the cell and comparing with the outcomes described by the Informational Model of Human Body, it is deduced that, the living organisms operate on the basis of three main streaming circuits assuring the living functions: (1) the metabolic matter-related circuit; (2) the operative informational circuit; (3) the epigenetic informational circuit for the gradual integration of information in the central informational structure – DNA. It is founded on these bases the Informational Model of the Living Structures, and the Informational System of the Living Structures (ISLS), with similar functions on the entire living scale size, from unitary to multicellular living structures, composed by seven informational systems, namely [CASI (center of acquisition and storing of information), CDC (center of decision and command), IRSS (info-reactive sentient system), MIS (maintenance info-system), GTS (genetic transmission system), IGG (info-genetic generator) and IC (info-connection)]ISLS, and are identified the specific functions of each of them. The living structures operate thus like self-“polarized" bipolar info-matter informational devices by means of the stand-by metabolic matter-related circuit, and react/respond to the external/internal informational stimuli, which modulate their functionality, returning an external reaction signal (“attitude"), for adaptation and survival. (shrink)

Objective: Reference values have gained universal acceptance as the most powerful material that helps the decision-making-implementation process of the clinical laboratory. These values ​​may be affected by the geographical location, dietary habits, and other lifestyle changes of individuals applying to the clinical laboratory. Our study aims to determine the reference ranges for the biochemistry test panel, thyroid function tests, and insulin hormone levels, which are frequently needed by clinicians for the province of Gaziantep, with samples obtained from healthy individuals. (...) -/- Materials and Methods: In the study phase, the selection of reference individuals was carried out using the direct method a priori. For the study group, healthy individuals (224 men, 243 women) aged 18-45 were selected. Reference intervals (95% limit) were calculated according to the non-parametric method. -/- Results: When the reference intervals obtained in our study were compared with the reference intervals of the manufacturer, there were differences (> 10% lower or higher) in the upper and lower limits in urea (female and male), creatinine (male), HDL (female), AST (female and male), ALT (female), GGT (female), ALP (common), Lipase (common), CK (male), iron (male), TSH (female and male) markers. Male and female reference intervals for HDL, AST, ALT, and TSH differed significantly. Manufacturer reference ranges for these parameters were common to both sexes. -/- Conclusion: As a result, differences were determined between most of the reference intervals obtained in our study and the reference intervals we routinely use. We think the difference in the reference intervals is due to the differences in dietary habits and environmental factors. (shrink)

The premise of biological modularity is an ontological claim that appears to come out of practice. We understand that the biological world is modular because we can manipulate different parts of organisms in ways that would only work if there were discrete parts that were interchangeable. This is the foundation of the BioBrick assembly method widely used in synthetic biology. It is one of a number of methods that allows practitioners to construct and reconstruct biological pathways and devices using DNA (...) libraries of standardized parts with known functions. In this paper, we investigate how the practice of synthetic biology reconfigures biological understanding of the key concepts of modularity and evolvability. We illustrate how this practice approach takes engineering knowledge and uses it to try to understand biological organization by showing how the construction of functional parts and processes can be used in synthetic experimental evolution. We introduce a new approach within synthetic biology that uses the premise of a parts-based ontology together with that of organismal self-organization to optimize orthogonal metabolic pathways in E. coli. We then use this and other examples to help characterize semisynthetic categories of modularity, parthood, and evolvability within the discipline. (shrink)

The present investigation has been designed to study the effect of sub lethal concentrations of Nickel on the serum metabolites of Channa punctatus after exposure to 45 days. The present study shows that serum metabolites such as glucose and protein were significantly decreased while lipid was significantly increased. Thus, the result provides an overview of the manipulation of fish, Channa punctatus as a biomarker of heavy metals through alternation in serum biochemical parameters.

Introduction: Metabolic syndrome (MetS) is an endocrinopathy with a combination of cardiovascular and metabolic compounds. In our study, it is expected to obtain results showing that mortality rate, loss of workforce, and treatment costs due to disorders caused by MetS can be reduced by physical exercise. The study analyses the effect of moderate exercise training on this Apolipoprotein E (ApoE), Apolipoprotein CIII (ApoCIII), adiponectin, resistin, interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α) which are thought to have a role (...) in the deterioration of glucose and lipid metabolism in MetS. -/- Methods: This clinical experimental study consists of 3 groups. The MetS+E (n=24) group, which included the participants who agreed to participate in the exercise program in addition to their medical treatment, the MetS (n=23) group who received medical treatment but did not exercise, and the Control+E (n=25) group, which included healthy volunteers who had the same protocol as MetS+E ApoE, ApoCIII, adiponectin, resistin, IL-6, and TNF-α plasma levels of all participants were measured both at the beginning of the study and at the end of the protocol. -/- Results: At the end of the study we reached the following findings; insulin and Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) levels decreased in exercise groups (p=0,03). ApoCIII levels increased in all the groups after the study (p<0,01). IL-6 levels decreased in MetS+E (p<0,01) and Control+E (p=0,037). ApoE (p=0,01) and TNF-α (p=0,037) levels decreased only in the Control+E group. -/- Conclusion: Training showed metabolic, anti-inflammatory, and physical improvements independent of ApoE and ApoCIII in those with MetS. (shrink)

Abstract: Background: Vitamin D insufficiency/deficiency prevalent in all age groups across the world is common in obesity and may play an important role in the risk factors of metabolic syndrome (MS). Objectives: This cross-sectional study is to evaluate the relationship between levels of adiponectin and circulating 25(OH)D, and its effect on metabolic biomarker among overweight/obese female students. Methods: Three hundred female students; with mean age 20.9 ± 3.2 years were attending the Aljouf University, Sakaka, Saudi Arabia. They were (...) randomly selected from university during the studying year 2015 – 2016. Anthropometric and biochemical indices were determined. Results: The study showed 19% of the female’s student were either overweight or obese (15% and 4%, respectively). The frequency of MS diagnosis among the students was 17%, with 13% and 4% had either three or four risk factors, respectively. Overweight/obese subjects had significantly worse anthropometric and biochemical characteristics, including waist/hip ratio, blood pressure (BP), fasting blood glucose (BG), insulin, insulin resistance (HOMA-IR), triglyceride levels (TG), low-density lipoprotein cholesterol levels (LDL-C), leptin, adiponectin, leptin/adiponectin ratio and high-density lipoprotein cholesterol levels (HDL-C) compared to normal weight. Of the subjects diagnosed with MS, 59% had mild and 8.6% had severe 25(OH)D deficiency. There was negative association between 25(OH)D and both FBG and HOMA-IR among young women obese/overweight. Conclusion: In our study, it suggested that low level of adiponectin was strongly correlated with low 25(OH)D levels. Also, the prevalence of MS tends to increase with high occurrence rate of low circulating 25(OH)D levels that is, known cause poor glycemic control and prediction of cardiovascular outcomes. (shrink)

The studies carried out in recent years on the molecular dynamics of consciousness, especially in relation to diseases such as major depression and bipolar disorder, on man considered as a synthesis of nature and culture, in their interdisciplinary and transdisciplinary expression, prompted us to carry out the molecular logic involving the human component of Christ (Christ-Man). On the basis of evidence presented in the Holy Scriptures, regarding the hours that preceded his death, we tend, in the light of the molecular (...) pathway related to mood disorders, to attribute a possible form of depression to Christ-Man, without of course, undermining the faith in the transcendent nature of the Christ-God. (shrink)

The biochemistry of geotropism in plants and gravisensing in e.g. cyanobacteria or paramacia is still not well understood today [1]. Perhaps there are more ways than one for organisms to sense gravity. The two best known relatively old explanations for gravity sensing are sensing through the redistribution of cellular starch statoliths and sensing through redistribution of auxin. The starch containing statoliths in a gravity field produce pressure on the endoplasmic reticulum of the cell. This enables the cell to sense (...) direction. Alternatively, there is the redistribution of auxin under the action of gravity. This is known as the Cholodny-Went hypothesis [2], [3]. The latter redistribution coincides with a redistribution of electrical charge in the cell. With the present study the aim is to add a mathematical unified field explanation to gravisensing. (shrink)

Starting from a philosophical perspective, which states that the living structures are actually a combination between matter and information, this article presents the results on an analysis of the bipolar information-matter structure of the human organism, distinguishing three fundamental circuits for its survival, which demonstrates and supports this statement, as a base for further development of the informational model of consciousness to a general informational model of the human organism. For this, it was examined the Informational System of the Human (...) Body and its components from the perspective of the physics/information/neurosciences concepts, showing specific functions of each of them, highlighting the correspondence of these centers with brain support areas and with their projections in consciousness, which are: Center of Acquisition and Storing of Information (CASI) reflected in consciousness as memory, Center of Decision and Command (CDC) (decision), Info-Emotional Center (IES) (emotions), Maintenance Informational System (MIS) (personal status), Genetic Transmission System (GTS) (associativity/genetic transmission) and Info Genetic Generator (IGG) related by the body development and inherited behaviors. The Info Connection (IC), detected in consciousness as trust and confidence can explain the Near-Death Experiences (NDEs) and associated phenomena. This connection is antientropic and informational, because from the multitude of uncertain possibilities is selected a certain one, helping/supporting the survival and life. The human body appears therefore as a bipolar structure, connected to two poles: information and matter. It is argued that the survival, which is the main objective of the organism, is complied in three main ways, by means of: (i) the reactive operation for adaptation by attitude; (ii) the info-genetic integration of information by epigenetic processes and genetic transmission of information for species survival, both circuits (i) and (ii) being associated to the information pole; (iii) maintenance of the material body (defined as informed matter) and its functions, associated to the matter pole of the organism. It results therefore that the informational system of the human body is supported by seven informational circuits formed by the neuro-connections between the specific zones of the brain corresponding to the informational subsystems, the cognitive centers, the sensors, transducers and execution (motor/mobile) elements. The fundamental informational circuits assuring the survival are the reactive circuit, expressible by attitude, the epigenetic/genetic circuit, absorbing and codifying information to be transmitted to the next generations, and the metabolic circuit, connected to matter (matter pole). The presented analysis allows to extend the informational modeling of consciousness to an Informational Model of Consciousness and Organism, fully describing the composition/functions of the organism in terms of information/matter and neurosciences concept. (shrink)

Scientific models share one central characteristic with fiction: their relation to the physical world is ambiguous. It is often unclear whether an element in a model represents something in the world or presents an artifact of model building. Fiction, too, can resemble our world to varying degrees. However, we assign a different epistemic function to scientific representations. As artifacts of human activity, how are scientific representations allowing us to make inferences about real phenomena? In reply to this concern, philosophers of (...) science have started analyzing scientific representations in terms of fictionalization strategies. Many arguments center on a dyadic relation between the model and its target system, focusing on structural resemblances and “as if” scenarios. This chapter provides a different approach. It looks more closely at model building to analyze the interpretative strategies dealing with the representational limits of models. How do we interpret ambiguous elements in models? Moreover, how do we determine the validity of model-based inferences to information that is not an explicit part of a representational structure? I argue that the problem of ambiguous inference emerges from two features of representations, namely their hybridity and incompleteness. To distinguish between fictional and non-fictional elements in scientific models my suggestion is to look at the integrative strategies that link a particular model to other methods in an ongoing research context. To exemplify this idea, I examine protein modeling through X-ray crystallography as a pivotal method in biochemistry. (shrink)

Chemical kinds (e.g. gold) are generally treated as having timelessly fixed identities. Biological kinds (e.g. goldfinches) are generally treated as evolved and/or evolving entities. So what kind of kind is a biochemical kind? This paper defends the thesis that biochemical molecules are clustered chemical kinds, some of which–namely, evolutionarily conserved units–are also biological kinds.On this thesis, a number of difficulties that have recently occupied philosophers concerned with proteins and kinds are shown to be resolved or dissolved.

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)

The conditions animals experience during the early developmental stages of their lives can have critical ongoing effects on their future health, welfare, and proper development. In this paper we draw on evolutionary theory to improve our understanding of the processes of developmental programming, particularly Predictive Adaptive Responses (PAR) that serve to match offspring phenotype with predicted future environmental conditions. When these predictions fail, a mismatch occurs between offspring phenotype and the environment, which can have long-lasting health and welfare effects. Examples (...) include metabolic diseases resulting from maternal nutrition and behavioral changes from maternal stress. An understanding of these processes and their evolutionary origins will help in identifying and providing appropriate developmental conditions to optimize offspring welfare. This serves as an example of the benefits of using evolutionary thinking within veterinary science and we suggest that in the same way that evolutionary medicine has helped our understanding of human health, the implementation of evolutionary veterinary science (EvoVetSci) could be a useful way forward for research in animal health and welfare. (shrink)

I consider some hitherto unexplored examples of teleological language in the sciences. In explicating these examples, I aim to show (a) that such language is not the sole preserve of the biological sciences, and (b) that not all such talk is reducible to the ascription of functions. In chemistry and biochemistry, scientists explaining molecular rearrangements and protein folding talk informally of molecules rearranging “in order to” maximize stability. Evolutionary biologists, meanwhile, often speak of traits evolving “in order to” optimize (...) some fitness-relevant variable. I argue that in all three contexts such locutions are best interpreted as shorthands for more detailed explanations which, were we to spell them out in full, would show that the relevant process would robustly converge towards the same end-point despite variation in initial conditions. This suggests that, in biology, such talk presupposes a substantial form of adaptationism. The upshot is that such shorthands may be more applicable in the physical sciences than the biological. (shrink)

Understanding computation as “a process of the dynamic change of information” brings to look at the different types of computation and information. Computation of information does not exist alone by itself but is to be considered as part of a system that uses it for some given purpose. Information can be meaningless like a thunderstorm noise, it can be meaningful like an alert signal, or like the representation of a desired food. A thunderstorm noise participates to the generation of meaningful (...) information about coming rain. An alert signal has a meaning as allowing a safety constraint to be satisfied. The representation of a desired food participates to the satisfaction of some metabolic constraints for the organism. Computations on information and representations will be different in nature and in complexity as the systems that link them have different constraints to satisfy. Animals have survival constraints to satisfy. Humans have many specific constraints coming in addition. And computers will compute what the designer and programmer ask for. We propose to analyze the different relations between information, meaning and representation by taking an evolutionary approach on the systems that link them. Such a bottom-up approach allows starting with simple organisms and avoids an implicit focus on humans, which is the most complex and difficult case. To make available a common background usable for the many different cases, we use a systemic tool that defines the generation of meaningful information by and for a system submitted to a constraint [Menant, 2003]. This systemic tool allows to position information, meaning and representations for systems relatively to environmental entities in an evolutionary perspective. We begin by positioning the notions of information, meaning and representation and recall the characteristics of the Meaning Generator System (MGS) that link a system submitted to a constraint to its environment. We then use the MGS for animals and highlight the network nature of the interrelated meanings about an entity of the environment. This brings us to define the representation of an item for an agent as being the network of meanings relative to the item for the agent. Such meaningful representations embed the agents in their environments and are far from the Good Old Fashion Artificial Intelligence type ones. The MGS approach is then used for humans with a limitation resulting of the unknown nature of human consciousness. Application of the MGS to artificial systems brings to look for compatibilities with different levels of Artificial Intelligence (AI) like embodied-situated AI, the Guidance Theory of Representations, and enactive AI. Concerns relative to different types of autonomy and organic or artificial constraints are highlighted. We finish by summarizing the points addressed and by proposing some continuations. (shrink)

Is shadowboxing an effective form of functional exercise? What physiological and morphological changes result from an exercise program based exclusively on shadowboxing for 3 weeks? To date, no empirical research has focused specifically on addressing these questions. Since mixed martial arts (MMA) is the fastest growing sport in the world, and since boxing and kickboxing fitness classes are among the most popular in gyms and fitness clubs worldwide, the lack of research on shadowboxing and martial arts-based fitness programs in the (...) extant literature is a shortcoming that the present article aims to address. This case study involved a previously sedentary individual engaging in an exercise program based exclusively on shadowboxing for 3 weeks. Body composition and heart rate data were collected before, throughout, and upon completion of the 3-week exercise program to determine the effectiveness of shadowboxing for functional fitness purposes. An original shadowboxing program prepared by an Everlast Master Instructor and NASM Certified Personal Trainer (NASM-CPT) and Performance Enhancement Specialist (NASM-PES) was used for this 3-week period. The original shadowboxing program with goals, techniques, and combinations to work on throughout the 3-week program is included in this article. This case study demonstrates that a 3-week exercise program based exclusively on shadowboxing can increase aerobic capacity, muscle mass, bone mass, basal metabolic rate, and daily calorie intake, and decrease resting heart rate, fat mass, body fat percentage, and visceral fat rating in a previously sedentary individual. The results of this research demonstrate that shadowboxing can be a safe and effective form of exercise leading to morphological and physiological improvements including fat loss and increased aerobic capacity. The results of this research also demonstrate that the Tanita BC-1500 is a reliable tool for individuals to evaluate their own fitness progress over time. (shrink)

Living agency is subject to a normative dimension (good-bad, adaptive-maladaptive) that is absent from other types of interaction. We review current and historical attempts to naturalize normativity from an organism-centered perspective, identifying two central problems and their solution: (1) How to define the topology of the viability space so as to include a sense of gradation that permits reversible failure, and (2) how to relate both the processes that establish norms and those that result in norm-following behavior. We present a (...) minimal metabolic system that is coupled to a gradient-climbing chemotactic mechanism. Studying the relationship between metabolic dynamics and environmental resource conditions, we identify an emergent viable region and a precarious region where the system tends to die unless environmental conditions change. We introduce the concept of normative field as the change of environmental conditions required to bring the system back to its viable region. Norm-following, or normative action, is defined as the course of behavior whose effect is positively correlated with the normative field. We close with a discussion of the limitations and extensions of our model and some final reflections on the nature of norms and teleology in agency. (shrink)

Assembly of minimal genomes revealed many genes encoding unknown functions. Three overlooked functional categories account for some of them. Cells are prone to make errors and age. As a first key function, discrimination between proper and changed entities is indispensable. Discrimination requires management of information, an authentic, yet abstract, cur- rency of reality. For example proteins age, sometimes very fast. The cell must identify, then get rid of old proteins without destroying young ones. Implementing discrimination in cells leads to the (...) second set of functions, usually ignored. Being abstract, information must nevertheless be embodied into material entities, with unavoidable idiosyncratic properties. This brings about novel unmet needs. Hence, the buildup of cells elicits specific but awkward material implementations, ‘kludges’ that become essential under particular settings, while difficult to identify. Finally, a third functional category char- acterizes the need for growth, with metabolic implementations allowing the cell to put together the growth of its cytoplasm, membranes, and genome, spanning different spatial dimensions. Solving this metabolic quandary, critical for engineering novel synthetic biology chassis, uncovered an unexpected role for CTP synthetase as the coordinator of nonhomothetic growth. Because a significant number of SynBio constructs aim at creating cell factories we expect that they will be attacked by viruses (it is not by chance that the function of the CRISPR system was identified in industrial settings). Substantiating the role of CTP, natural selection has dealt with this hurdle via synthesis of the antimetabolite 30-deoxy-30,40-didehydro- CTP, recruited for antiviral immunity in all domains of life. (shrink)

This project begins with the selective sensory experience suggested by lngarden followed by an insensitivity he insinuates to digestive processes. This is juxtaposed with an oenological explanation of phenomenal sedimentation offered by Jean-Luc Marion. It compares the dynamics of time in the former with the those of wine in the latter. Emphasis is given to lngarden's insinuation of time as fluid, liquid, or aquatic. It revisits Ingarden's physiological explanations of partially-open systems by way of the bilateral excretion and absorption of (...) semi-permeable cellular membranes. The importance he eventually grants to inner secretion is considered alongside perspiration and salivation collateral to skin and membranes. It suggests that Ingarden's interest in thermoregulation, partial permeation, and secretion invites alternative conceptions of temporal consciousness in physiological experiences, beyond sequential and linear clock-time and/or Kantian intuition. Temporality experienced as temperance becomes discernible at a permeable point in which the sedimentation of Husserl, the maturation of Marion, and the fluidity and secretion of Ingarden mix and mingle into the taste of time. (shrink)

This chapter argues that scientific and philosophical progress in our understanding of the living world requires that we abandon a metaphysics of things in favour of one centred on processes. We identify three main empirical motivations for adopting a process ontology in biology: metabolic turnover, life cycles, and ecological interdependence. We show how taking a processual stance in the philosophy of biology enables us to ground existing critiques of essentialism, reductionism, and mechanicism, all of which have traditionally been associated (...) with substance ontology. We illustrate the consequences of embracing an ontology of processes in biology by considering some of its implications for physiology, genetics, evolution, and medicine. And we attempt to locate the subsequent chapters of the book in relation to the position we defend. (shrink)

In searching for life in extraterrestrial space, it is essential to act based on an unequivocal definition of life. In the twentieth century, life was defined as cells that self-replicate, metabolize, and are open for mutations, without which genetic information would remain unchangeable, and evolution would be impossible. Current definitions of life derive from statistical mechanics, physics, and chemistry of the twentieth century in which life is considered to function machine like, ignoring a central role of communication. Recent observations show (...) that context-dependent meaningful communication and network formation (and control) are central to all life forms. Evolutionary relevant new nucleotide sequences now appear to have originated from social agents such as viruses, their parasitic relatives, and related RNA networks, not from errors. By applying the known features of natural languages and communication, a new twenty-first century definition of life can be reached in which communicative interactions are central to all processes of life. A new definition of life must integrate the current empirical knowledge about interactions between cells, viruses, and RNA networks to provide a better explanatory power than the twentieth century narrative. (shrink)

Function talk is a constant across different life sciences. From macro-evolution to genetics, functions are mentioned everywhere. For example, a limb’s function is to allow movement and RNA polymerases’ function is to transcribe DNA. Biochemistry is not immune from such a characterization; the biochemical world seems to be a chemical world embedded within biological processes. Specifically, biochemists commonly ascribe functions to biomolecules and classify them accordingly. This has been noticed in the recent philosophical literature on biochemical kinds. But while (...) a lot has been written on biological and psychological functions, little has been said explicitly about biochemical fuctions. Here, I explore functional attribution to biochemical molecules. I argue that if we accept this attribution, then biochemical functions are constituted by chemical dispositional properties that causally contribute to selected biological processes. In section 2, I discuss the controversy concerning the characterization of biochemical functions. In section 3, I consider whether a biological or a chemical under- standing of function can be applied to biochemical functions, illustrating the account with the example of vitamin B12. The result is that none of the theories on their own provides an adequate characterization. In section 4, I present an account of biochemical functions. In section 5, I assess this account taking into consideration common requirements for a theory of functions and an objection. (shrink)

The aim of this paper is to provide a theoretical framework to understand how multicellular systems realize functionally integrated physiological entities by organizing their intercellular space. From a perspective centered on physiology and integration, biological systems are often characterized as organized in such a way that they realize metabolic self-production and self-maintenance. The existence and activity of their components rely on the network they realize and on the continuous management of the exchange of matter and energy with their environment. (...) One of the virtues of the organismic approach focused on organization is that it can provide an understanding of how biological systems are functionally integrated into coherent wholes. Organismic frameworks have been primarily developed by focusing on unicellular life. Multicellularity, however, presents additional challenges to our understanding of biological systems, related to how cells are capable to live together in higher-order entities, in such a way that some of their features and behaviors are constrained and controlled by the system they realize. Whereas most accounts of multicellularity focus on cell differentiation and increase in size as the main elements to understand biological systems at this level of organization, we argue that these factors are insufficient to provide an understanding of how cells are physically and functionally integrated in a coherent system. In this paper, we provide a new theoretical framework to understand multicellularity, capable to overcome these issues. Our thesis is that one of the fundamental theoretical principles to understand multicellularity, which is missing or underdeveloped in current accounts, is the functional organization of the intercellular space. In our view, the capability to be organized in space plays a central role in this context, as it enables (and allows to exploit all the implications of) cell differentiation and increase in size, and even specialized functions such as immunity. We argue that the extracellular matrix plays a crucial active role in this respect, as an evolutionary ancient and specific (non-cellular) control subsystem that contributes as a key actor to the functional specification of the multicellular space and to modulate cell fate and behavior. We also analyze how multicellular systems exert control upon internal movement and communication. Finally, we show how the organization of space is involved in some of the failures of multicellular organization, such as aging and cancer. (shrink)

Synthetic biology (SynBio) covers two main areas: application engineering, exemplified by metabolic engi- neering, and the design of life from artificial building blocks. As the general public is often reluctant to embrace synthetic approaches, preferring nature to artifice, its immediate future will depend very much on the public’s reaction to the unmet needs created by the pervasive demands of sustainability. On the other hand, this reluctance should not have a negative impact on research that will now take into account (...) the existence of the multiple transitions that cells face over time. The ages of life—birth, development, maturation, senescence and death—reflect specific key transitions and have, until now, rarely been taken into account in SynBio designs. This results in a mismatch between novelty and the very long evolutionary time that led to the existing chassis [remember that this is the common term used to describe the cellular framework as seen by synthetic biologists (de Lorenzo & Danchin, 2008)]. It also implies that, in general, transitions between growth stages will be taken into account with the appro- priate embodiment of highly specific processes. This is particularly important when adapting new models to their host, whether natural or artificial. Adaptation fol- lows two stages, short-term accommodation of new entities and long-term assimilation into the cell as a whole. This requires discrimination between classes of entities. We suggest that proteins playing the essential role of Maxwell’ demons, here named Maxwell’s dis- criminators (MxDs) to refer to their original function, will permit the assimilation and accommodation of artificial constructs. As a consequence, we can foresee that class discrimination, beyond mere recognition, will be implemented in SynBio 2.0, leading to an authentic par- adigm shift (Kuhn, 1996), based on conceptions that embody information as a genuine currency of reality. (shrink)

● Any given placement (e.g. Sun in Taurus; Mars in Capricorn; Mercury in the third house) is necessarily common to tens of thousands of people. Saturn in the ninth house, for example, will not behave the same or produce the same effects in the twenty or one hundred charts in which we find it there. In each case Saturn will behave in accordance with the rest of the astrographic/chart composition (as if we stayed in the same hotel in different epochs (...) or different people contracted the same disease; our stay will be different each time, according to the epoch, and each person’s symptoms will too, be different, according to their individual biochemistry; not to mention that each chart or astrography, like each genetic code or sequence, is unrepeatable). Certainly, “no planet can produce, on its own, what only the combined or concerted action of all can” (BUSTAMANTE, 2023, SPICA magazine, pp. 93-111). Hence the synergistic nature of the interpretative exercise (i.e., the whole is greater than all its parts). The fundamental component of the mathematical expression of the interpretive exercise is: astrological triangulation, the functional denomination for what we know as synthesis (WEISS, 1946; LEO, 1983, HAND, 1981). In order to demonstrate its usefulness, as well as the convenience of its mathematical expression, we have chosen two individuals (JEFFREY DAHMER, STEVEN SPIELBERG) whose astrographies do not—according to the community—explain their lives. The rest of the astrographies correspond to those of serial killers JOHN WAYNE GACY, DAVID CARPENTER, and TED BUNDY. ● We explain, by means of algebraic notations, the synthesis and the functional values that make up the synthesis. ● We take the Moon and Neptune as relevant bodies for the purpose of diagnosing or studying endocrine or neurohormonal issues, and Mars, Pluto, and Saturn as relevant planets for the purpose of inferring violence or sinister behaviour, upon the case, and quadratures or oppositions—and conjunctions—between Venus and the Moon, the Moon and Neptune, and the Sun or Venus and Neptune or Uranus as indicators of neurohormonal disorders and/or sexual deviance (APA definition) . ● We consider quadratures (90º) or oppositions (180º)—and conjunctions—between Mercury or the Moon and Saturn, or between Mars or the Moon and Saturn, Uranus, Neptune, and/or Pluto as powerful indications of violence or mental disorders, upon the case. ● We have also regarded Sagittarius as a sign as expansive and abundant as its ruler, Jupiter, according to the best of its characterisations (or as an exceptionally swift and wild sign, according to other characterisations), and the fifth region of a natal chart as one closely related to fortune in a broad sense (material and immaterial). ● Because we advocate the idea that orbs should be predicated of the planet (size, speed), not the aspect itself, the gas giants (Jupiter, Saturn, Uranus, and Neptune) and the Sun have been granted up to 10º of orb (or 12º, in the case of broad influence ). We understand aspectual relationships as angular relationships held between two or more celestial bodies placed in signs with at least one property in common (according to our molecular theory of the ecliptic, compatible with the optical theory of the aspects from the Hellenistic tradition). (shrink)

From the school yard to the workplace, there’s no charge more damning than “you’re being unfair!” Born out of democracy and raised in open markets, fairness has become our de facto modern creed. The very symbol of American ethics—Lady Justice—wears a blindfold as she weighs the law on her impartial scale. In our zealous pursuit of fairness, we have banished our urges to like one person more than another, one thing over another, hiding them away as dirty secrets of our (...) humanity. In Against Fairness, polymath philosopher Stephen T. Asma drags them triumphantly back into the light. Through playful, witty, but always serious arguments and examples, he vindicates our unspoken and undeniable instinct to favor, making the case that we would all be better off if we showed our unfair tendencies a little more kindness—indeed, if we favored favoritism. Conscious of the egalitarian feathers his argument is sure to ruffle, Asma makes his point by synthesizing a startling array of scientific findings, historical philosophies, cultural practices, analytic arguments, and a variety of personal and literary narratives to give a remarkably nuanced and thorough understanding of how fairness and favoritism fit within our moral architecture. Examining everything from the survival-enhancing biochemistry that makes our mothers love us to the motivating properties of our “affective community,” he not only shows how we favor but the reasons we should. Drawing on thinkers from Confucius to Tocqueville to Nietzsche, he reveals how we have confused fairness with more noble traits, like compassion and open-mindedness. He dismantles a number of seemingly egalitarian pursuits, from classwide Valentine’s Day cards to civil rights, to reveal the envy that lies at their hearts, going on to prove that we can still be kind to strangers, have no prejudice, and fight for equal opportunity at the same time we reserve the best of what we can offer for those dearest to us. Fed up with the blue-ribbons-for-all absurdity of "fairness" today, and wary of the psychological paralysis it creates, Asma resets our moral compass with favoritism as its lodestar, providing a strikingly new and remarkably positive way to think through all our actions, big and small. (shrink)

This paper aims to provide a philosophical and theoretical account of biological communication grounded in the notion of organisation. The organisational approach characterises living systems as organised in such a way that they are capable to self-produce and self-maintain while in constant interaction with the environment. To apply this theoretical framework to the study of biological communication, we focus on a specific approach, based on the notion of influence, according to which communication takes place when a signal emitted by a (...) sender triggers a change in the behaviour of the receiver that is functional for the sender itself. We critically analyse the current formulations of this account, that interpret what is functional for the sender in terms of evolutionary adaptations. Specifically, the adoption of this etiological functional framework may lead to the exclusion of several phenomena usually studied as instances of communication, and possibly even of entire fields of investigation such as synthetic biology. As an alternative, we reframe the influence approach in organisational terms, characterising functions in terms of contributions to the current organisation of a biological system. We develop a theoretical account of biological communication in which communicative functions are distinguished from other types of biological functions described by the organisational account (e.g. metabolic, ecological, etc.). The resulting organisational-influence approach allows to carry out causal analyses of current instances of phenomena of communication, without the need to provide etiological explanations. In such a way it makes it possible to understand in terms of communication those phenomena which realise interactive patterns typical of signalling interactions – and are usually studied as such in scientific practice – despite not being the result of evolutionary adaptations. Moreover, this approach provides operational tools to design and study communicative interactions in experimental fields such as synthetic biology. (shrink)

In this paper some classical representational ideas of Hertz and Duhem are used to show how the dichotomy between representation and intervention can be overcome. More precisely, scientific theories are reconstructed as complex networks of intervening representations (or representational interventions). The formal apparatus developed is applied to elucidate various theoretical and practical aspects of the in vivo/in vitro problem of biochemistry. Moreover, adjoint situations (Galois connections) are used to explain the relation berween empirical facts and theoretical laws in a (...) new way. (shrink)

Purpose: The purpose of the discussion is to call for an experimental trial in order to optimize the sociology of knowledge in the astronomical and cosmological sciences from a cognitive science and developmental psychology perspective. The potential of such experimental trial may also correlate developmental psychology with cosmology and astrophysics, therefore, contribute to public health from an astrobiological perspective. -/- Method: The discussion adopts a philosophizing method for the multidisciplinary and trans-disciplinary proposal, with the hypothesis that proton decay in cosmology (...) is correlative to neuronal development in human biochemistry. The method adopts a humanitarian paradigm of pragmatism in natural mutation from cosmic changes, in an exploratory heuristics for hydro-sampling of mutational potentials from environmental factors in cosmological large-scale structure. -/- Result: With an initial assessment on existing technologies, the potentials of the big data trend in astronomy and astrophysics can be applied to data analysis with solid-state electrolytes in sensor baselines to nuclear medicine methods. (shrink)

The present thesis explores some metaphysical issues concerning biochemical kinds and the relations between chemical and biological properties and phenomena. The main result of this thesis is that there is something sui generis about biochemical kinds. This result is motivated by two theoretical steps. The first is characterising biochemical functions as weakly emergent from the chemical structure [Chapter 3, Chapter 6]. The second is via an account for which biochemical kinds are natural categories [Chapter 4, Chapter 7]. The thesis comprises (...) four parts. Part I [Chapter 1, Chapter 2] aims to offer the methodological and conceptual tools that underpin this research. Chapter 1 presents the debate on the unity of science and the motivation of the research. Chapter 2 presents the account of natural kinds that will be used throughout the thesis. Part II [Chapter 3, Chapter 4] offers a detailed metaphysical analysis of the molecular gene. Chapter 3 argues that molecular genes are weakly emergent from nucleic acids. Chapter 4 argues that the category "molecular gene" can be deemed a natural kind, following the account presented in Chapter 2. Part III [Chapter 5, Chapter 6, Chapter 7] explores some of the themes related to biochemical kinds and generalises some of the results from Part II. Chapter 5 considers biochemical functions and how functional attribution should be interpreted for biochemical molecules. Chapter 6 considers the relation between biochemical functions and structure, spelt in terms of weak emergence and explores unity in biochemistry. Chapter 7 considers the topic of biochemical kinds per se and argues that biochemical kinds are natural categories. Part IV [Chapter 8] elucidates the main outcome and the implications that this research can have for future discussion in the philosophy and metaphysics of biochemistry and the unity of science. (shrink)

The biological sciences study (bio)complex living systems. Research directed at the mechanistic explanation of the "live" state truly requires a pluralist research program, i.e. BioComplexity research. The program should apply multiple intra-level and inter-level theories and methodologies. We substantiate this thesis with analysis of BioComplexity: metabolic and modular control analysis of metabolic pathways, emergence of oscillations, and the analysis of the functioning of glycolysis.

Intermediary metabolism molecules are orchestrated into logical pathways stemming from history (L-amino acids, D-sugars) and dynamic constraints (hydrolysis of pyrophosphate or amide groups is the driving force of anabolism). Beside essential metabolites, numerous variants derive from programmed or accidental changes. Broken down, variants enter standard pathways, producing further variants. Macromolecule modification alters enzyme reactions specificity. Metabolism conform thermodynamic laws, precluding strict accuracy. Hence, for each regular pathway, a wealth of variants inputs and produces metabolites that are similar to but not (...) the exact replicas of core metabolites. As corollary, a shadow, paralogous metabolism, is associated to standard metabolism. We focus on a logic of paralogous metabolism based on diversion of the core metabolic mimics into pathways where they are modified to minimize their input in the core pathways where they create havoc. We propose that a significant proportion of paralogues of well-characterized enzymes have evolved as the natural way to cope with paralogous metabolites. A second type of denouement uses a process where protecting/deprotecting unwanted metabolites - conceptually similar to the procedure used in the laboratory of an organic chemist - is used to enter a completely new catabolic pathway. (shrink)

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

Let us start by some general definitions of the concept of complexity. We take a complex system to be one composed by a large number of parts, and whose properties are not fully explained by an understanding of its components parts. Studies of complex systems recognized the importance of “wholeness”, defined as problems of organization (and of regulation), phenomena non resolvable into local events, dynamics interactions in the difference of behaviour of parts when isolated or in higher configuration, etc., in (...) short, systems of various orders (or levels) not understandable by investigation of their respective parts in isolation. In a complex system it is essential to distinguish between ‘global’ and ‘local’ properties. Theoretical physicists in the last two decades have discovered that the collective behaviour of a macro-system, i.e. a system composed of many objects, does not change qualitatively when the behaviour of single components are modified slightly. Conversely, it has been also found that the behaviour of single components does change when the overall behaviour of the system is modified. There are many universal classes which describe the collective behaviour of the system, and each class has its own characteristics; the universal classes do not change when we perturb the system. The most interesting and rewarding work consists in finding these universal classes and in spelling out their properties. This conception has been followed in studies done in the last twenty years on second order phase transitions. The objective, which has been mostly achieved, was to classify all possible types of phase transitions in different universality classes and to compute the parameters that control the behaviour of the system near the transition (or critical or bifurcation) point as a function of the universality class. This point of view is not very different from the one expressed by Thom in the introduction of Structural Stability and Morphogenesis (1975). It differs from Thom’s program because there is no a priori idea of the mathematical framework which should be used. Indeed Thom considers only a restricted class of models (ordinary differential equations in low dimensional spaces) while we do not have any prejudice regarding which models should be accepted. One of the most interesting and surprising results obtained by studying complex systems is the possibility of classifying the configurations of the system taxonomically. It is well-known that a well founded taxonomy is possible only if the objects we want to classify have some unique properties, i.e. species may be introduced in an objective way only if it is impossible to go continuously from one specie to another; in a more mathematical language, we say that objects must have the property of ultrametricity. More precisely, it was discovered that there are conditions under which a class of complex systems may only exist in configurations that have the ultrametricity property and consequently they can be classified in a hierarchical way. Indeed, it has been found that only this ultrametricity property is shared by the near-optimal solutions of many optimization problems of complex functions, i.e. corrugated landscapes in Kauffman’s language. These results are derived from the study of spin glass model, but they have wider implications. It is possible that the kind of structures that arise in these cases is present in many other apparently unrelated problems. Before to go on with our considerations, we have to pick in mind two main complementary ideas about complexity. (i) According to the prevalent and usual point of view, the essence of complex systems lies in the emergence of complex structures from the non-linear interaction of many simple elements that obey simple rules. Typically, these rules consist of 0–1 alternatives selected in response to the input received, as in many prototypes like cellular automata, Boolean networks, spin systems, etc. Quite intricate patterns and structures can occur in such systems. However, what can be also said is that these are toy systems, and the systems occurring in reality rather consist of elements that individually are quite complex themselves. (ii) So, this bring a new aspect that seems essential and indispensable to the emergence and functioning of complex systems, namely the coordination of individual agents or elements that themselves are complex at their own scale of operation. This coordination dramatically reduces the degree of freedom of those participating agents. Even the constituents of molecules, i.e. the atoms, are rather complicated conglomerations of subatomic particles, perhaps ultimately excitations of patterns of superstrings. Genes, the elementary biochemical coding units, are very complex macromolecular strings, as are the metabolic units, the proteins. Neurons, the basic elements of cognitive networks, themselves are cells. In those mentioned and in other complex systems, it is an important feature that the potential complexity of the behaviour of the individual agents gets dramatically simplified through the global interactions within the system. The individual degrees of freedom are drastically reduced, or, in a more formal terminology, the factual space of the system is much smaller than the product of the state space of the individual elements. That is one key aspect. The other one is that on this basis, that is utilizing the coordination between the activities of its members, the system then becomes able to develop and express a coherent structure at a higher level, that is, an emergent behaviour (and emergent properties) that transcends what each element is individually capable of. (shrink)

It is increasingly clear that children's excessive consumption of products high in added sugar causes obesity and obesity-related health problems like type 2 diabetes, cardiovascular disease, and metabolic syndrome. Less clear is how best to address this problem through public health policy. In contrast to policies that might conflict with adult's right to self-determination — for example sugar taxes and soda bans — this article proposes that children's access to products high in added sugars should be restricted in the (...) same way that children's access to tobacco products is restricted. The article first considers how the recommended policy will protect a child's right to an open future while not violating parental rights. The article then explores how the implementation of the recommended policy can help transform the social meaning of sugar and thereby curb the parental supply of added sugar to children — a central cause of obesity. The article also addresses several potential objections. (shrink)

It should now be recognized that codes are central to life and to understanding its more complex forms, including human culture. Recognizing the ‘conventional’ nature of codes provides solid grounds for rejecting efforts to reduce life to biochemistry and justifies according a place to semantics in life. The question I want to consider is whether this is enough. Focussing on Eigen’s paradox of how a complex code could originate, I will argue that along with Barbieri’s efforts to account for (...) the origins of life based on the ribosome and then to account for the refined codes through a process of ambiguity reduction, something more is required. Barbieri has not provided an adequate account of emergence, or the basis for providing such an account. I will argue that Stanley Salthe has clarified to some extent the nature of emergence by conceptualizing it as the interpolation of new enabling constraints. Clearly, codes can be seen as enabling constraints. How this actually happens, though, is still not explained. Stuart Kauffman has grappled with this issue and shown that it radically challenges the assumptions of mainstream science going back to Newton. He has attempted to reintroduce real possibilities or potentialities into his ontology, and argued that radically new developments in nature are associated with realizing adjacent possibles. This is still not adequate. What is also involved, I will suggest, utilizing concepts developed by the French natural philosopher Gilbert Simondon, is ‘transduction’ as part of ‘ontogenesis’ of individuals in a process of ‘individuation’, that is, the emergence of ‘individuals’ from preindividual fields or milieux. (shrink)

In his Target Article, Terrence Deacon develops simple models that assist in understanding the role of RNA in the origins of life. However, his models fail to adequately represent an important evolutionary dynamic. Central to this dynamic is the selection that impinges on RNA molecules in the context of their association with proto-metabolisms. This selection shapes the role of RNA in the emergence of life. When this evolutionary dynamic is appropriately taken into account, it predicts a role for RNA that (...) is consistent with the Managed-Metabolism Hypothesis about the origins of life, and inconsistent with Deacon’s account. (shrink)

Pranayamic breathing, defined as a manipulation of breath movement, has been shown to contribute to a physiologic response characterized by the presence of decreased oxygen consumption, decreased heart rate, and decreased blood pressure, as well as increased theta wave amplitude in EEG recordings, increased parasympathetic activity accompanied by the experience of alertness and reinvigoration. The mechanism of how pranayamic breathing interacts with the nervous system affecting metabolism and autonomic functions remains to be clearly understood. It is our hypothesis that voluntary (...) slow deep breathing functionally resets the autonomic nervous system through stretchinduced inhibitory signals and hyperpolarization currents propagated through both neural and non-neural tissue which synchronizes neural elements in the heart, lungs, limbic system and cortex. During inspiration, stretching of lung tissue produces inhibitory signals by action of slowly adapting stretch receptors (SARs) and hyperpolarization current by action of fibroblasts. Both inhibitory impulses and hyperpolarization current are known to synchronize neural elements leading to the modulation of the nervous system and decreased metabolic activity indicative of the parasympathetic state. In this paper we propose pranayama’s physiologic mechanism through a cellular and systems level perspective,involving both neural and non-neural elements. This theoretical description describes a common physiological mechanism underlying pranayama and elucidate the role of the respiratory and cardiovascular system on modulating the autonomic nervous system. Along with facilitating the design of clinical breathing techniques for the treatment of autonomic nervous system and other disorders, this model will also validate pranayama as a topic requiring more research. (shrink)

The latest draft (posted 05/14/22) of this short, concise work of proof, theory, and metatheory provides summary meta-proofs and verification of the work and results presented in the Theory and Metatheory of Atemporal Primacy and Riemann, Metatheory, and Proof. In this version, several new and revised definitions of terms were added to subsection SS.1; and many corrected equations, theorems, metatheorems, proofs, and explanations are included in the main text. The body of the text is approximately 18 pages, with 3 sections; (...) 1, an Introduction (with a 108 page listing of key terms & definitions), sect. 2, the Results, sect. 3, Discussion (commentary & predictions), and sect. 4, Works Cited. As much as possible, the style is intended for readability and understanding by very bright children (with some interest & knowledge of maths, etc.) and very interested nonprofessionals. The results of this project also enable upgrades of number theory, set theory, proof theory, metamathematics, the foundations of science, and quantum mechanics theory (etc.). (shrink)

The “nature or nurture” problem concerning the debate on the innate features with respect to the acquired ones is approached in terms of information, from the perspective of the Informational Model of Consciousness. This model reveals seven distinct informational systems reflected in consciousness as informational centers, i.e. memory (Iknow-Ik), decisional info-operational center (Iwant-Iw), emotions (Ilove-Il), metabolic operations (Iam-Ia), genetic transmission (Icreate-Ic), genetic info-generation (Icreated-Icd) and the anti-entropic center (Ibelieve-Ib). Ib is a life-assisting beneficial center, because it is opposed to (...) the entropic action of matter, eliminating or reducing the uncertainty characteristic of unknown possibilities to certainty, and inducing in this way the trust and confidence in own actions. The pro and contra arguments of the “nature or nurture” are shortly presented, noting the large range of divergent opinions and concepts on the approached problem. It is shown that the information concept acting both as informal and matter-related information, specifically referred to the embodiment/ disembodiment mechanisms for the transmission of information during the epigenetic processes, can coherently approach and explain the transgenerational transmission of the traits acquired during the life span of the predecessors. The concepts of tendency, affinity, propensity, predisposition, aptitude, vocation and talent, specific for inheritable properties described by Icd are discussed, pointing out the large pallet and variety of such concepts describing the evidences detected by external observers on the inherited behaviors, and that of self-perceived by the implicated individual, as a silent voice of whose are no longer. The external manifestation of such inherited features and traits depends on practice, because the characteristic operation of the nervous system and of epigenetic processes is based on repetition and/or intensive practice, but these are permanently guided by the silent voice of those who are no longer, with various signal intensities. (shrink)

There are two fundamentally distinct kinds of biological theorizing. "Formal biology" focuses on the relations, captured in formal laws, among mathematically abstracted properties of abstract objects. Population genetics and theoretical mathematical ecology, which are cases of formal biology, thus share methods and goals with theoretical physics. "Compositional biology," on the other hand, is concerned with articulating the concrete structure, mechanisms, and function, through developmental and evolutionary time, of material parts and wholes. Molecular genetics, biochemistry, developmental biology, and physiology, which (...) are examples of compositional biology, are in serious need of philosophical attention. For example, the very concept of a "part" is understudied in both philosophy of biology and philosophy of science. ;My dissertation is an attempt to clarify the distinction between formal biology and compositional biology and, in so doing, provide a clear philosophical analysis, with case studies, of compositional biology. Given the social, economic, and medical importance of compositional biology, understanding it is urgent. For my investigation, I draw on the philosophical fields of metaphysics and epistemology, as well as philosophy of biology and philosophy of science. I suggest new ways of thinking about some classic philosophy of science issues, such as modeling, laws of nature, abstraction, explanation, and confirmation. I hint at the relevance of my study of two kinds of biological theorizing to debates concerning the disunity of science. (shrink)

Introduction: the objective of this investigation is to analyses the advances of understanding in the epigenetic processes and to extract conclusions concerning the information-based evolution from the perspective of the Informational Model of Consciousness (IMC). Analysis of epigenetic mechanisms: it is shown that the study of the epigenetic mechanisms are of increasing interest not only to discover the responsible mechanisms of some diseases, but also to observe the acquisition and transmission mechanisms of some traits to the next generation/ transgenerations, without (...) affecting the DNA sequences. These advances were especially supported by the spectacular progresses in the high technological tools like digital microfluidic techniques and semiconductor-based detection systems, allowing to apply sequencing methods of DNA and to observe its structural modifications. The specific typical steps of the epigenetic mechanisms are analysed, showing that these mechanisms could be fully described in terms of information, as signal transmission agents embodying or disembodying information in three different stages and under specific conditions, including especially the signal persistence as a main conditional epigenetic factor. Results concerning the information-assisted evolution from the perspective of IMC: the epigenetic mechanisms are discussed as a function of each component of the informational system of the organism, consisting in memory, decisional operability, emotional reactivity, metabolic driving processes, genetic transmission, genetic info-generator and the info-connection explaining the special extra-power properties of the mind. It is shown that the epigenetic mechanisms could be related to the specific functions of each informational component, mainly exhibiting five levels of integration of information as matter-related information, culminating with the stable integration in the procreation cells and transmission to the next generation. The results were extended to explain the transgenerational adaptive processes of isolated population groups. Conclusion: the epigenetic mechanisms discussed within IMC allow to understand the transgenerational adaptation as an information-assisted proces. (shrink)

To enable microbial colonisation of the gut mucosa, the intestinal immune system must not only react to danger signals but also recognize cues that indicate safety. Safety recognition, paradoxically, is mediated by the same environmental sensors that are involved in signalling danger. Indeed, in addition to their well established role in inducing inflammation in response to stress signals, pattern recognition receptors (PRRs) and a variety of metabolic sensors also promote gut-microbiota symbiosis by responding to "microbial symbiosis factors", "resolution-associated molecular (...) patterns", markers of energy extraction and other signals indicating the absence of pathogenic infection and tissue damage. Here we focus on how the paradoxical role of immune receptors and other environmental sensors define the microbiota signature of the individual. (shrink)

Synthetic biology is a field of research that concentrates on the design, construction, and modification of new biomolecular parts and metabolic pathways using engineering techniques and computational models. By employing knowledge of operational pathways from engineering and mathematics such as circuits, oscillators, and digital logic gates, it uses these to understand, model, rewire, and reprogram biological networks and modules. Standard biological parts with known functions are catalogued in a number of registries (e.g. Massachusetts Institute of Technology Registry of Standard (...) Biological Parts). Biological parts can then be selected from the catalogue and assembled in a variety of combinations to construct a system or pathway in a microbe. Through the innovative re-engineering of biological circuits and the optimization of certain metabolic pathways, biological modules can be designed to reprogram organisms to produce products or behaviors. Synthetic biology is what is known as a “platform technology”. That is, it generates highly transferrable theoretical models, engineering principles, and know-how that can be applied to create potential products in a wide variety of industries. Proponents suggest that applications of synthetic biology may be able to provide scientific and engineered solutions to a multitude of worldwide problems from health to energy. Synthetic biology research has already been successful in constructing microbial products which promise to offer cheaper pharmaceuticals such as the antimalarial synthetic drug artemisinin, engineered microbes capable of cleaning up oil spills, and the engineering of biosensors that can detect the presence of high concentrations of arsenic in drinking water. One of the potential benefits of synthetic biology research is in its application to biofuel production. It is this application which is the focus of this entry. The term “biofuel” has referred generally to all liquid fuels that are sourced from plant or plant byproducts and are used for energy necessary for transportation vehicles (Thompson 2012). Biofuels that are produced using synthetic biological techniques re-engineer microbes into biofuel factories are a subset of these. (shrink)