Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed (...) studies of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. (shrink)

In conceptual modeling (CM) as a subdiscipline of software engineering, current proposed ontologies (categorical analysis of entities) are typically established through whole adoption of philosophical theories (e.g. Bunge’s). In this paper, we pursue an interdisciplinary research approach to develop a diagrammatic-based ontological foundation for CM using philosophical ontology as a secondary source. It is an endeavor to escape an offshore procurement of ontology from philosophy and implant it in CM. In such an effort, the CM diagrammatic language plays (...) an important role in contrast to dogmatic philosophical languages’ obsession with abstract entities. Specifically, this paper is about developing a descriptive (in contrast to formal) ontology that a modeler accepts as a supplementary account of reality when using thinging machines (TMs; i.e. a reality that uncovers the ontology of things that TM modeling discusses or “talks about,” akin to the ontology of natural language). Although existence is a well-established notion, we defend subsistence (Stoic term) as a supplementary mode of reality (e.g. reflection of event). The aim here is aligned toward developing CM notions and processes that are firm enough. Classical analysis of being per se (e.g. identity, substance, classes, objects) is de-emphasized in this work; nevertheless, philosophical concepts form an acknowledged authority to compare to. As a case study, such a methodology is applied to the notion of information that provides a common-sense understanding of the world. This application would enhance understanding of the TM methodology and clarify some of the issues that shed light on the question of the nature of information as an important concept in software engineering. Information is defined as about events; that is, it is about existing things. It is viewed as having a subsisting nature that exists only through being “carried on” by other things. The results seem to indicate a promising approach to define information and understand its nature. (shrink)

Efforts to bridge emotion theory with neurobiology can be facilitated by dynamic systems (DS) modeling. DS principles stipulate higher-order wholes emerging from lower-order constituents through bidirectional causal processes cognition relations. I then present a psychological model based on this reconceptualization, identifying trigger, self-amplification, and self-stabilization phases of emotion-appraisal states, leading to consolidating traits. The article goes on to describe neural structures and functions involved in appraisal and emotion, as well as DS mechanisms of integration by which they interact. These (...) mechanisms include nested feedback interactions, global effects of neuromodulation, vertical integration, action-monitoring, and synaptic plasticity, and they are modeled in terms of both functional integration and temporal synchronization. I end by elaborating the psychological model of emotion–appraisal states with reference to neural processes. (shrink)

This paper analyses the technoscientific objective of building a synthetic cell from a Jungian perspective. After decades of fragmentation and specialisation, the synthetic cell symbolises a turn towards restored wholeness, both at the object pole and at the subject pole. From a Jungian perspective, it is no coincidence that visual representations of synthetic cells often reflect an archetypal, mandala-like structure. As a symbol of restored unity, the synthetic cell mandala compensates for technoscientific fragmentation via active imagination, providing (...) a visual aid for the technoscientific turn towards reintegration. Although the biotechnological desire to reconstruct life in vitro has been compared to alchemy before, a Jungian analysis allows us to make this comparison more specific and precise. The problem of archetypal images, however, is that alluring prospects of reintegration may underestimate and obfuscate the deficiencies and tensions at work in the current situation. As a projection of a future wholeness, it fosters optimism, but may also function as a misleading façade, covering up collisions and complexities. This can be averted by the conscious employment of the mandala as a symbolic scaffold fostering processes of individuation and working through. (shrink)

This chapter focuses on a novel class of models used in frontier research in the bioengineering sciences – in vitro simulation models – that provide the basis for biological experimentation. These bioengineered models are hybrid constructions, composed of living tissues or cells and engineered materials. Specifically, it discusses the processes through which in vitro models were built, experimented with, and justified in a tissue engineering lab. It examines processes of design, construction, experimentation, evaluation, and redesign of in vitro simulation models, (...) in general, as instances of building the source analogy (as distinguished from retrieving an analogy), which figures prominently in creative frontier scientific research. Building the analogical source is a bootstrapping process, which furthers the articulation, as well as the solution of the problem. -/- . (shrink)

Cancer biology features the ascription of normal functions to parts of cancers. At least some ascriptions of function in cancer biology track local normality of parts within the global abnormality of the aberration to which those parts belong. That is, cancer biologists identify as functions activities that, in some sense, parts of cancers are supposed to perform, despite cancers themselves having no purpose. The present paper provides a theory to accommodate these normal function ascriptions—I call it the Modeling Account (...) of Normal Function (MA). MA comprises two claims. First, normal functions are activities whose performance by the function-bearing part contributes to the self-maintenance of the whole system and, thereby, results in the continued presence of that part. Second, MA holds that models of system-level activities that are (partly) constitutive of self-maintenance are improved by including a representation of the relevant function-bearing part and by making reference to the activity/activities that part performs which contribute(s) to those system-level activities. I contrast MA with two other accounts that seek to explicate the ascription of normal functions in biology, namely, the organizational account and the selected effects account. Both struggle to extend to cancer biology. However, I offer ecumenical readings which allow them to recover some ascriptions of normal function to parts of cancers. So, though I contend that MA excels in this respect, the purpose of this paper is served if it provides materials for bridging the gap between cancer biology, philosophy of cancer, and the literature on function. (shrink)

This paper has a dual character, combining a philosophical ontological exploration with a conceptual modeling approach in systems and software engineering. Such duality is already practiced in software engineering, in which the current dominant modeling thesis is object orientation. This work embraces an anti-thesis that centers solely on the process rather than emphasizing the object. The approach is called occurrence-only modeling, in which an occurrence means an event or process where a process is defined as an orchestrated (...) net of events that form a semantical whole. In contrast to object orientation, in this occurrence-only modeling objects are nothing more than long events. We apply this paradigm to (1) a UML/BPMN inventory system in simulation engineering and (2) an event-based system that represents medical occurrences that occur on a timeline. The aim of such a venture is to enhance the field of conceptual modeling by adding yet a new alternative methodology and clarifying differences among approaches. Conceptual modeling’s importance has been recognized in many research areas. An active research community in simulation engineering demonstrates the growing interest in conceptual modeling. In the clinical domains, temporal information elucidates the occurrence of medical events (e.g., visits, laboratory tests). These applications give an opportunity to propose a new approach that includes (a) a Stoic ontology that has two types of being, existence and subsistence; (b) Thinging machines that limit activities to five generic actions; and (c) Lupascian logic, which handles negative events. With such a study, we aim to substantiate the assertion that the “occurrence only” approach is a genuine philosophical base for conceptual modeling. The results in this paper seem to support such a claim. (shrink)

Metaphors allow us to come to terms with abstract and complex information, by comparing it to something which is structured, familiar and concrete. Although modern science is “iconoclastic”, as Gaston Bachelard phrases it, scientists are at the same time prolific producers of metaphoric images themselves. Synthetic biology is an outstanding example of a technoscientific discourse replete with metaphors, including textual metaphors such as the “Morse code” of life, the “barcode” of life and the “book” of life. This paper focuses on (...) a different type of metaphor, however, namely on the archetypal metaphor of the mandala as a symbol of restored unity and wholeness. Notably, mandala images emerge in textual materials related to one of the new “frontiers” of contemporary technoscience, namely the building of a synthetic cell: a laboratory artefact that functions like a cell and is even able to replicate itself. The mandala symbol suggests that, after living systems have been successfully reduced to the elementary building blocks and barcodes of life, the time has now come to put these fragments together again. We can only claim to understand life, synthetic cell experts argue, if we are able to technically reproduce a fully functioning cell. This holistic turn towards the cell as a meaningful whole also requires convergence at the “subject pole”: the building of a synthetic cell as a practice of the self, representing a turn towards integration, of multiple perspectives and various forms of expertise. (shrink)

The paper explicates the stages of the author’s philosophical evolution in the light of Kopnin’s ideas and heritage. Starting from Kopnin’s understanding of dialectical materialism, the author has stated that category transformations of physics has opened from conceptualization of immutability to mutability and then to interaction, evolvement and emergence. He has connected the problem of physical cognition universals with an elaboration of the specific system of tools and methods of identifying, individuating and distinguishing objects from a scientific theory domain. The (...) role of vacuum conception and the idea of existence (actual and potential, observable and nonobservable, virtual and hidden) types were analyzed. In collaboration with S.Crymski heuristic and regulative functions of categories of substance, world as a whole as well as postulates of relativity and absoluteness, and anthropic and self-development principles were singled out. Elaborating Kopnin’s view of scientific theories as a practically effective and relatively true mapping of their domains, the author in collaboration with M. Burgin have originated the unified structure-nominative reconstruction (model) of scientific theory as a knowledge system. According to it, every scientific knowledge system includes hierarchically organized and complex subsystems that partially and separately have been studied by standard, structuralist, operationalist, problem-solving, axiological and other directions of the current philosophy of science. 1) The logico-linguistic subsystem represents and normalizes by means of different, including mathematical, languages and normalizes and logical calculi the knowledge available on objects under study. 2) The model-representing subsystem comprises peculiar to the knowledge system ways of their modeling and understanding. 3) The pragmatic-procedural subsystem contains general and unique to the knowledge system operations, methods, procedures, algorithms and programs. 4) From the viewpoint of the problem-heuristic subsystem, the knowledge system is a unique way of setting and resolving questions, problems, puzzles and tasks of cognition of objects into question. It also includes various heuristics and estimations (truth, consistency, beauty, efficacy, adequacy, heuristicity etc) of components and structures of the knowledge system. 5) The subsystem of links fixes interrelations between above-mentioned components, structures and subsystems of the knowledge system. The structure-nominative reconstruction has been used in the philosophical and comparative case-studies of mathematical, physical, economic, legal, political, pedagogical, social, and sociological theories. It has enlarged the collection of knowledge structures, connected, for instance, with a multitude of theoreticity levels and with an application of numerous mathematical languages. It has deepened the comprehension of relations between the main directions of current philosophy of science. They are interpreted as dealing mainly with isolated subsystems of scientific theory. This reconstruction has disclosed a variety of undetected knowledge structures, associated also, for instance, with principles of symmetry and supersymmetry and with laws of various levels and degrees. In cooperation with the physicist Olexander Gabovich the modified structure-nominative reconstruction is in the processes of development and justification. Ideas and concepts were also in the center of Kopnin’s cognitive activity. The author has suggested and elaborated the triplet model of concepts. According to it, any scientific concept is a dependent on cognitive situation, dynamical, multifunctional state of scientist’s thinking, and available knowledge system. A concept is modeled as being consisted from three interrelated structures. 1) The concept base characterizes objects falling under a concept as well as their properties and relations. In terms of volume and content the logical modeling reveals partially only the concept base. 2) The concept representing part includes structures and means (names, statements, abstract properties, quantitative values of object properties and relations, mathematical equations and their systems, theoretical models etc.) of object representation in the appropriate knowledge system. 3) The linkage unites a structures and procedures that connect components from the abovementioned structures. The partial cases of the triplet model are logical, information, two-tired, standard, exemplar, prototype, knowledge-dependent and other concept models. It has introduced the triplet classification that comprises several hundreds of concept types. Different kinds of fuzziness are distinguished. Even the most precise and exact concepts are fuzzy in some triplet aspect. The notions of relations between real scientific concepts are essentially extended. For example, the definition and strict analysis of such relations between concepts as formalization, quantification, mathematization, generalization, fuzzification, and various kinds of identity are proposed. The concepts «PLANET» and «ELEMENTARY PARTICLE» and some of their metamorphoses were analyzed in triplet terms. The Kopnin’s methodology and epistemology of cognition was being used for creating conception of the philosophy of law as elaborating of understanding, justification, estimating and criticizing legal system. The basic information on the major directions in current Western philosophy of law (legal realism, feminism, criticism, postmodernism, economical analysis of law etc.) is firstly introduced to the Ukrainian audience. The classification of more than fifty directions in modern legal philosophy is suggested. Some results of historical, linguistic, scientometric and philosophic-legal studies of the present state of Ukrainian academic science are given. (shrink)

We drive our lives permanently by decisions YES/NO, and even we no longer distinguish the elementary intermediary steps of such decisions most often, they form stereotyped chains that once triggered, they run unconsciously, daily facilitating our activities. We lead our lives actually by conscious decisions, each of such decisions establishing our future trajectory. The YES/NO dipole is actually the elemental evaluation and decisional unit in the informational transmission/reception equipment and lines and in computers, respectively. Based on a binary probabilistic system, (...) this is defined as a unit of information (Bit). We operate therefore as an informational system and we actually live in a bipolar universe, which is fundamentally informational. Indeed, the laws of nature and its equilibrium or steady state conditions are based on bipolar units with opposite characteristics, such as action/reaction, attraction/rejection, gravity/anti-gravity, matter/antimatter, entropy/anti-entropy, to enumerate just a few examples. As part of this bipolar universe, we are also bipolar entities connected to information and matter. Starting from the informational features of the human being, seven informational components are identified, forming the informational system of the human body, distinguished by their different functions, reflected at the conscious level through the center Iknow (the memory, including whole life experience), Iwant (decisions center), Iove (emotions), Iam (body status), Icreate (informational genetic transmitter), Icreated (genetic generator inherited from parents) and Ibelieve, which is the gateway to the antientropic component, favorable to maintain the life structure and functioning. Taking into account the characteristics of these centers, it is discussed the life cycle and are deduced suitable conclusions concerning an optimal, active lifestyle, that would contribute to a successful life, aging and destiny. (shrink)

This is a paper about the methodology of normative ethics. I claim that much work in normative ethics can be interpreted as modelling, the form of inquiry familiar from science, involving idealised representations. I begin with the anti-theory debate in ethics, and note that the debate utilises the vocabulary of scientific theories without recognising the role models play in science. I characterise modelling, and show that work with these characteristics is common in ethics. This establishes the plausibility of my interpretation. (...) Taking methodological inspiration from modelling in science gives us new tools for managing idealisations, and a new perspective on pluralism. I demonstrate why this interpretation is a fruitful way of interpreting ethics, by looking at three case studies. First, I return to the anti-theory debate and argue that modelling opens up a new middle ground. Second, I argue that a modelling lens offers a new way of understanding impossibility theorems in population ethics, and their bearing on ethics as a whole. Finally, I show how viewing our work as modelling can be deployed in debates within ethics, using the debate over prioritarianism as an example. I close with further methodological suggestions for those who choose to see themselves as modellers. I discuss the role of counterexamples, our responses to moral disagreement, and the training of new ethicists. (shrink)

The Hodgkin–Huxley (HH) model of the action potential is a theoretical pillar of modern neurobiology. In a number of recent publications, Carl Craver ([2006], [2007], [2008]) has argued that the model is explanatorily deficient because it does not reveal enough about underlying molecular mechanisms. I offer an alternative picture of the HH model, according to which it deliberately abstracts from molecular specifics. By doing so, the model explains whole-cell behaviour as the product of a mass of underlying low-level (...) events. The issue goes beyond cellular neurobiology, for the strategy of abstraction exhibited in the HH case is found in a range of biological contexts. I discuss why it has been largely neglected by advocates of the mechanist approach to explanation. 1 Introduction2 A Primer on the HH Model2.1 The basic qualitative picture2.2 The quantitative model3 Interlude: What Did Hodgkin and Huxley Think?4 Craver’s View4.1 Mechanistic explanation4.2 Sketches4.3 Craver's view: The HH model as a mechanism sketch5 An Alternative View of the HH Model5.1 Another look at the equations5.2 The discrete-gating picture5.3 The road paved by Hodgkin and Huxley5.4 Summary and comparison to Craver6 Conclusion: The HH Model and Mechanistic Explanation6.1 Sketches and abstractions6.2 Why has aggregative abstraction been overlooked? (shrink)

In a series of formal studies and less formal applications, Hong and Page offer a ‘diversity trumps ability’ result on the basis of a computational experiment accompanied by a mathematical theorem as explanatory background (Hong & Page 2004, 2009; Page 2007, 2011). “[W]e find that a random collection of agents drawn from a large set of limited-ability agents typically outperforms a collection of the very best agents from that same set” (2004, p. 16386). The result has been extremely influential as (...) an epistemic justification for diversity policy initiatives. Here we show that the ‘diversity trumps ability’ result is tied to the particular random landscape used in Hong and Page’s simulation. We argue against interpreting results on that random landscape in terms of ‘ability’ or ‘expertise.’ These concepts are better modeled on smother and more realistic landscapes, but keeping other parameters the same those are landscapes on which it is groups of the best performing that do better. Smoother landscapes seem to vindicate both the concept and the value of expertise. Change in other parameters, however, also vindicates diversity. With an increase in the pool of available heuristics, diverse groups again do better. Group dynamics makes a difference as well; simultaneous ‘tournament’ deliberation in a group in place of the ‘relay’ deliberation in Hong and Page’s original model further emphasizes an advantage for diversity. ‘Tournament’ 2 dynamics particularly shows the advantage of mixed groups that include both experts and non-experts. As a whole, our modeling results suggest that relative to problem characteristics and conceptual resources, the wisdom of crowds and the wisdom of the few each have a place. We regard ours as a step toward attempting to calibrate their relative virtues in different modelled contexts of intellectual exploration. (shrink)

"Living systems are cognitive systems, and living as a process is a process of cognition." -H.R. Maturana, The Biology of Cognition (1970/1980) Just as the cell has gradually come to be understood as a highly regulated and unctionally integrated whole, so too is the biosphere now recognized as a finely balanced ecological whole in which local disturbances can create world-wide climatic catastrophe. The oversimplified ideas of biology that characterized the field in its immature beginning led to the (...) theories of a progressive cumulative development or evolution to explain the present state of Nature. However, today, a more mature understanding of biology has brought with it the realization that Nature can not be the product of a gradual development, based only on the reductionist principles of chemistry and physics. In an ideal situation, where there are no strong interactions with the environment, isolated and purified chemicals may react in a mechanically simple manner, but in a living organism there are no isolated molecules. Everything within the cell interacts with everything else. The constituents of a cell are produced by the cell as much as they produce the cell itself. As the German philosopher Immanuel Kant understood, the unique judgment that allows us to identify a living organism as distinct from non-living matter, is that a living organism is both the cause and effect of itself. Thus, the life of a cell, as much as the life of the biosphere, can only be properly understood as an integrated organic whole. (shrink)

Today, the lipid bilayer structure is nearly ubiquitous, taken for granted in even the most rudimentary introductions to cell biology. Yet the image of the lipid bilayer, built out of lipids with heads and tails, went from having obscure origins deep in colloid chemical theory in 1924 to being “obvious to any competent physical chemist” by 1935. This chapter examines how this schematic, strictly heuristic explanation of the idea of molecular orientation was developed within colloid physical chemistry, and how (...) the image was transformed into a reflection of the reality and agency of lipid molecules in the biological microworld. Whereas in physical and colloid chemistry these images considered secondary to instrumental measurement and mathematical modeling of surface phenomena, in biology the manipulable image of the lipid on paper became an essential tool for the molecularization of the cell. (shrink)

It is well-known that the entangled quantum state of a composite object cannot be reduced to the states of its parts. This quantum holism provides a peculiar challenge to formulate an appropriate mereological model: When a system is in an entangled state, which objects are there on the micro and macro level, and which of the objects carries which properties? This paper chooses a modeling approach to answer these questions: It proceeds from a systematic overview of consistent mereological models (...) for entangled systems and discusses which of them is compatible with the quantum mechanical evidence (where quantum states are understood realistically). It reveals that entangled quantum systems neither describe undivided wholes nor objects that stand in irreducible relations. The appropriate model assumes that the entangled property is an irreducible non-relational plural property carried collectively by the micro objects, while there is no macro object. In this sense, quantum holism is an instance of property holism, not of object holism. (shrink)

In this essay, I argue that Valéry's poetic reflections offer valuable insights on the ancient (Aristotelian) ideal of beauty as perfection, which he rehabilitates and updates. I also show that these clarifications provide solutions to enduring aesthetic problems. To do this, I start from the modal vocabulary (necessary, possible, arbitrary) Valéry uses each time he wants to describe the relationship of an author to his composition. He therefore seems to have been deeply fascinated by the tension between the fact that (...) a creator is always free to compose what he wants, and the fact that the same creator wants his work or parts of it to be imposed on him, while he is in the midst of his creative process. Here comes into play the ideal in question, since the perfection of a work implies, among other things, that one cannot want to modify this work for the better (being already perfect). After a detour aiming to introduce the importance of the rules of composition and to refute the idea that this ideal would no longer have any relevance in a modern artistic perspective, I detail what could be called the "aesthetic holism" of Valéry, which retains from a work only its formal dimension, considered in an original way as a formal whole composed of other formal parts. It is therefore above all a form that must be perfected, against possible relative deprivations (lacks or defects). Then, I link (with the help of Wittgenstein) the modal vocabulary to this notion of form which, by posing compositional challenges, turns out to be essential to the understanding of beauty as perfection. -/- Dans cet essai, je soutiens que les réflexions poétiques de Valéry offrent des éclaircissements particulièrement précieux sur l’idéal ancien (Aristotélicien) de beauté comme perfection, qu’il réhabilite et réactualise. Je défends également l’idée que ces éclaircissements peuvent nous mettre sur la voie de solutions à des problèmes endurants de l’esthétique. Pour ce faire, je pars de l’usage remarquable que Valéry fait d’un vocabulaire modal (nécessaire, possible, arbitraire) chaque fois qu’il veut décrire de quelle manière un auteur se rapporte à sa composition. Il apparaît ainsi que ce qui a profondément fasciné Valéry, c’est le dilemme ou la tension selon laquelle tout en étant libre de composer comme il l’entend (en laissant libre cours à sa fantaisie), un créateur aspire néanmoins à ce que son œuvre ou les parties de cette dernière s’imposent à lui, pendant qu’il crée. Ici entre en jeu l’idéal en question, car la perfection d’une œuvre implique entre autre chose que nous ne puissions vouloir modifier cette œuvre pour le mieux (celle-ci étant justement déjà parfaite). Après un détour visant à introduire l’importance des règles de composition et à réfuter l’idée que cet idéal n’aurait plus de pertinence dans une perspective artistique moderne, je détaille ce que l’on pourrait appeler le « holisme esthétique » de Valéry, qui ne retient de la composition d’une œuvre que sa dimension formelle, envisagée de manière originale comme une totalité faite d’autres parties formelles. C’est donc avant toute chose une forme qu’il faut parfaire, contre d’éventuelles privations relatives (manques ou défauts). Il s’agit alors de connecter (à l’aide de Wittgenstein) ce vocabulaire modale à cette notion de forme qui, en posant des enjeux de composition, se révèle indispensable à la compréhension de la beauté comme perfection. Après une défense à contretemps des traditions formelles dans la création (puisque ce sont de telles traditions qui constituent les ressources par lesquelles un individu libre et autonome peut vouloir, non seulement se faire l’héritier de ces traditions, mais aussi se montrer original et innovant), je termine en appliquant les idées de Valéry au débat qui a opposé un camp « généraliste » à un camp « particulariste » en matière de raisons esthétiques. (shrink)

This paper aims at developing a logical theory of perspectival epistemic attitudes. After presenting a standard framework for modeling acceptance, where the epistemic space of an agent coincides with a unique epistemic cell, more complex systems are introduced, which are characterized by the existence of many connected epistemic cells, and different possible attitudes towards a proposition, both positive and negative, are discussed. In doing that, we also propose some interesting ways in which the systems can be interpreted on (...) well known epistemological standpoints. (shrink)

Conceptual spaces have become an increasingly popular modeling tool in cognitive psychology. The core idea of the conceptual spaces approach is that concepts can be represented as regions in similarity spaces. While it is generally acknowledged that not every region in such a space represents a natural concept, it is still an open question what distinguishes those regions that represent natural concepts from those that do not. The central claim of this paper is that natural concepts are represented by (...) the cells of an optimally designed similarity space. (shrink)

In this article, network science is discussed from a methodological perspective, and two central theses are defended. The first is that network science exploits the very properties that make a system complex. Rather than using idealization techniques to strip those properties away, as is standard practice in other areas of science, network science brings them to the fore, and uses them to furnish new forms of explanation. The second thesis is that network representations are particularly helpful in explaining the properties (...) of non-decomposable systems. Where part-whole decomposition is not possible, network science provides a much-needed alternative method of compressing information about the behavior of complex systems, and does so without succumbing to problems associated with combinatorial explosion. The article concludes with a comparison between the uses of network representation analyzed in the main discussion, and an entirely distinct use of network representation that has recently been discussed in connection with mechanistic modeling. (shrink)

We received several critical comments regarding the "The Science of Spiritual Biology." We reply to those criticisms in order to further clarify some of the important points that were made. It is only to be expected that a strong emotional response may be evoked by the revolution in scientific thinking that the modern paradigm of cognitive biology presents. We have to be prepared to accept that, and maintain the integrity of the scientific approach.

We received several critical comments regarding the "The Science of Spiritual Biology." We reply to those criticisms in order to further clarify some of the important points that were made. It is only to be expected that a strong emotional response may be evoked by the revolution in scientific thinking that the modern paradigm of cognitive biology presents. We have to be prepared to accept that, and maintain the integrity of the scientific approach.

The Tree of Life has traditionally been understood to represent the history of species lineages. However, recently researchers have suggested that it might be better interpreted as representing the history of cellular lineages, sometimes called the Tree of Cells. This paper examines and evaluates reasons offered against this cellular interpretation of the Tree of Life. It argues that some such reasons are bad reasons, based either on a false attribution of essentialism, on a misunderstanding of the problem of lineage identity, (...) or on a limited view of scientific representation. I suggest that debate about the Tree of Cells and other successors to the traditional Tree of Life should be formulated in terms of the purposes these representations may serve. In pursuing this strategy, we see that the Tree of Cells cannot serve one purpose suggested for it: as an explanation for the hierarchical nature of taxonomy. We then explore whether, instead, the tree may play an important role in the dynamic modeling of evolution. As highly-integrated complex systems, cells may influence which lineage components can successfully transfer into them and how they change once integrated. Only if they do in fact have a substantial role to play in this process might the Tree of Cells have some claim to be the Tree of Life. (shrink)

Today the whole world is facing a very difficult time due to corona virus which initially originated in Wuhan city of China. In China an unusual pneumonia was noticed earlier which later recognized as a pandemic. There have been two events in the past wherein crossover of animal corona viruses to humans has resulted in severe disease, one was SARS-CoV and the other was MERS-CoV. The genetic sequence of the COVID19 showed more than 80% similarities to SARS-CoV and 50% (...) to the MERSCoV. Corona viruses are enveloped positive sense single-stranded RNA virus belongs to a large family in which all strains of the family do not have virulent capacity. World Health Organisation has classified COVID-19 as a β CoV of group 2B. Structurally, SARS-CoV-2 has four main structural proteins and several accessory proteins through which it enters into the cell. This virus enters the through ACE2 receptors, which are found on various organs in human body. After entering into one body, it enters to another body via transmission through sneezing, coughing etc. People who have had diabetes, chronic respiratory disease, cardiovascular disease, or even high blood pressure and cancer are at higher risk of coronavirus. (shrink)

According to cultural evolutionary theory in the tradition of Boyd and Richerson, cultural evolution is driven by individuals' learning biases, natural selection, and random forces. Learning biases lead people to preferentially acquire cultural variants with certain contents or in certain contexts. Natural selection favors individuals or groups with fitness-promoting variants. Durham (1991) argued that Boyd and Richerson's approach is based on a "radical individualism" that fails to recognize that cultural variants are often "imposed" on people regardless of their individual decisions. (...) Fracchia and Lewontin (2005) raised a similar challenge, suggesting that the success of a variant is often determined by the degree of power backing it. With power, a ruler can impose beliefs or practices on a whole population by diktat, rendering all of the forces represented in cultural evolutionary models irrelevant. It is argued here, based on work by Boehm (1999, 2012), that, from at least the time of the early Middle Paleolithic, human bands were controlled by powerful coalitions of the majority that deliberately guided the development of moral norms to promote the common good. Cultural evolutionary models of the evolution of morality have been based on false premises. However, Durham (1991) and Fracchia and Lewontin's (2005) challenge does not undermine cultural evolutionary modeling in nonmoral domains. (shrink)

This paper aims to provide a theoretical framework for explaining the subjective character of pain experience in terms of what we will call ‘embodied predictive processing’. The predictive processing (PP) theory is a family of views that take perception, action, emotion and cognition to all work together in the service of prediction error minimisation. In this paper we propose an embodied perspective on the PP theory we call the ‘embodied predictive processing (EPP) theory. The EPP theory proposes to explain pain (...) in terms of processes distributed across the whole body. The prediction error minimising system that generates pain experience comprises the immune system, the endocrine system, and the autonomic system in continuous causal interaction with pathways spread across the whole neural axis. We will argue that these systems function in a coordinated and coherent manner as a single complex adaptive system to maintain homeostasis. This system, which we refer to as the neural-endocrine-immune (NEI) system, maintains homeostasis through the process of prediction error minimisation. We go on to propose a view of the NEI ensemble as a multiscale nesting of Markov blankets that integrates the smallest scale of the cell to the largest scale of the embodied person in pain. We set out to show how the EPP theory can make sense of how pain experience could be neurobiologically constituted. We take it to be a constraint on the adequacy of a scientific explanation of subjectivity of pain experience that it makes it intelligible how pain can simultaneously be a local sensing of the body, and, at the same time, a more global, all-encompassing attitude towards the environment. Our aim in what follows is to show how the EPP theory can meet this constraint. (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)

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)

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)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support (...) advanced vaccine data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

continent. 1.1 : 3-13. / 0/ – Introduction I want to propose, as a trajectory into the philosophically weird, an absurd theoretical claim and pursue it, or perhaps more accurately, construct it as I point to it, collecting the ground work behind me like the Perpetual Train from China Mieville's Iron Council which puts down track as it moves reclaiming it along the way. The strange trajectory is the following: Kant's critical philosophy and much of continental philosophy which has followed, (...) has been a defense against horror and madness. Kant's prohibition on speculative metaphysics such as dogmatic metaphysics and transcendental realism, on thinking beyond the imposition of transcendental and moral constraints, has been challenged by numerous figures proceeding him. One of the more interesting critiques of Kant comes from the mad black Deleuzianism of Nick Land stating, “Kant’s critical philosophy is the most elaborate fit of panic in the history of the Earth.” And while Alain Badiou would certainly be opposed to the libidinal investments of Land's Deleuzo-Guattarian thought, he is likewise critical of Kant's normative thought-bureaucracies: Kant is the one author for whom I cannot feel any kinship. Everything in him exasperates me, above all his legalism—always asking Quid Juris? Or ‘Haven’t you crossed the limit?’—combined, as in today’s United States, with a religiosity that is all the more dismal in that it is both omnipresent and vague. The critical machinery he set up has enduringly poisoned philosophy, while giving great succour to the academy, which loves nothing more than to rap the knuckles of the overambitious [….] That is how I understand the truth of Monique David-Menard’s reflections on the properly psychotic origins of Kantianism. I am persuaded that the whole of the critical enterprise is set up to to shield against the tempting symptom represented by the seer Swedenborg, or against ‘diseases of the head’, as Kant puts it. An entire nexus of the limits of reason and philosophy are set up here, namely that the critical philosophy not only defends thought from madness, philosophy from madness, and philosophy from itself, but that philosophy following the advent of the critical enterprise philosophy becomes auto-vampiric; feeding on itself to support the academy. Following Francois Laruelle's non-philosophical indictment of philosophy, we could go one step further and say that philosophy operates on the material of what is philosophizable and not the material of the external world. [1] Beyond this, the Kantian scheme of nestling human thinking between our limited empirical powers and transcendental guarantees of categorical coherence, forms of thinking which stretch beyond either appear illegitimate, thereby liquefying both pre-critical metaphysics and the ravings of the mad in the same critical acid. In rejecting the Kantian apparatus we are left with two entities – an unsure relation of thought to reality where thought is susceptible to internal and external breakdown and a reality with an uncertain sense of stability. These two strands will be pursued, against the sane-seal of post-Kantian philosophy by engaging the work of weird fiction authors H.P. Lovecraft and Thomas Ligotti. The absolute inhumanism of the formers universe will be used to describe a Shoggothic Materialism while the dream worlds of the latter will articulate the mad speculation of a Ventriloquil Idealism. But first we must address the relation of philosophy to madness as well as philosophy to weird fiction. /1/ – Philosophy and Madness There is nothing that the madness of men invents which is not either nature made manifest or nature restored. Michel Foucault. Madness and Civilization. The moment I doubt whether an event that I recall actually took place, I bring the suspicion of madness upon myself: unless I am uncertain as to whether it was not a mere dream. Arthur Schopenhauer. The World as Will and Idea, Vol. 3. Madness is commonly thought of as moving through several well known cultural-historical shifts from madness as a demonic or otherwise theological force, to rationalization, to medicalization psychiatric and otherwise. Foucault's Madness and Civilization is well known for orientating madness as a form of exclusionary social control which operated by demarcating madness from reason. Yet Foucault points to the possibility of madness as the necessity of nature at least prior to the crushing weight of the church. Kant’s philosophy as a response to madness is grounded by his humanizing of madness itself. As Adrian Johnston points out in the early pages of Time Driven pre-Kantian madness meant humans were seized by demonic or angelic forces whereas Kantian madness became one of being too human. Madness becomes internalized, the external demonic forces become flaws of the individual mind. Foucault argues that, while madness is de-demonized it is also dehumanized during the Renaissance, as madmen become creatures neither diabolic nor totally human reduced to the zero degree of humanity. It is immediately clear why for Kant, speculative metaphysics must be curbed – with the problem of internal madness and without the external safeguards of transcendental conditions, there is nothing to formally separate the speculative capacities for metaphysical diagnosis from the mad ramblings of the insane mind – both equally fall outside the realm of practicality and quotidian experience. David-Menard's work is particularly useful in diagnosing the relation of thought and madness in Kant's texts. David-Menard argues that in Kant's relatively unknown “An Essay on the Maladies of the Mind” as well as his later discussion of the Seer of Swedenborg, that Kant formulates madness primarily in terms of sensory upheaval or other hallucinatory theaters. She writes: “madness is an organization of thought. It is made possible by the ambiguity of the normal relation between the imaginary and the perceived, whether this pertains to the order of sensation or to the relations between our ideas” Kant's fascination with the Seer forces Kant between the pincers of “aesthetic reconciliation” – namely melancholic withdrawal – and “a philosophical invention” – namely the critical project. Deleuze and Guattari's schizoanalysis is a combination and reversal of Kant's split, where an aesthetic over engagement with the world entails prolific conceptual invention. Their embrace of madness, however, is of course itself conceptual despite all their rhizomatic maneuvers. Though they move with the energy of madness, Deleuze and Guattari save the capacity of thought from the fangs of insanity by imbuing materiality itself with the capacity for thought. Or, as Ray Brassier puts it, “Deleuze insists, it is necessary to absolutize the immanence of this world in such a way as to dissolve the transcendent disjunction between things as we know them and as they are in themselves”. That is, whereas Kant relied on the faculty of judgment to divide representation from objectivity Deleuze attempts to flatten the whole economy beneath the juggernaut of ontological univocity. Speculation, as a particularly useful form of madness, might fall close to Deleuze and Guattari’s shaping of philosophy into a concept producing machine but is different in that it is potentially self destructive – less reliant on the stability of its own concepts and more adherent to exposing a particular horrifying swath of reality. Speculative madness is always a potential disaster in that it acknowledges little more than its own speculative power with the hope that the gibbering of at least a handful of hysterical brains will be useful. Pre-critical metaphysics amounts to madness, though this may be because the world itself is mad while new attempts at speculative metaphysics, at post-Kantian pre-critical metaphysics, are well aware of our own madness. Without the sobriety of the principle of sufficient reason we have a world of neon madness: “we would have to conceive what our life would be if all the movements of the earth, all the noises of the earth, all the smells, the tastes, all the light – of the earth and elsewhere, came to us in a moment, in an instant – like an atrocious screaming tumult of things”. Speculative thought may be participatory in the screaming tumult of the world or, worse yet, may produce its spectral double. Against theology or reason or simply commonsense, the speculative becomes heretical. Speculation, as the cognitive extension of the horrorific sublime should be met with melancholic detachment. Whereas Kant's theoretical invention, or productivity of thought, is self -sabotaging, since the advent of the critical project is a productivity of thought which then delimits the engine of thought at large either in dogmatic gestures or non-systematizable empirical wondrousness. The former is celebrated by the fiction of Thomas Ligotti whereas the latter is espoused by the tales of H.P. Lovecraft. /2/ – Weird Fiction and Philosophy. Supernatural horror, in all its eerie constructions, enables a reader to taste treats inconsistent with his personal welfare. Thomas Ligotti Songs of a Dead Dreamer. I choose weird stories because they suit my inclination best—one of my strongest and most persistent wishes being to achieve,momentarily, the illusion of some strange suspension or violation of the galling limitations of time, space, and natural law which forever imprison us and frustrate our curiosity about the infinite cosmic spaces beyond the radius of our sight and analysis H.P. Lovecraft. “Notes on Writing Weird Fiction” Lovecraft states that his creation of a story is to suspend natural law yet, at the same time, he indexes the tenuousness of such laws, suggesting the vast possibilities of the cosmic. The tension that Lovecraft sets up between his own fictions and the universe or nature is reproduced within his fictions in the common theme of the unreliable narrator; unreliable precisely because they are either mad or what they have witnessed questions the bounds of material reality. In “The Call of Cthulhu” Lovecraft writes: The most merciful thing in the world, I think, is the inability of the human mind to correlate all its contents. We live on a placid island of ignorance in the midst of black seas of infinity, and it was not meant that we should voyage far. The sciences, each straining in its own direction, have hitherto harmed us little; but some day the piecing together of dissociated knowledge will open up such terrifying vistas of reality, and of our frightful position therein, that we shall either go mad from the revelation or flee from the deadly light into the peace and safety of a new dark age. Despite Lovecraft's invocations of illusion, he is not claiming that his fantastic creations such as the Old Ones are supernatural but, following Joshi, are only ever supernormal. One can immediately see that instead of nullifying realism Lovecraft in fact opens up the real to an unbearable degree. In various letters and non-fictional statements Lovecraft espoused strictly materialist tenets, ones which he borrowed from Hugh Elliot namely the uniformity of law, the denial of teleology and the denial of non-material existence. Lovecraft seeks to explore the possibilities of such a universe by piling horror upon horror until the fragile brain which attempts to grasp it fractures. This may be why philosophy has largely ignored weird fiction – while Deleuze and Guattari mark the turn towards weird fiction and Lovecraft in particular, with the precursors to speculative realism as well as contemporary related thinkers have begun to view Lovecraft as making philosophical contributions. Lovecraft's own relation to philosophy is largely critical while celebrating Nietzsche and Schopenhauer. This relationship of Lovecraft to philosophy and philosophy to Lovecraft is coupled with Lovecraft's habit of mercilessly destroying the philosopher and the figure of the academic more generally in his work, a destruction which is both an epistemological destruction and an ontological destruction. Thomas Ligotti's weird fiction which he has designated as a kind of “confrontational escapism” might be best described in the following quote from one of his shortstories, “The human phenomenon is but the sum of densely coiled layers of illusion each of which winds itself on the supreme insanity. That there are persons of any kind when all there can be is mindless mirrors laughing and screaming as they parade about in an endless dream”. Whereas Lovecraft's weirdness draws predominantly from the abyssal depths of the uncharted universe, Ligotti's existential horror focuses on the awful proliferation of meaningless surfaces that is, the banal and every day function of representation. In an interview, Ligotti states: We don't even know what the world is like except through our sense organs, which are provably inadequate. It's no less the case with our brains. Our whole lives are motored along by forces we cannot know and perceptions that are faulty. We sometimes hear people say that they're not feeling themselves. Well, who or what do they feel like then? This is not to say that Ligotti sees nothing beneath the surface but that there is only darkness or blackness behind it, whether that surface is on the cosmological level or the personal. By addressing the implicit and explicit philosophical issues in Ligotti's work we will see that his nightmarish take on reality is a form of malevolent idealism, an idealism which is grounded in a real, albeit dark and obscure materiality. If Ligotti's horrors ultimately circle around mad perceptions which degrade the subject, it takes aim at the vast majority of the focus of continental philosophy. While Lovecraft's acidic materialism clearly assaults any romantic concept of being from the outside, Ligotti attacks consciousness from the inside: Just a little doubt slipped into the mind, a little trickle of suspicion in the bloodstream, and all those eyes of ours, one by one, open up to the world and see its horror [...] Not even the solar brilliance of a summer day will harbor you from horror. For horror eats the light and digests it into darkness. Clearly, the weird fiction of Lovecraft and Ligotti amount to a anti-anthrocentric onslaught against the ramparts of correlationist continental philosophy. /3/ – Shoggothic Materialism or the Formless Formless protoplasm able to mock and reflect all forms and organs and processes—viscous agglutinations of bubbling cells—rubbery fifteen-foot spheroids infinitely plastic and ductile—slaves of suggestion, builders of cities—more and more sullen, more and more intelligent, more and more amphibious, more and more imitative—Great God! What madness made even those blasphemous Old Ones willing to use and to carve such things? H.P. Lovecraft. “At the Mountains of Madness” On the other hand, affirming that the universe resembles nothing and is only formless amounts to saying that the universe is something like a spider or spit. Georges Bataille. “Formless”. The Shoggoths feature most prominently in H.P. Lovecraft's shortstory “At the Mountains of Madness” where they are described in the following manner: It was a terrible, indescribable thing vaster than any subway train – a shapeless congeries of protoplasmic bubbles, faintly self -luminous, and with myriads of temporary eyes forming and un-forming as pustules of greenish light all over the tunnel-filling front that bore down upon us, crushing the frantic penguins and slithering over the glistening floor that it and its kind had swept so evilly free of all litter. The term is a litmus test for materialism itself as the Shoggoth is an amorphous creature. The Shoggoths were living digging machines bio engineered by the Elder Things, and their protoplasmic bodies being formed into various tools by their hypnotic powers. The Shoggoths eventually became self aware and rose up against their masters in an ultimately failed rebellion. After the Elder Ones retreated into the oceans leaving the Shoggoths to roam the frozen wastes of the Antarctic. The onto-genesis of the Shoggoths and their gross materiality, index the horrifyingly deep time of the earth a concept near and dear to Lovecraft's formulation of horror as well as the fear of intelligences far beyond, and far before, the ascent of humankind on earth and elsewhere. The sickly amorphous nature of the Shoggoths invade materialism at large, where while materiality is unmistakably real ie not discursive, psychological, or otherwise overly subjectivist, it questions the relation of materialism to life. As Eugene Thacker writes: The Shoggoths or Elder Things do not even share the same reality with the human beings who encounter them—and yet this encounter takes place, though in a strange no-place that is neither quite that of the phenomenal world of the human subject or the noumenal world of an external reality. Amorphous yet definitively material beings are a constant in Lovecraft's tales. In his tale “The Dream-Quest of Unknown Kadatth” Lovecraft describes Azathoth as, “that shocking final peril which gibbers unmentionably outside the ordered universe,” that, “last amorphous blight of nethermost confusion which blashphemes and bubbles at the centre of all infinity,” who, “gnaws hungrily in inconceivable, unlighted chambers beyond time”. Azathoth's name may have multiple origins but the most striking is the alchemy term azoth which is both a cohesive agent and a acidic creation pointing back to the generative and the decayed. The indistinction of generation and degradation materially mirrors the blur between the natural and the unnatural as well as life and non-life. Lovecraft speaks of the tension between the natural and the unnatural is his short story “The Unnameable.” He writes, “if the psychic emanations of human creatures be grotesque distortions, what coherent representation could express or portray so gibbous and infamous a nebulousity as the spectre of a malign, chaotic perversion, itself a morbid blasphemy against Nature?”. Lovecraft explores exactly the tension outlined at the beginning of this chapter, between life and thought. At the end of his short tale Lovecraft compounds the problem as the unnameable is described as “a gelatin—a slime—yet it had shapes, a thousand shapes of horror beyond all memory”. Deleuze suggests that becoming-animal is operative throughout Lovecraft's work, where narrators feel themselves reeling at their becoming non-human or of being the anomalous or of becoming atomized. Following Eugene Thacker however, it may be far more accurate to say that Lovecraft's tales exhibit not a becoming-animal but a becoming-creature. Where the monstrous breaks the purportedly fixed laws of nature, the creature is far more ontologically ambiguous. The nameless thing is an altogether different horizon for thought. The creature is either less than animal or more than animal – its becoming is too strange for animal categories and indexes the slow march of thought towards the bizarre. This strangeness is, as aways, some indefinite swirling in the category of immanence and becoming. Bataille begins “The Labyrinth” with the assertion that being, to continue to be, is becoming. More becoming means more being hence the assertion that Bataille's barking dog is more than the sponge. This would mean that the Shoggotth is altogether too much being, too much material in the materialism. Bataille suggests that there is an immanence between the eater and the eaten, across the species and never within them. That is, despite the chaotic storm of immanence there must remain some capacity to distinguish the gradients of becoming without reliance upon, or at least total dependence upon, the powers of intellection to parse the universe into recognizable bits, properly digestible factoids. That is, if we undo Deleuze's aforementioned valorization of sense which, for his variation of materialism, performed the work of the transcendental, but refuse to reinstate Kant's transcendental disjunction between thing and appearance, then it must be a quality of becoming-as-being itself which can account for the discernible nature of things by sense. In an interview with Peter Gratton, Jane Bennett formulates the problem thusly: What is this strange systematicity proper to a world of Becoming? What, for example, initiates this congealing that will undo itself? Is it possible to identify phases within this formativity, plateaus of differentiation? If so, do the phases/plateaus follow a temporal sequence? Or, does the process of formation inside Becoming require us to theorize a non-chronological kind of time? I think that your student’s question: “How can we account for something like iterable structures in an assemblage theory?” is exactly the right question. Philosophy has erred too far on the side of the subject in the subject-object relation and has furthermore, lost the very weirdness of the non-human. Beyond this, the madness of thought need not override. /4/ - Ventriloquial Idealism or the Externality of Thought My aim is the opposite of Lovecraft's. He had an appreciation for natural scenery on earth and wanted to reach beyond the visible in the universe. I have no appreciation for natural scenery and want the objective universe to be a reflection of a character. Thomas Ligotti. “Devotees of Decay and Desolation.” Unless life is a dream, nothing makes sense. For as a reality, it is a rank failure [….] Horror is more real than we are. Thomas Ligotti. “Professor Nobody's Little Lectures on Supernatural Horror”. Thomas Ligotti's tales are rife with mannequins, puppets, and other brainless entities which of replace the valorized subject of philosophy – that of the free thinking human being. His tales such as “The Dream of the Manikin” aim to destroy the rootedness of consciousness. James Trafford has connected the anti-egoism of Ligotti to Thomas Metzinger – where the self is at best an illusion and we plead desperately for someone else to acknowledge that we are real. Trafford has stated it thus, “Life is played out as an inescapable puppet show, an endless dream in which the puppets are generally unaware that they are trapped within a mesmeric dance of whose mechanisms they know nothing and over which they have no control”. An absolute materialism, for Ligotti, implies an alienation of the idea which leads to a ventriloquil idealism. As Ligotti notes in an interview, “the fiasco and nightmare of existence, the particular fiasco and nightmare of human existence, the sense that people are puppets of powers they cannot comprehend, etc.” And then further elaborates that,“[a]ssuming that anything has to exist, my perfect world would be one in which everyone has experienced the annulment of his or her ego. That is, our consciousness of ourselves as unique individuals would entirely disappear”. The externality of the idea leads to the unfortunate consequence of consciousness eating at itself through horror which, for Ligotti, is more real than reality and goes beyond horror-as-affect. Beyond this, taking together with the unreality of life and the ventriloquizing of subjectivity, Ligotti's thought becomes an idealism in which thought itself is alien and ultimately horrifying. The role of human thought and the relation of non-relation of horror to thought is not completely clear in Ligotti's The Conspiracy Against the Human Race. Ligotti argues in his The Conspiracy Against the Human Race,that the advent of thought is a mistake of nature and that horror is being in the sense that horror results from knowing too much. Yet, at the same time, Ligotti seems to suggest that thought separates us from nature whereas, for Lovecraft, thought is far less privileged – mind is just another manifestation of the vital principal, it is just another materialization of energy. In his brilliant “Prospects for Post-Copernican Dogmatism” Iain Grant rallies against the negative definition of dogmatism and the transcendental, and suggests that negatively defining both over-focuses on conditions of access and subjectivism at the expense of the real or nature. With Schelling, who is Grant's champion against the subjectivist bastions of both Fichte and Kant, Ligotti's idealism could be taken as a transcendental realism following from an ontological realism. Yet the transcendental status of Ligotti's thought move towards a treatment of the transcendental which may threaten to leave beyond its realist ground. Ligotti states: Belief in the supernatural is only superstition. That said, a sense of the supernatural, as Conrad evidenced in Heart of Darkness, must be admitted if one's inclination is to go to the limits of horror. It is the sense of what should not be- the sense of being ravaged by the impossible. Phenomenally speaking, the super-natural may be regarded as the metaphysical counterpart of insanity, a transcendental correlative of a mind that has been driven mad. Again, Ligotti equates madness with thought, qualifying both as supernatural while remaining less emphatic about the metaphysical dimensions of horror. The question becomes one of how exactly the hallucinatory realm of the ideal relates to the black churning matter of Lovecraft's chaos of elementary particles. In his tale “I Have a Special Plan for This World” Ligotti formulates thus: A: There is no grand scheme of things. B: If there were a grand scheme of things, the fact – the fact – that we are not equipped to perceive it, either by natural or supernatural means, is a nightmarish obscenity. C: The very notion of a grand scheme of things is a nightmarish obscenity. Here Ligotti is not discounting metaphysics but implying that if it does exist the fact that we are phenomenologically ill-equipped to perceive that it is nightmarish. For Ligotti, nightmare and horror occur within the circuit of consciousness whereas for Lovecraft the relation between reality and mind is less productive on the side of mind. It is easier to ascertain how the Kantian philosophy is a defense against the diseases of the head as Kant armors his critical enterprise from too much of the world and too much of the mind. The weird fiction of both Lovecraft and Ligotti demonstrates that there is too much of both feeding into one another in a way that corrodes the Kantian schema throughly, breaking it down into a dead but still ontologically potentiated nigredo. The haunting, terrifying fact of Ligotti's idealism is that the transcendental motion which brought thought to matter, while throughly material and naturalized, brings with it the horror that thought cannot be undone without ending the material that bears it either locally or completely. Thought comes from an elsewhere and an elsewhen being-in-thought. The unthinkable outside thought is as maddening as the unthought engine of thought itself within thought which doesn't exist except for the mind, the rotting décor of the brain. /5/ - Hyperstitional Transcendental Paranoia or Self -Expelled Thought Weird fiction has been given some direct treatment in philosophy in the mad black Deleuzianism of Nick Land. Nick Land along with others in the 1990s created the Cyber Culture Research Unit as well as the research group Hyperstition. The now defunct hyperstitional website, an outgrowth of the Cyber Culture Research Unit, defined hyperstition in the following fourfold: 1-Element of effective culture that makes itself real. 2-Fictional quantity functional as a time-traveling device. 3-Coincidence intensifier. 4-Call to the Old Ones. The distinctively Lovecraftian character of hyperstition is hard to miss as is its Deleuzo-Guattarian roots. In the opening pages of A Thousand Plateaus Deleuze and Guattari write, “We have been criticized for over-quoting literary authors. But when one writes, the only question is which other machine the literary machine can be plugged into”. The indisinction of literature and philosophy mirrors the mess of being and knowing as post-correlationist philosophy, where philosophy tries to make itself real where literature, especially the weird, aims itself at the brain-circuit of horror. The texts of both Lovecraft and Ligotti work through horror as epistemological plasticity meeting with proximity as well as the deep time of Lovecraft and the glacially slow time of paranoia in Ligotti. Against Deleuze, and following Brassier, we cannot allow the time of consciousness, the Bergsonian time of the duree, to override natural time, but instead acknowledge that it is an unfortunate fact of existence as a thinking being. Horror-time, the time of consciousness, with all its punctuated moments and drawn out terrors, cannot compare to the deep time of non-existence both in the unreachable past and the unknown future. The crystalline cogs of Kant's account of experience as the leading light for the possibility of metaphysics must be throughly obliterated. His gloss of experience in Prolegomena to any Future Metaphysics could not be more sterile: Experience consists of intuitions, which belong to the sensibility, and of judgments, which are entirely a work of the understanding. But the judgments which the understanding makes entirely out of sensuous intuitions are far from being judgments of experience. For in the one case the judgment connects only the perceptions as they are given in sensuous intuition [....] Experience consists in the synthetic connection of appearances in consciousness, so far as this connection is necessary. Here it is difficult to dismiss the queasiness that Kant's legalism induces upon sight for both Badiou and David-Menard. Kant's thought becomes, as Foucault says when reflecting on Sade's text in relation to nature, “the savage abolition of itself”. For Badiou, Kant's philosophy simply closes off too much of the outside, freezing the world of thought in an all too limited formalism. Critical philosophy is simply the systematized quarantine on future thinking, on thinking which would threaten the formalism which artificially grants thought its own coherency in the face of madness. Even the becoming-mad of Deleuze, while escaping the rumbling ground, makes grounds for itself, mad grounds but grounds which are thinkable in their affect. The field of effects allows for Deleuze's aesthetic and radical empiricism, in which effects and/or occasions make up the material of the world to be thought as a chaosmosis of simulacra. Given a critique of an empiricism of aesthetics, of the image, it may be difficult to justify an attack on Kantian formalism with the madness of literature, which does not aim to make itself real but which we may attempt to make real. That is, how do Lovecraft's and Ligotti's materials, as materials for philosophy to work on, differ from either the operative formalisms of Kant or the implicitly formalized images of Deleuzian empiricism? It is simply that such texts do not aim to make themselves real, and make claims to the real which are more alien to us than familiar, which is why their horror is immediately more trustworthy. This is the madness which Blanchot discusses in The Infinite Conversation through Cervantes and his knight – the madness of book-life, of the perverse unity of literature and life a discussion which culminates in the discussion of one of the weird's masters, that of Kafka. The text is the knowing of madness, since madness, in its moment of becoming-more-mad, cannot be frozen in place but by the solidifications of externalizing production. This is why Foucault ends his famous study with works of art. Furthermore extilligence, the ability to export the products of our maligned brains, is the companion of the attempts to export, or discover the possibility of intelligences outside of our heads, in order for philosophy to survive the solar catastrophe. To borrow again from Deleuze, writing is inseparable from becoming. The mistake is to believe that madness is reabsorbed by extilligence, by great works, or that it could be exorcised by the expelling of thought into the inorganic or differently organic. Going out of our heads does not guarantee we will no longer mean we cannot still go out of our minds. This is simply because of the outside, of matter, or force, or energy, or thing-in-itself, or Schopenhauerian Will. In Lovecraft’s “The Music of Erich Zahn” an “impoverished student of metaphysics” becomes intrigued by strange viol music coming from above his room. After meeting the musician the student discovers that each night he plays frantic music at a window in order to keep some horridness at bay, some “impenetrable darkness with chaos and pandemonium”. The aesthetic defenses provided by the well trained brain can bear the hex of matter for so long, the specter of unalterability within it which too many minds obliterate, collapsing everything before the thought of thought as thinkable or at least noetically mutable on our own terms. Transcendental paranoia is the concurrent nightmare and promise of Paul Humphrey's work, of being literally out of our minds. It is the gothic counterpart of thinking non-conceptually but also of thinking never belonging to any instance of purportedly solid being. As Bataille stated, “At the boundary of that which escapes cohesion, he who reflects within cohesion realizes there is no longer any room for him” Thought is immaterial only to the degree that it is inhuman, it is a power that tries, always with failure, to ascertain its own genesis. Philosophy, if it can truly return to the great outdoors, if it can leave behind the dead loop of the human skull, must recognize not only the non-priority of human thought, but that thought never belongs to the brain that thinks it, thought comes from somewhere else. To return to the train image from the beginning “a locomotive rolling on the surface of the earth is the image of continuous metamorphosis” this is the problem of thought, and of thinking thought, of being no longer able to isolate thought, with only a thought-formed structure. [1] One of the central tenets of Francois Laruelle's non-philosophy is that philosophy has traditionally operated on material already presupposed as thinkable instead of trying to think the real in itself. Philosophy, according to Laruelle, remains fixated on transcendental synthesis which shatters immanence into an empirical datum and an a prori factum which are then fused by a third thing such as the ego. For a critical account of Laruelle's non-philosophy see Ray Brassier's Nihil Unbound. (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 ‘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. Graphical Abstract. (shrink)

The behavior/structure methodological dichotomy as locus of scientific inquiry is closely related to the issue of modeling and theory change in scientific explanation. Given that the traditional tension between structure and behavior in scientific modeling is likely here to stay, considering the relevant precedents in the history of ideas could help us better understand this theoretical struggle. This better understanding might open up unforeseen possibilities and new instantiations, particularly in what concerns the proposed technological modification of the human (...) condition. The sequential structure of this paper is twofold. The contribution of three philosophers better known in the humanities than in the study of science proper are laid out. The key theoretical notions interweaving the whole narrative are those of mechanization, constructability and simulation. They shall provide the conceptual bridge between these classical thinkers and the following section. Here, a panoramic view of three significant experimental approaches in contemporary scientific research is displayed, suggesting that their undisclosed ontological premises have deep roots in the Western tradition of the humanities. This ontological lock between core humanist ideals and late research in biology and nanoscience is ultimately suggested as responsible for pervasively altering what is canonically understood as “human”. (shrink)

Climatology is a paradigmatic complex systems science. Understanding the global climate involves tackling problems in physics, chemistry, economics, and many other disciplines. I argue that complex systems like the global climate are characterized by certain dynamical features that explain how those systems change over time. A complex system's dynamics are shaped by the interaction of many different components operating at many different temporal and spatial scales. Examining the multidisciplinary and holistic methods of climatology can help us better understand the nature (...) of complex systems in general. -/- Questions surrounding climate science can be divided into three rough categories: foundational, methodological, and evaluative questions. "How do we know that we can trust science?" is a paradigmatic foundational question (and a surprisingly difficult one to answer). Because the global climate is so complex, questions like "what makes a system complex?" also fall into this category. There are a number of existing definitions of `complexity,' and while all of them capture some aspects of what makes intuitively complex systems distinctive, none is entirely satisfactory. Most existing accounts of complexity have been developed to work with information-theoretic objects (signals, for instance) rather than the physical and social systems studied by scientists. -/- Dynamical complexity, a concept articulated in detail in the first third of the dissertation, is designed to bridge the gap between the mathematics of contemporary complexity theory (in particular the formalism of "effective complexity" developed by Gell-Mann and Lloyd [2003]) and a more general account of the structure of science generally. Dynamical complexity provides a physical interpretation of the formal tools of mathematical complexity theory, and thus can be used as a framework for thinking about general problems in the philosophy of science, including theories, explanation, and lawhood. -/- Methodological questions include questions about how climate science constructs its models, on what basis we trust those models, and how we might improve those models. In order to answer questions about climate modeling, it's important to understand what climate models look like and how they are constructed. Climate model families are significantly more diverse than are the model families of most other sciences (even sciences that study other complex systems). Existing climate models range from basic models that can be solved on paper to staggeringly complicated models that can only be analyzed using the most advanced supercomputers in the world. I introduce some of the central concepts in climatology by demonstrating how one of the most basic climate models might be constructed. I begin with the assumption that the Earth is a simple featureless blackbody which receives energy from the sun and releases it into space, and show how to model that assumption formally. I then gradually add other factors (e.g. albedo and the greenhouse effect) to the model, and show how each addition brings the model's prediction closer to agreement with observation. After constructing this basic model, I describe the so-called "complexity hierarchy" of the rest of climate models, and argue that the sense of "complexity" used in the climate modeling community is related to dynamical complexity. -/- With a clear understanding of the basics of climate modeling in hand, I then argue that foundational issues discussed early in the dissertation suggest that computation plays an irrevocably central role in climate modeling. "Science by simulation" is essential given the complexity of the global climate, but features of the climate system--the presence of non-linearities, feedback loops, and chaotic dynamics--put principled limits on the effectiveness of computational models. This tension is at the root of the staggering pluralism of the climate model hierarchy, and suggests that such pluralism is here to stay, rather than an artifact of our ignorance. Rather than attempting to converge on a single "best fit" climate model, we ought to embrace the diversity of climate models, and view each as a specialized tool designed to predict and explain a rather narrow range of phenomena. Understanding the climate system as a whole requires examining a number of different models, and correlating their outputs. This is the most significant methodological challenge of climatology. -/- Climatology's role contemporary political discourse raises an unusually high number of evaluative questions for a physical science. The two leading approaches to crafting policy surrounding climate change center on mitigation (i.e. stopping the changes from occurring) and adaptation (making post hoc changes to ameliorate the harm caused by those changes). Crafting an effective socio-political response to the threat of anthropogenic climate change, however, requires us to integrate multiple perspectives and values: the proper response will be just as diverse and pluralistic as the climate models themselves, and will incorporate aspects of both approaches. I conclude by offering some concrete recommendations about how to integrate this value pluralism into our socio-political decision making framework. (shrink)

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of (...) kidney and skin. (shrink)

Resonance can trigger of a series of quantum events and therefore induce several changes related to consciousness at micro as well as macro level within a living system. Therapeutic effects have been observed in several religious meditative and healing practices, which use resonance in the form of chanting and prayers. A living system may have many resonant frequencies due to their degrees of freedom, where each can vibrate as a harmonic oscillator supporting the progression of vibrations as waves that moves (...) as a ripple within the whole system. A cell as an organism or cells in multicellular organisms act as resonating bodies that trigger of oscillation of oscillatory proteins of the cytoskeletal network. The resulting protein conformational changes generate a conscious moment that is regulated via electron tunneling, delocalization and superposition in space time geometry. Consciousness or sentience are phenomenal characteristics of every cell and even though we don’t know the “why” we surely can predict and hypothesize the “how” of consciousness to be quantum computed, which enables the cell to understand and judge perceptions giving it a prospect to behave as per will. (shrink)

June 2022 A Revolutionary New Metaphysics, Based on Consciousness, and a Call to All Philosophers We are in a unique moment of our history unlike any previous moment ever. Virtually all human economies are based on the destruction of the Earth, and we are now at a place in our history where we can foresee if we continue on as we are, our own extinction. As I write, the planet is in deep trouble, heat, fires, great storms, and record flooding, (...) weather patterns drastic everywhere. Capitalism has been so successful in supplying us with an endless array of consumer items, that we have never noticed there is a cost. But there is a cost, the cost is the very life of the Earth herself, and now the day of reckoning is here. Days of reckoning are most often days of rath. But I am hoping that this is a day of major Awakening over the entire planet. We have caused a crisis so great for the Earth we can hardly get our minds around it. But I am proposing that deeply embedded in the crisis are ideas, about who and what the Earth is, Ourselves, and what we are here for. I am proposing that this is a call to all philosophy and philosophers to rethink ourselves from the ground up. The human race has never gotten the Earth right and now we must, for the Earth is the true foundation for civilization. We are in deep trouble with the Earth, and it owes to the fact that the great male thinkers never got the Earth right, they could never make the connection between the life of mind and the life of the Earth. I am proposing that deeply embedded in the crisis we are in are ideas. And that in fact the planet is in the grip of a false metaphysics, and scientific image of nature that really comes most recently from Descartes. His conviction that matter, and with it the Earth, are simply the weighable, the measurable the extended in space and time, utterly devoid of any inner life of mind thoughts or Consciousness. This view of matter and the Earth goes back to the very dawn of thought, Descartes is just its most recent and comprehensive version of things. This view of matter is really a false metaphysics that dominates most of the modern world and underpins the whole scientific image of nature itself. I am proposing this is a false metaphysics and offering a new version of things based on Consciousness. If there is a single idea fueling and driving the destruction of the planet, it is the conviction that the Earth is something without Consciousness. When you intend to ravage and savage the planet, turn it into consumer items to be converted into money in the bank, first pretend that all of the bright beings in the natural world are devoid of Consciousness, just “things” you do not have to have any conscious about destroying them. I am proposing that this term Consciousness, that has appeared as term and a problem for modern science, is the key to getting ourselves right with the Earth. I propose this new theory for science will ramify into every other disciplines as well, and the ways we think just about everything. This old paradigm based on a false theory of matter, has run its course, it has brought us to the brink of our own extinction. We need new ideas, and we need them now. You will find my recent work in the Scientific God Journal under the title: Consciousness as the Organizing Principle, and a very complete version of my arguments for this term Consciousness, along with radical reinterpretation of modern science itself, on the Galileo Commission site. It is a radical moment for all of the thinkers among us, take this as my small contribution to rethinking ourselves in new terms, based on my understanding that the true basis for the whole of Being, the Universe, the Cosmos, and with them Ourselves, is this term Consciousness. And unpack it. And I predict that with this term Consciousness every intractable human problem in both science and the modern world will go down like a line of dominos before it. And so, here are a few new ideas I would offer you. These are the times of the Reappearance of the Feminine, a great Awakening as of Springtime after a long dark and lonely Winter. We are leaving behind us an old civilization based on male dominance, fear lies and control, now in decay, disease, and death disintegrating all around us. We are moving into a whole new civilization based on Love and Truth. A new civilization requires new basic terms values and first principles. And so, I return to Descartes. 1. Just over 300 years ago a young man travelling with the army found himself stranded in a foreign town in a bare room lit by a candle with nothing to do but think. And in a couple of nights Descartes laid the entire thought foundations for modern science and most of the modern world. It isn’t clear that modern philosophers with their funding sources of grants, their graduate students, their reputation and all the perks and privileges of academia can do any better. Descartes claimed there are just two principles in the Universe, Matter and Mind. God was pure mind; human beings were mind and matter. And we are the only ones on the planet with mind. Everything else all of the bright array of beings who share the planet with us are simply matter. And matter? The weighable the measurable the extended in space and time utterly devoid of any inner life of thoughts, feelings, or Consciousness This classification was a boon for developing science. Scientists did not have to worry about any inner life in nature, ideas or Consciousness, they could just set about weighing and measuring, as they have until the present day. But it was a disaster for the Earth. Earth was once worshiped as a Goddess. With Descartes she became almost overnight “things.” Simply commodities and resources, an endless of supply of consumer items, to be turned into money in the bank. And now Descartes concept of matter is up for us. If there is a single idea that is enabling and driving the destruction of the Earth, it is the conviction that Earth is something without Consciousness. This whole scientific image of nature as something devoid of Consciousness is driving the destruction of the Earth, and driving us all insane, and it needs to change. Ever since Descartes formulated Dualism, scientists and philosophers have been trying to get rid of it. They have done this by attempting to make matter the fundamental term of reality, and to explain mind or Consciousness in terms of matter. And now, Consciousness has emerged as term and a problem for modern science. 2. The prevailing Universe picture has been mainly based on the belief that Consciousness appears only at the end of evolution in ourselves and some of the higher animals when matter attains “a certain state of complexity” and it is produced by neurons in the brain. But Consciousness is nothing real in itself, the neurons are doing the work, Consciousness is simply a byproduct of neural activity. As William James summed up this position, not his: Consciousness is to the brain as a shadow to the runner, it runs beside him but never influences his stride. And so, the great problem of neuroscience: How do neurons produce Consciousness? So far, no one has been able to say how. All we have is parallelism. Two processes are running in parallel a train of neural events and a train of Consciousness events. And so, which one is primary? The face of neuroscience and much of the modern world is that the neural events are what is really real, Consciousness is secondary. The conviction that Consciousness is something produced by neurons is so deeply held and has been so for so long, that it seems like an obvious fact. It is in fact an assumption and a theory, and it could all well be the other way around. The scientific image of nature as something devoid of Consciousness is now up for us. It has enabled the destruction of the Earth, and we are now at a unique place in our own evolution where we can foresee if we continue on as we are, our own extinction. And so, there are the best reasons for rethinking Descartes concepts of matter. Scientists and philosophers have been trying to escape dualism by making matter the fundamental term. And now, this has not worked. In a nutshell: The mind body problem, the “hard problem of Consciousness” ---how do neurons in the brain, atoms and molecules give rise to ideas thoughts and feelings and who what and where is the “I” who sees them? And then, the near-death experience. I remind you of the truth of the near-death experience. The body in the bed is brain dead eeg flat, but the patient, pure Consciousness is hovering at the ceiling watching the doctors work over the body below, able to read dials he could not have seen from the bed, sometimes able to events in the corridor beyond the room, all subsequently confirmed by the doctors. Evidence as good as it gets that the patient really was out of his body. And so, the patient is able to see without eyes, hear without ears and to think and remember without a brain. There is not a single scientific principle that can account for this. And I am proposing that the near-death experience is a threshold and a key for a much deeper understanding of the Universe. These three problems are so hard they cannot be solved by present scientific principles and therefore call all present principles and ways of thought into question. When your axioms cannot account for the data, it is time to drop them and find better fundamental terms. We have not been able to solve the problems of Consciousness with the assumption that matter is the most basic and fundamental term. And so, if Cartesian dualism is to be overcome at all, we need to try it the other way around. 3. We are in the position of Copernicus. Remember Copernicus? He was making his calculations on the assumption that the Earth was the center of the Universe until they became so unwieldy that he decided to try it all the other way around. To make the sun the center, the Earth revolving around it. And lo, all of his data fell neatly into place. I am proposing a whole new Universe picture. Evolution makes us continuous with every other being, Consciousness would not be in us if it were not in them also, and then, in the atoms and molecules and cells that make up living beings. I propose to make Consciousness the most basic term and see what follows. I am in fact, proposing a new Copernican Revolution, that Consciousness is the true basis for the Universe and the right fundamental term, for science itself all other disciplines as well, and the whole of the modern world. And I predict that every intractable problem in science or the modern world, will go down like a line of dominos before it. In a nutshell: Consciousness and not matter is “first and fundamental” in the Universe, it is there from the very “Beginning” everything has it and all of the true causalities, the explanatory principles belong to it. Not to matter. What then is matter? All matter is an Appearance of something much more real, Consciousness. All matter is an expression of Consciousness, even the least little bit of matter contains Consciousness, and is an expression of Consciousness. And so, we revise the scientific image of nature. Science at present is two termed, matter/energy. It needs to become three termed: Matter/energy/Consciousness, with the recognition that all of the basic principles, the true causalities of events, and of the Universe belong to Consciousness. And now physics. To accommodate this new Universe picture physics needs to alter just one term, energy. All energy contains Consciousness, that idea alone will change our world forever. The animals the trees the plants are just as conscious as we are, as is the Earth herself, a continuum of many forms of Consciousness of which our own is one. The Earth consists of interacting and intersecting forms of Consciousness, Consciousness within Consciousness within Consciousness within Consciousness. A remarkable work has just appeared entitled “Beyond Words What Animals Feel and Think.” Describing in detail how like ourselves all of the animals are. And the more we can see how like us everything else really is, the harder it will be for us to do them all in, in the interest of turning them into consumer items. And so, here is a new principle of understanding, that entails completely new forms of explanation, and a whole new Universe picture to be spelled out in terms of Consciousness and its various properties. This is a Universe that is aware awake and Enspirited throughout. And so, there is only one principle, not two. And so, how does Consciousness work? There is “no mind/body problem.” My Consciousness is aligning the Consciousness of neurons in the brain, that aligns the Consciousness of all other cells in the body, that aligns the Consciousness of molecules and atoms themselves. Mainly from the top down, but also interactive, and not reduction to the purely physical forces. 4. And so, here is a radical new Universe picture, and with it a new way to think about the Universe itself, the Earth, Ourselves, and Spirit. It requires a complete revision of both of the terms of modern science itself. The problem of the modern world owes in deep measure to Descartes concept of matter as something devoid of interior life. But he is only the most powerful and simple expression of a whole tradition of thought that predates him, that goes back to the very dawn of thought itself. It owes to the conviction of both Plato and Aristotle that the Earth was something devoid of reason, or mind, and therefore something to be held in complete contempt. We are emerging from a civilization based on contempt for the Earth, and down the road, it will become contempt for the body, sex, women, the Native people, and people of color everywhere. And so, this entire tradition is now up for us, it has brought us to the brink of our own extinction, and we need to get beyond it. I am proposing that this term Consciousness is the way out. The missing piece of the puzzle and the idea whose time has come. And it will enable us to move into a completely new civilization based on respect for the Earth, women, sex, people of color, that honors everyone and has a place for all. Revolutions in science occur when new data show up that cannot be accounted for by existing paradigms (Thomas Kuhns: The Structure of Scientific Revolutions). Consciousness, and all the properties and problems of Consciousness are just such data, and they compel a new scientific revolution. But we are a scientific age. A new Copernican revolution in science is such as revolution everywhere. And Consciousness is the key to getting every other reality at all levels and depths right as well. It will enable us finally to get the Earth right, get ourselves right with the Earth, and with one another. Archimedes: Give me a place to stand, and I will move the world. I am proposing a new synthesis among our fundamental terms in which this term Consciousness is the new lynchpin. And so, I return once more to Descartes. Descartes in the Mediations was a dualist, they were two realities interacting in the pineal gland mind and body. But Descartes age was high on “Cartesianisms,” on Descartes concept of matter. Animals were simply cleverly wired machines (Hobbes called them automata). Rumor had it that Descartes followers went about kicking dogs reasoning that their howls were not due to any feelings of pain, but simply the wiring of the machine. We have been doing this to the Earth ever since, and now the Earth is not going to stand for it any longer. It is time we all woke up. There is no matter in Descartes sense of it, or in Plato and Aristotle’s sense of it. This old concept of matter is embedded in all of the crisis and catastrophes---fires, drought, pandemics, over population, the disintegrating economies, our ways of life, capitalism and consumerism themselves. All matter is Enspirited, contains Consciousness, and is an expression of Consciousness. Now I tell you something about Descartes you may not know. In the Mediations was a dualist, there are minds and bodies. But by the end of his life, he knew the truth. Descartes guided his whole life by these vivid dreams, and toward the end of his life he had this dream: He saw the Universe as a giant machine and in the heart of the machine propelling the whole, was Consciousness. And so, out of the shades and shadows and into the light of day. Here is a renewed and a new science, a new cosmology. And with it, a revolutionary new metaphysics. The whole of the modern world is in the grip of a false metaphysics, based on Descartes theory of matter. Here is a new, and finally true metaphysics based on the single term, Consciousness. 5. And in all my works, I spell out this new metaphysics based on Consciousness, and what it means for how we think about virtually everything: The Universe, the Earth, Ourselves, and Spirit. Of who, what and where Spirit is, that we may connect with Spirit everywhere. There is only one term for the Universe, and not two, this single term Consciousness, that manifests itself in two modes: Consciousness in Form, Consciousness Formless. And so, here is a sketch of what this new term Consciousness really means. For four great aspects of the real, four new cornerstones for a whole new civilization on Earth, based on Love and Truth. A. For the Universe: New causalities, all matter is an expression of Consciousness, awake and aware, Enspirited throughout, which has a place for the causalities of love ideas intent plan and purpose, what Aristotle called final causality, that for the sake of which. And it has a place for subjectivity, the greatest mystery in the whole of the Universe, knowable only in ourselves, but there in everything else as well, bedrock in the chain of causalities. The buck stops here. Here are two very different Universe pictures. The Cartesian Universe consists of things, pushed, and pulled around by the physical forces that function blind. The true Universe consists of selves and not things. Selves at least in ourselves, are organized and focused about an I, an I am, or a sense of self in everything, ever other being dear to itself. Just one aspect of subjectivity. And so, it is Consciousness all the way down, and subjectivity all the way down. Science proceeds on the basis of the negligible of what it can leave out as unimportant. Subjectivity is the ultimate animating principle of the Universe. What Descartes really did was to strip from nature what is most essential about it, its animating principle Consciousness. And so, we come out of a long history of “clunk.” The great male thinkers have killed creation. First in concepts and now in the lived life. And so, after centuries of fruitless search, not all of it in vain, finally, and just in time the true basic principle for the Universe has shown up in virtually all disciplines, this term Consciousness. B. And so, the Earth: What does this term Consciousness really mean for the Earth? It means that all of the bright array of beings around us have Consciousness. And the more we can realize how like us they are, the harder it will be to do them all in. Is this what it really means to be “made in the image of Spirit?” To destroy ever other living being? The god of Genesis is a creator god who has created billions and billions of living forms. Man, taking himself to be made in the image of Spirit has destroyed virtually all of it. The Earth is not things, not commodities and resources, not an endless array of consumer goods. The Earth consists of conscious living spiritual beings like ourselves, who need to be honored and respected, nurtured and cared for, to be Loved. And if the human race can finally pull it off and bring Love here and start helping the Earth rather than destroying her, even our vast numbers now at 8 billion, may not matter. Deeply embedded in the modern world is a false cosmology based on the hitherto useful but ultimately false metaphysics of Descartes. In particular it owes to Descartes concepts of matter, and of the Earth, as something devoid of Consciousness. And now this concept is up for us. If there is a single idea enabling and driving the destruction of the planet, it is the conviction that the Earth is something devoid of Consciousness. And we all have a vested interest in keeping this false concept in place. When you intend to ravage and savage the Earth, to turn it into consumer items, and money in the bank, first pretend she has no Consciousness that way we need not have any conscious about it. We are in deep trouble with the planet. Virtually all human economies are based on the destruction of the Earth, and we are now at a place in our history where we can foresee if we continue on as we are, our own extinction. And so, here are a few new guiding principles for the planet, based on Consciousness. Consciousness has field properties. The Earth is Consciousness throughout, connected and interconnected throughout, intersecting and interacting fields of Consciousness of which our own is one. To harm one is to harm all. Only this understanding of the Earth can set our destructive technologies, and capitalism, their goals, and their limits. The real problem with capitalism, and with civilization itself is it has no true understanding of the Earth, all the exquisite networks and webworks that connect all beings with one another. Nor it is about to admit that the Earth is our “life support system,” reason gone insane in the modern world. We are destroying our life support system, capitalism is the full expression of the human death wish in the modern world, and it needs to change. And now, let the barriers between ourselves and all other beings go down. C. And so, Ourselves. This new Universe picture based on Consciousness opens into and has a place for new concepts of human identity. In particular, it has a place for reincarnation, a process whereby one Consciousness dons’ bodies again and again and lays them down. This is a process wholly impossible on materialistic theories. This new view of things puts a higher perspective on Freudian determinism, which is a partial knowing in a greater account. We are something more than the victims of genes drives and childhood. We are immortally eternal evolving spiritual beings who take on a cycle of earthly lives in order to achieve certain goals and abilities, and then, our earthly cycle complete, we depart the Earth plane for other areas of the Universe physical or purely spiritual, to continue our evolution elsewhere. The scientific evidence for reincarnation is increasing on all sides, see for example the work of Michael Newton, a mainstream scientist forced to confront the fact of reincarnation. A completely new reincarnational picture is now emerging everywhere. We choose our parents for abilities we could acquire through them. We all come here with reasons for being here, and we all have free will, an original property of Consciousness, and we work out our issues accordingly. We all come here with the same reason for being here. It is to experience the Earth plane and human society at all levels and depths, in every social role, every climate, both sexes male and female and in all races. We are all here to acquire a deep understanding of the Earth plane with all its challenges and all of its present problems. We are not here to devour and consume the Earth, but to honor her for the learning experience she makes available for us. And so, reincarnation is the great equalizer, the fundamental basis for any bill of rights. Many of the problems of the modern world owe to the fact that reincarnation has not been taught in the West. Reincarnation was the center piece of Jesus teachings. It was banned by a fourth century council that decided the populous could best be controlled through fear. They edited all mention of reincarnation from the scriptures, and inserted fear terms instead, a judgmental god, and so on. If reincarnation had been taught, there would have been no suppression of women, but the gift of both sexes would have been honored and developed. And there would have been no reason for contempt for people of color because who they are, we have been or will be. There is no reason to look down on anyone when we know that our own identity includes membership in theirs. The truth of reincarnation needs to be the foundation for getting ourselves right with the Earth, and with one another. D. And so, Spirit. This new Universe picture, based on Consciousness, has a place for Spirit as simply Infinite Consciousness. All universes all worlds are formed out of this Consciousness, divine and sacred throughout. And Spirit is everywhere in the Earth and can be connected everywhere. And the Native North American people had things right. Everything has its own Spirit, and without contradiction is also an expression of Spirit. And what I am really doing in terms of concepts of modern science is presenting the Native North American version of the Real. And this new Universe picture has a place for the essential insight of all religions almost smothered by church tradition: Love. Not an emotion but a great Oneness, that can be found everywhere, even in a busy city street. But especially in the Earth, that is levels and depths of Oneness everywhere. And so, for the first time in their long and bitter antagonistic history, science and religion now share a common base with this term Spirit, the lynchpin in a new conceptual framework. And I offer an interpretation of where we are in our history, this present moment of historical grace, and these tumultuous times in which we live, the return of the Goddess and the Divine Feminine, the Reappearance of the Feminine in history, the Advent of Women, this great Awakening, as of Springtime after a long dark Winter, the Awakening, the Second Coming. And so, stay tuned! (shrink)

The relations between life and cogntion have been addressed through different perspectives [Stewart 1996, Boden 2001, Bourgine and Stewart 2004, van Duijn & all 2006, Di Paolo 2009]. We would like here to address that subject by relating life to cognition through a process of meaning generation. Life emerged on earth as a far from thermodynamic equilibrium performance that had to maintain herself. Life is charactertized by a ‘stay alive’ constraint that has to be satisfied (such constraint can be included (...) in the constraint of being able to maintain far from equilibrium thermodynamic conditions [Bickhard 2011]). The local ‘stay alive‘ constraint has to be satisfied in an environment containing elements potentially supportive or harmfull. A key activity for the living entity is to characterize these elements in terms of meaningfulness relatively to the ‘stay alive’ constraint. This process can be modeled with an existing tool where a system submitted to an internal constraint generates meaningful information characterizing elements of the environment: the Meaning Generator System (MGS) [Menant, 2003, 2014 a]. In a few words: when a system submitted to an internal constraint receives from the environment an information that has a connection with the constraint it generates a meaning usable for the implementation of an action satisfying the constraint.The generated meaning is the connection existing between the received information and the constraint. The MGS models this process and interfaces to the action implementation for constraint satisfaction The meaning is generated by and for the system. The MGS grounds meaning generation in constraint satisfaction and links the living entity to her environment in a relational process. A simple example is with a paramecium close to a drop of acid. The paramecium which is submitted to a ‘stay alive’ constraint will move away from the acid area. The received information ‘presence of acid’ generates the meaning ‘acid not compatible with the ‘stay alive’ constraint‘ which triggers the moving away action (that example is close to Varela’s bacteria swimming up a sugar gradient. What the MGS brings in addition is a modeling of the significance of the chemical gradient for the organism). The action implemented to satisfy the constraint modifies the environment and the received information, establishing an interactive process linking the living entity to her environment. During its evolution animal life has elaborated new constraints (like ‘live group life’) and new functions enriching meaning generation and action scenarios. As a result the build up of meaningful representations has improved the constraint satisfaction processes of animals, embedding them in their environments in relational and interactive terms [Menant, 2011]. Cognition can be defined by proposing that ‘a system is cognitive if and only if sensory inputs serve to trigger actions in a specific way, so as to satisfy a viability constraint’ [Bourgine, Stewart 2004]. Cognition can also be considered as exemplifying a ‘vital criterion of responsiveness’ [Boden, 2001 ]. Consequently the MGS can be positioned as an elementary and generic version of animal cognition. For animal life, meaning generation for internal constraint satisfaction links life and cognition in a relational and interactive process. Cognition for human life is more complex as new performances have to be taken into account like self-consciousness and free-will. Meaning generation at human level is a challenging subject as human constraints are not clearly understood [Menant, 2011]. Many research activities are in process looking for some understanding of human mind [Philpapers]. One area of investigation is an evolutionary approach to self-consciousness using meaning generation where anxiety limitation comes up as a generic human constraint [Menant, 2014 b]. Assuming that we can have clear enough an understanding of some human constraints, we can look at the MGS for partly extending to humans the link between life and cognition that has been established for animals. So overall, we can consider that the MGS approach makes available an evolutionary link between life and cognition for animals, and partly for humans. A characteristic of the proposed system approach to meaning generation is the possibility to use it for any type of agent, be it organic (with intrinsic constraints ) or artificial (with derived constraints). Such characterization of agents through meaning generation can be used to discriminate artificial itelligence from human intelligence (see the MGS usage to support Searle’s chinese room argument [Menant, 2013]). On a more general basis, the proposed system approach can positions the MGS as a simple model for an internal source of normativity. It’s usage as a simple building block allows a bottom-up modeling for normativity in the sensorimotor approach. The ‘stay alive’ constraint could also be taken as a starting point for an evolutionary grounding of sensorimotor norms ‘in the biological normativity of the agent as a whole’ [Di Paolo & all 2014]. The proposed presentation will develop the points summarized here above and position them relatively to the autopoietic and enactive approaches. Several possible continuations will also be highlighted. (shrink)

In a very general sense, hybrid can be understood to be any organism that is the product of two (or more) organisms where each parent belongs to a different kind. For example; the offspring from two or more parent organisms, each belonging to a separate species (or genera), is called a “hybrid”. “Hybridity” refers to the phenomenal character of being a hybrid. And “hybridization ” refers to both natural and artificial processes of generating hybrids. These processes include mechanisms of selective (...) cross-breeding and cross-fertilization of parents of different species for the purpose of producing hybrid offspring. In addition to these processes, “hybridization ” also refers to natural and artificial processes of whole genome duplication that result in the doubling or trebling of the sets of chromosomes of the organism. This entry provides an overview of the impact of hybridity on agriculture. It begins with an historical sketch that traces the early horticulturalists’ and naturalists’ investigations of hybrids. This starts with the observations of Thomas Fairchild and Georges-Louis Leclerc, Comte de Buffon; and leads to the explanation of its mechanism by Gregor Mendel, James Watson and Francis Crick, and Ernst Mayr; and the eventual manipulation of hybrids and hybridization by Barbara McClintock. Following this, the reader is introduced to a number of key terms and concepts in use within current research as well as highlighting diverse ethical concerns that center on hybridization. Recent research that attempts to ascertain the role of hybridization in adaptive change will be introduced. This will include research on the evolution of crop species, increased biodiversity, and the use of hybrids to manipulate phenotypically desirable traits in agricultural crops. The focus of the discussion is on a particularly significant type of naturally occurring hybridization, polyploidy hybridization. Polyploids are organisms which have more than two complete genomes in each cell. This kind of hybridization is ubiquitous among crop plants. The role of polyploidy in plant evolution and the affects of polyploidy on plants and animals will be reviewed. A critical discussion of its agricultural value in the production of fertile polyploid hybrids highlights key epistemological, ontological, and ethical issues. These are illuminated with reference to the distinct processes of artificial and natural hybridization. A survey of these different kinds of hybridization includes the ethical and economic impacts of hybridity on global nutrition, the environment, and considerations of some practical implications for the agricultural industry. Tracking the role of hybrids, the process of hybridization, and the current impacts of it for agriculture requires knowledge of the history of its early conceptualization, understanding, and use. This is the topic of the following section. (shrink)

This paper revisits the “Hwang case,” which shook Korean society and the world of stem cell research in 2005 with the fraudulent claim of creating patient-specific embryonic stem cells. My goal is to overcome a human-centered, Korea-oriented narrative, by illustrating how materials can have an integral role in the construction and judgment of fraud. To this end, I pay attention to Woo Suk Hwang’s lab at Seoul National University as a whole, including human and nonhuman agents, that functioned (...) as what I call sociomaterial technology, and Gerald P. Schatten at the University of Pittsburgh, Hwang’s collaborator, who played a crucial role in demonstrating the potency of this technology to the members of the scientific community. By recasting the whole event as the “case of Hwang and Schatten,” I argue that fraud is, like all knowledge claims, a sociotechnical construct, and that matters of fraud are locally judged. Fraud leaves its mark on materials, but I show that material evidence alone never tells the whole story and instead can be used to limit the range of responsibility. (shrink)

Undoubtedly the Penrose-Hameroff Orch OR model may be considered as a good theory for describing information processing mechanisms and holistic phenomena in the human brain, but it doesn’t give us satisfactory explanation of human perception. In this work a new approach explaining our perception is introduced, which is in good agreement with Orch OR model and other mainstream science theories such as string theory, loop quantum gravity and holographic principle. It is shown that human perception cannot be explained in the (...) terms of elementary particles and we should introduce new indivisible holistic objects with geometry based on smooth infinitesimal analysis - elastic membranes. The example of such a membrane is our Universe which is an indivisible whole. It is shown that our perception may be considered as the result of elastic oscillations of two dimensional (2D) elastic membranes with closed topology embedded in our bodies. Only one elastic membrane responsible for its perceptions will correspond to the selected organism, but there may be other membranes, even at the cell level. In other words, reality may be considered as the process of time evolution of holistic energetically very weak macro objects - elastic membranes with the geometry based on smooth infinitesimal analysis. An embedded membrane in this multidimensional world will look different for the external and internal observers: from the outside it will look like a material object with smooth infinitesimal geometry, while from the inside our Universe-like space-time fabric. When interacting with elementary particles and other membranes, a membrane will transform their energy into its elastic energy (a new form of energy) - the energy of stretching of the infinitesimal segments. The theory postulates that these elastic deformations will not be observable from the point of view of the internal observer. Heisenberg’s uncertainty principle will work in this physics only from the point of view of the internal observer. For the external observer each embedded elastic membrane may be stretched and even a very small region will become observable. For example, living organisms play the role of internal observers of the Universe, and at the same time they serve as external observers for 2D membranes embedded into our Universe. We can observe our 2D self-membranes through our perceptions, which are encoded in elastic oscillations of the elastic membrane. According to the theory, elastic membranes occupy energetically favorable positions around microtubules involved into Orch OR. The theory not only gives us a really multidimensional holistic picture of reality, but it also provides us with a new method for understanding such phenomena as perception, self-awareness and will. (shrink)

Forty-two years ago, Capra published “The Tao of Physics” (Capra, 1975). In this book (page 17) he writes: “The exploration of the atomic and subatomic world in the twentieth century has …. necessitated a radical revision of many of our basic concepts” and that, unlike ‘classical’ physics, the sub-atomic and quantum “modern physics” shows resonances with Eastern thoughts and “leads us to a view of the world which is very similar to the views held by mystics of all ages and (...) traditions.“ This article stresses an analogous situation in biology with respect to a new theoretical approach for studying living systems, Integral Biomathics (IB), which also exhibits some resonances with Eastern thought. Stepping on earlier research in cybernetics1 and theoretical biology,2 IB has been developed since 2011 by over 100 scientists from a number of disciplines who have been exploring a substantial set of theoretical frameworks. From that effort, the need for a robust core model utilizing advanced mathematics and computation adequate for understanding the behavior of organisms as dynamic wholes was identified. At this end, the authors of this article have proposed WLIMES (Ehresmann and Simeonov, 2012), a formal theory for modeling living systems integrating both the Memory Evolutive Systems (Ehresmann and Vanbremeersch, 2007) and the Wandering Logic Intelligence (Simeonov, 2002b). Its principles will be recalled here with respect to their resonances to Eastern thought. (shrink)

Religion has a considerable influence over the public’s attitudes towards science and technologies. The objective of the paper is to understand the ethical and religious problems concerning the use of embryo for research in assisting conception for infertile couples from the perspective of Catholic Christians. This paper seeks to explain our preliminary reflections on how religious communities particularly the Catholic Christian communities respond to and assess the ethics of reproductive technologies and embryo research. Christianity as a whole lacks a (...) unified and definitive statement on when an embryo becomes a person, although fundamentalist Christians tend to be opposed to embryo experimentation. Roman Catholics tend to believe that the embryo should be treated as human life from the moment of conception or fertilisation. As opposed to this preconception I have tried to point out that a foetus is a clump of cells and lacks individuality as a conscientious human being and thus can be used for research for therapeutic reason. The paper concluded that the Church accepts techniques on embryo that respect their life. So they would allow procedures that are akin with healing and improvement of life without involving undue risks. The Church feels children should arise out of act of love between man and his wife in co-operation with God. In this regard, it may be pointed out though the creation of a child through a conjugal act in a wed lock is the preferred method since it is the most natural, least expensive one. But that does not mean, it should be the only acceptable means to conception. To state a child born using ARTs would be less perfect compared to a child born through conjugal act of husband and wife is absurd one to be mentioned. (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)

Gregor Mendel (1822-1884) was the first to explain that certain 'traits' were inherited in plants from one generation to the next. These would later become known as genes. Frederich Miescher in 1869 analyzed a substance from the nucleus of cells, which he therefore called nuclein. Further study of nuclein revealed that it contained elements like hydrogen, oxygen, nitrogen and phosphorous, with a specific ratio of nitrogen to phosphorous. Then in 1878 Albrecht Kossel determined that nuclein contained nucleic acid, from which (...) he isolated five nucleobases (nitrogen compounds now referred to by the letters C, G, A, T, U representing cytosine, guanine, adenine, thymine, and uracil). It was also discovered that ribose, a sugar was present in the nuclein compound. What Miescher had isolated from the cell nucleus was actually what would latter be identified as DNA (Deoxyribonucleic acid). C. H. Waddington (1905 - 1975) first proposed the term “epigenetics” in 1942 to describe the region between the gene and the whole organism (phenotype) [3]. Today, what is called the epigenome refers to all the chromosomal modifications, DNA modifications, chromatin protein modifications and their complexes. It is the epigenome that determines both the expression of the genes and their inheritance. R. A. Jorgenson reports [4], "Many of these modifications appear to be “programmable” and to be “read out” to influence chromosomal functions." Nobel laureate Barbara McClintock stated this revolutionary proposal more clearly in her Nobel lecture [5], “to determine the extent of knowledge the cell has of itself, and how it utilizes this knowledge in a ‘thoughtful’ manner when challenged.” In 1960 R. A. Brinks suggested that chromosomes possess a paragenetic function in addition to their genetic function [7]. The physical nature of the paragenetic function is characterized by the variety of forms or states of chromatin that can reside at any genetic locus. While the genetic function is stable, the paragenetic function is labile and programmable in ontogeny. It is this latter function that allows organisms to transfer informational macromolecules (RNA and proteins) in a systematic and regulated manner over what is known as the “RNA information superhighway.” Given this capacity, organisms may be able to store information at numerous genetic loci in the form of paragenetic chromatin states, which can be reprogrammed during ontogeny or environmental stress [8]. This reprogrammable system could operate over the whole organism as a storage device, allowing it to make informed ‘decisions' during growth and development, or in response to the environment. Such processing capacity could be considered a form of ‘intelligence,' which also could be passed on to future generations. The study of the flow of information within and between cells and organisms represents the cutting edge of modern biological research. While physical correlates of cognitive behavior in living organisms are being discovered, it does not spell reduction to such correlates. The electronic activity within the physical components of a radio, for example, may be minutely determined, but ultimately it is not merely the electrical activity that produces the intelligent speech that is heard. Only the intelligent person whose voice is being broadcast through the radio can explain that. Without the broadcaster, the radio would sit silently even though fully functional. An organism without its living agency also appears to be devoid of metabolic activity although all the chemical components are fully present. How to connect life to matter will be the ultimate challenge that has to be met. This will prove to be a philosophical problem we hope to address in the near future. (shrink)

Introduction. Taking into account the priorities of the state policy in the field of economic and innovative development of the Perm region, assessment of the regional potential of the digital economy, the strategic importance of economic activities implemented by SMEs for the economy of the region and the country as a whole, the actual impact of the norms on the instruments of development of small and medium-sized enterprises in the Perm region is assessed. The purpose of this study is (...) to improve the regional regulatory platform of tools for the development of small and medium-sized businesses in the Perm region in order to gain the status of an investment-attractive region in the digital economy of the Russian Federation, taking into account the Strategy of the information society in the Russian Federation, which will ultimately contribute to the development of e-business in the Perm region, rehabilitation and competitiveness of the economy of the Perm region in the global market. Methodology. The General methodological basis of the study was the dialectical- materialistic method of cognition of legal reality, which allowed to study the tools of development of small and medium-sized businesses in the Perm region in their development, to consider the problems of tools for the integrated development of small and medium-sized businesses in the Perm region, taking into account the changed socio-economic conditions in inseparable unity with other related tools relevant to the needs of digitalization of society. Such universal scientific methods as analysis and synthesis of doctrinal and normative materials were used in the work. In addition, special legal methods were used: the method of legal modeling, which allows to design possible legal situations using digital tools for the development of small and medium- sized businesses in the Perm region; the method of systematic interpretation used in assessing the actual impact of regional norms on the tools of development of small and medium-sized businesses in the Perm region. Results. The article proposes a new tool for the development of SMEs as a regional electronic platform for the promotion of goods, works and services of SMEs in the Perm region. Attention is paid to the level of digital literacy of SMEs and consumers of their goods, works and services: the conclusion about the lack of digital competence. Conclusion. It is necessary to improve the regional regulatory platform taking into account economic trends: it is important to introduce digital competencies everywhere, including at the professional level in relation to SMEs in the Perm region, in order to increase the business activity of young people and other representatives of the working population. As for the actual introduction of new tools for the development of small and medium-sized businesses in the Perm region, we propose that the regional legislator develop a new electronic information platform at the expense of the regional budget to promote goods, works and services sold by SMEs in the Perm region. We believe that the measures proposed by us to enhance the economic activity of SMEs can be perceived by other regions. (shrink)

Never was dogmatic reductionism helpful in conceiving the phenomenon of life. The post-genomic era has made it clear that genes alone cannot explain the functioning of whole organisms. Already each cell represents a unique, non-recurring individual. Recent progress in developmental biology has conveyed new perspectives both on the makings of individual organisms (ontogeny), as on evolutionary change (Evo-Devo). The genome (the entirety of all genes) of an animal remains constant from fertilization onwards in each cell. The realization (...) of genes requires molecular environments, in particular pertinent to the cytoplasm of the unfertilized egg. Individuality of an organism therefore is not only determined by its genome, but is shaped through developmental processes (it needs time!). Organisms can only exist through mutual interplays with their respective (molecular and cellular) environments at all levels of organization. Thus, life can be conceived of as endless networks of communication, e.g. as a mutual continuum, connecting all individuals, all species and all generations within their given environments. Evolutionarily, nature does not select fitting genes, but rather viable traits. The presented concepts render it unlikely that it was genes that founded our living world, but rather that distinct environments shaped “genes” (of whatever chemical nature) which proved to be “life-suitable”. (shrink)

Wormhole is a popular tool for interstellar travel in science fiction. It connects two different space-time points directly although such an astrophysical object is not yet observed, but in 2015, researchers in Spain created a tiny magnetic wormhole for the first time ever. They used it to connect two regions of space so that a magnetic field could travel 'invisibly' between them. This article presents a model of making a wormhole of light on the principle of conversion of energy so (...) that light going from one end could come out of another end; hence it can be called a wormhole of light. Materials including solar cell, amplified speaker, one way walkie talkie, alligator clips, light emitting diode, transistors and clapping switch have been used. The method of conversion of energy is used and light is transferred into sound first and then back into light. The preparation of such wormhole of light is split into two parts. One end includes a circuit that would accept light through a box and the other end would provide light coming from another box. In order to utilize a wormhole of light to two locales of room the goal was to make light travel between them. Sound made from light would travel the distance between the two boxes. For this purpose a one way walkie-talkie will provide the connection between the two boxes and thus as a whole it would work as a wormhole of light. (shrink)

The paper begins with a retrospective of the debates on the origin of life: the virus or the cell? The virus needs a cell for replication, instead the cell is a more evolved form on the evolutionary scale of life. In addition, the study of viruses raises pressing conceptual and philosophical questions about their nature, their classification, and their place in the biological world. The subject of pandemics is approached starting from the existentialism of Albert Camus and (...) Sartre, the replacement of the exclusion ritual with the disciplinary mechanism of Michel Foucault, and about the Gaia hypothesis, developed by James Lovelock and supported in the current pandemic by Bruno Latour. The social dimensions of pandemics, their connection to global warming, which has led to an increase in infectious diseases, and the deforestation of large areas, which have caused viruses to migrate from their native area (their "reservoir") are highlighted below. The ethics of pandemics is approached from several philosophical points of view, of which the most important in a crisis of such global dimensions is utilitarianism which involves maximizing benefits for society in direct conflict with the usual (Kantian) view of respect for people as individuals. After a retrospective of the COVID-19 virus that caused the current pandemic, its life cycle and its history, with an emphasis on the philosophy of death, the concept of biopower initially developed by Foucault is discussed, with reference to the practice of modern states of control of the populations and the debate generated by Giorgio Agamben who states that what is manifested in this pandemic is the growing tendency to use the state of emergency as a normal paradigm of government. An interesting and much debated approach is the one generated by the works of Slavoj Žižek, who states that the current pandemic has led to the bankruptcy of the current "barbaric" capitalism, wondering if the path that humanity will take is a neo-communism. Another important negative effect is desocialization, with the conclusion of some philosophers that we cannot exist independently of our relationships with others, that a person's humanity depends on the humanity of those around him. The last section is dedicated to forecasting what the world will look like after the pandemic, and there are already signs of a paradigm shift, including the sudden disappearance of the "wall" ideology: a cough was enough to make it suddenly impossible to avoid the responsibility that every individual has it towards all living beings for the simple fact that he is part of this world, and of the desire to be part of it. The whole is always involved in part, because everything is, in a sense, in everything and in nature there are no autonomous regions that are an exception. The COVID-19 pandemic seems to restore the supremacy that once belonged to politics. One of the virtues of the virus is its ability to generate a more sober idea of ​​freedom: to be free means to do what needs to be done in a specific situation. -/- CONTENTS: -/- Abstract Introduction 1 Viruses 1.1 Ontology 2 Pandemics 2.1 Social dimensions 2.2 Ethics 3 COVID-19 3.1 Biopolitics 3.2 Neocommunism 3.3 Desocialising 4 Forecasting Bibliography -/- DOI: 10.13140/RG.2.2.31039.74405/1. (shrink)