Life distinguishes itself from non-life in taking advantage of the cohesion of temporal origin which non-life cannot afford. The temporal cohesion letting the local participants adhere to each other in a contemporaneous manner refers to an instance of the precedent product being pulled into the subsequent production. Setting the precedent is equivalent to preparing the conditions for the subsequent to follow. A concrete implementation of the cohesion of temporal origin, compared with the spatial cohesion common in physics, is found in (...) the natural construction of a reaction cycle with use of the temporal affinity exerted from the immediate local environment. That construction is a temporally local phenomenon in the experiential domain, rather than in the theoretical. The cohesion originating in the local environment is due to the local act of measurement by the environment. A major component of the local environment to each reactant in the reaction cycle is the cycle itself. The cohesion specific to the reaction cycle rests upon the fact that every reaction product from the upstream production in the cycle comes to be fed upon by the immediate downstream production. Every production constituting the reaction cycle is temporally adjacent to and contemporaneous with the similar others residing in the whole cycle, in sharp contrast to the case of the open-ended linear chain of reaction. One externalist scheme of appreciating the internalist enterprise of constructing a durable reaction cycle in a contemporaneous manner may become possible as referring to the Bayesian probability. The durable reaction cycle may be made actual with probability unity under the condition that the products from the preceding production come with the protocol for the similar production to come subsequently. (shrink)

One common denominator between biosemiotics and quantum physics is the participation of agents detecting their surroundings. In biosemiotics, any biological agents as the internal observers including the molecular and cellular ones are involved in detecting their surroundings. Likewise, the physicist as the external observer is also involved in detecting what should be all about the physical world with use of a wide variety of sophisticated measurement apparatuses. On the other hand, the difference between the two is in the nature of (...) the agents of detection involved there. One obvious difference is that although the physicist can report the results of measurement with use of the symbolic language, the biological beings take the indexical act of measurement to simply be a matter of experiencing. The internal observers are phenomenological in constructing something durable as participating in the construction of the phenomenon. In a similar vein, the external observer is also phenomenological in getting into interpreting the constructed durable class property of an object with use of the symbolic language. In particular, the potential use of phenomenology is not limited only to the phenomenologist as the external observer. A possible integration of both the internal and external observers may be sought within quantum phenomenology allowing for the external observer to descriptively make access to the durable objects the internal observers could eventually have constructed. The internal observers are ubiquitous in the environment that functions as the absorbers of whatever quantum particles available there. (shrink)

We are concerned with two modes of describing the dynamics of natural systems. Global descriptions require simultaneous global coordination of all dynamical operations. Global dynamics, including mechanics, remain invariant in the absence of external perturbation. But, failing impossible global coordination, dynamical operations could actually become coordinated only locally. In local records, as in global ones, the law of the excluded middle would be strictly observed, but without global coordination it could only be fullfilled sequentially by passing causative factors forward onto (...) subsequent contiguous operations.The local dynamics of sequential operations would be indefinite with regard to how commitments will be made which will avoid violating the law of the excluded middle, but any resulting record will be as definite as if there had been global coordination. While maintaining an agential capacity for making contingent choices internally, local dynamics could be cumulated into a global record of seemingly simultaneous operations. Natural selection within a framework of local dynamics would have a capacity for making opportunistic commitments, but its effects in a posterior record can be reduced to the mechanistic neodarwinian version as if there had been a global dynamics. However, the resulting global description falsifies the actual material nature of the dynamics. (shrink)

The Schrödinger equation for quantum mechanics, which is approachable in third-person description, takes for granted tenseless time that does not distinguish between different tenses such as past, present, and future. The time-reversal symmetry grounded upon tenseless time globally may, however, be broken once measurement in the form of exchanging indivisible quantum particles between the measured and the measuring intervenes. Measurement breaks tenseless time locally and distinguishes different tenses. Since measurement is about the material process of feeding and acting upon the (...) quantum resources already available from any material bodies to be measured internally, the agency of measurement is sought within the environment in the broadest sense. Most indicative of internal measurement of the environmental origin are chemical reactions in the reaction environment. Temporality naturalized in chemical reactions proceeding as being subjected to frequent interventions of internal measurement is approachable in second-person description because of the participation of multiple agents of measurement there. The use of second-person description is found in the appraisal of the material capacity of generating, distinguishing, and integrating different tenses. An essence of the temporality to be naturalized is within the genesis of different tenses. A most conspicuous exemplar of naturalized temporality is sought in the origins of life conceivable exclusively on the material ground. (shrink)

Chemical affinity is by itself inclusive of the action of a sign. Naturalization of the action of a sign is latent in the material organization holding its own identity by means of the exchange of material. A concrete experimental example is the citric acid cycle running in the absence of biological enzymes. The carbon atoms to be exchanged round the cycle serve as the signs for holding the cycle as a natural system. The action of a sign operates in the (...) present progressive tense and is also descriptively approachable in the same tense, as implying that a natural system holding its own identity assumes the first-person status acting for its own sake. The action of a sign is thus addressable in first person descriptions on the level of the supporting material system that can recognize the sign as such from within. Furthermore, if the action of a sign happens to precipitate the record registered in the present perfect tense, the record itself will be approachable in third person descriptions in the present tense. When one can relate the record of an earlier event to that of a later one, what is called information will come up. Information to be externalized and objectified is about the completed outcome from the action of a sign that is accessible in third person descriptions in the present tense. Conversely, if the action of a sign is carried by a natural system holding its own identity in a manner to be registered in the present perfect tense after the event, information will appear in a proper form of bookkeeping as relating the memory to anticipation on the part of the material agency. Although information in the present has the capacity of relating the past to future in the present tense as avoiding direct confrontation with the dynamic nature of the present or now head on, the action of a sign facing the present squarely is competent enough to address and decipher the generative capacity of information itself operating in the present progressive tense. (shrink)

Anticipatory acts or predictive behavior are prerequisites for living organisms to sustain their survival when escaping from a predator, catching prey, or schooling. For example, catching prey requires that the predator perform some procedures that are equivalent to estimating the directional movement of the prey, its speed and its distance relative to the predator. Underlying these procedures is time experience, which does not adhere to man-made mechanical clocks. Living organisms keep time based on the local activities of each participant and (...) form ecological clocks together. The timekeeping of ecological clocks has been called E-series time, which is interactive in character and consists of mutual alignment of timing that is co-adjusted to each other’s movements and rhythms. A main objective of our current work is to illustrate how E-series time is used for flows of anticipatory acts. To explain such predictive moves and their efforts based on how the perspective of the immediate future affects the present, we resort to the organismic activity of revising the preceding acts in retrospect and semiotic scaffolding that extends beyond simple linear causality. Special attention is paid to the construction of the notion of retrocausal scaffolding, which is a series of dialogical punctuations or mutual coordination of rhythms for the joint production of the present moment of now. Retrocausal scaffolding is synonymous with negotiated anticipation, which is a semiotic/communicative account of revising the preceding acts in the present moment. (shrink)

Reinforcement learning has recently received much attention as a learning method for complicated systems, e.g., robot systems. It does not need prior knowledge and has higher capability of reactive and adaptive behaviors. However increase in dimensionality of the action-state space makes it diffcult to accomplish learning. The applicability of the existing reinforcement learning algorithms are effective for simple tasks with relatively small action-state space. In this paper, we propose a new reinforcement learning algorithm: “Q-learning with Dynamic Structuring of Exploration Space (...) Based on Genetic Algorithm ”. The algorithm is applicable to systems with high dimensional action and interior state spaces, for example a robot with many redundant degrees of freedom. To demonstrate the effectiveness of the proposed algorithm simulations of obstacle avoidance by a 50 links manipulator have been carried out. It is shown that effective behavior can be learned by using the proposed algorithm. (shrink)

Reinforcement learning is very effective for robot learning. Because it does not need priori knowledge and has higher capability of reactive and adaptive behaviors. In our previous works, we proposed new reinforcement learning algorithm: “Q-learning with Dynamic Structuring of Exploration Space Based on Genetic Algorithm (QDSEGA)”. It is designed for complicated systems with large action-state space like a robot with many redundant degrees of freedom. And we applied it to 50 link manipulator and effective behavior is acquired. However optimality and (...) fault tolerance of the proposed algorithm were not considered and to demonstrate effectiveness of the proposed algorithm other applications are necessary. Acquiring of locomotion patterns by a multi-legged robot is a very interesting problem. As it has many redundant degrees of freedom, application of usual reinforcement learning is difficult and an optimal locomotion has not been acquired using previous reinforcement learning algorithm. And the redundancy of the robot is effective to the fault tolerance and various locomotion patterns can be acquired for adapting the faults of the legs. In this paper, we applied QDSEGA to acquiring of locomotion pattern by the multi-legged robot and considered the optimality and fault tolerance. Effective behavior has been obtained by using our proposed algorithm. (shrink)

Timing adjustment is an important ability for living organisms. Wild animals need to act at the right moment to catch prey or escape a predator. Land plants, although limited in their movement, need to decide the right time to grow and bloom. Humans also need to decide the right moment for social actions. Although scientists can pinpoint the timing of such behaviors by observation, we know extremely little about how living organisms as actors or players decide when to act – (...) such as the exact moment to dash or pounce. The time measurements of an outsider-observer and the insider-participants are utterly different. We explain how such essential operations of timing adjustment and temporal spanning, both of which constitute a single regulated set, can be carried out among organisms. For this purpose, we have to reexamine the ordinary conception of time. Our specific explanatory tools include the natural movement known as the upbeat (anacrusis) in music, a rhythmic push for the downbeat that follows, which predicts future moves as an anticipatory lead-in. The scheme is situated in and is the extension of our formulation of E-series time, i.e., timing co-adjusted through interaction, which is derived from the semiotic/communicative perspectives. We thereby demonstrate that a prediction-based timing system is not mechanical but communicative and entails meanings for future anticipation. (shrink)

Molecular imprints of organisms serving as both the agents and the products of the underlying sign activities are quantum mechanical in their origins. In particular, molecules in any reaction networks constituting a biological organism are semiotic or context-dependent in the sense that their activities reside within the proper coordination of the entire networks. The origin of life could have been related to a specific aspect of molecular semiotics, especially in the transition from molecules as the physical symbols of material units (...) to molecules as the semiotic signs having the capacity of pointing to something else other than the molecules themselves. Quantum mechanical underpinning of the molecular imprints leading to the emergence of life is in the appraisal of the material capacities of both coherent assimilation and decoherent dissociation already latent in the imprints. One empirical evidence suggesting the likelihood of both coherent assimilation and decoherent dissociation in prebiotic settings could have been found in synthetic chemical reactions running in hydrothermal circulation of seawater through hot vents in the Haedean ocean on the primitive Earth. (shrink)

(1993). Evolving dissipative structures viewed from the eyes of molecules. World Futures: Vol. 38, Theoretical Achievements and Practical Applications of General Evolutionary Theory, pp. 149-156.

This paper proposes an agent community based information retrieval method, which uses agent communities to manage and look up information related to users. An agent works as a delegate of its user and searches for information that the user wants by communicating with other agents. The communication between agents is carried out in a peer-to-peer computing architecture. In order to retrieve information related to a user query, an agent uses two histories : a query/retrieved document history(Q/RDH) and a query/sender agent (...) history(Q/SAH). The former is a list of pairs of a query and retrieved documents, where the queries were sent by the agent itself. The latter is a list of pairs of a query and sender agents and shows ``who sent what query to the agent''. This is useful to find a new information source. Making use of the Q/SAH is expected to cause a collaborative filtering effect, which gradually creates virtual agent communities, where agents with the same interests stay together. Our hypothesis is that a virtual agent community reduces communication loads to perform a search. As an agent receives more queries, then more links to new knowledge are achieved. From this behavior, a ``give and take''(or positive feedback) effect for agents seems to emerge. We implemented this method with Multi-Agents Kodama which has been developed in our laboratory, and conducted preliminary experiments to test the hypothesis. The empirical results showed that the method was much more efficient than a naive method employing 'broadcast' techniques only to look up a target agent. (shrink)

Enzymes are remarkable molecules which make metabolism possible. Their processing powers are considerable for not only are they catalysts they also contribute to information processing, integration, coherence and memory in the cell. This complex of attributes suggests that a complementary perspective to enzyme nature and activity is needed related to what enzymes and verbs have in common. The value of this kind of thinking is that it shifts the focus from objects and mechanisms to processes and information. In order to (...) support this idea a number of features which enzymes and verbs share are discussed including, context-dependence, occurrence, cases, voice, mood and glue/integrative capacities. The paper concludes with some reflections on the utility of a view of enzymes as verbs. (shrink)

The idea behind this special theme journal issue was to continue the work we have started with the INBIOSA initiative (www.inbiosa.eu) and our small inter-disciplinary scientific community. The result of this EU funded project was a white paper (Simeonov et al., 2012a) defining a new direction for future research in theoretical biology we called Integral Biomathics and a volume (Simeonov et al., 2012b) with contributions from two workshops and our first international conference in this field in 2011. The initial impulse (...) for this effort was given a year earlier by a publication of one of the guest editors of this issue (Simeonov, 2010) in this journal. This time we wish to provide a broader forum and more space to elaborate in detail some of the most interesting concepts we have encountered in our discussions, as well as to invite some new contributions of particular interest in the field. Another goal we had in mind was to collect and review as many provocative perspectives as possible on the same key topic we are interested before making a decision to follow a more focused notion that would lead to a funded research program. Therefore we welcomed the generous suggestion of Professor Denis Noble, FRS, who is also editor of this journal to prepare a special theme issue entitled: “Can biology create a profoundly new mathematics and computation?” It has taken a while to invite and collect the contributions. Most of them had a couple of revision cycles and adjustments after having been thoroughly discussed with colleagues, incl. the editors of this issue. We think that the result we have obtained at the end is a satisfactory one, since we succeeded to integrate a diversity of original, but sometimes controversial and mutually excluding concepts organized within chapters of a self-contained volume. The task of compiling all this was not easy at all. Despite our efforts to position the articles of different authors and themes in a way allowing their easy comprehension and relation to each other within the individual chapters, some of them still require a sort of introduction to dissolve possible ambiguities. This is what we are going to do in the following few paragraphs with the hope that the reader (and some of the authors) would excuse our failures. (shrink)

We develop a semiotic scheme of time, in which time precipitates from the repeated succession of punctuating the progressive tense by the perfect tense. The underlying principle is communication among local participants. Time can thus be seen as a meaning-making, semiotic system in which different time codes are delineated, each having its own grammar and timekeeping. The four time codes discussed are the following: the subjective time having tense, the objective time without tense, the static time without timekeeping, and the (...) inter-subjective time of the E-series. Living organisms adopt a time code called the E-series, which emerges through the local synchronization among organisms or parts of organisms. The inter-subjective time is a new theoretical dimension resulting from the time-aligning activities of interacting agents. Such synchronization in natural settings consists of incessant mutual corrections and adjustments to one’s own punctuation, which is then constantly updated. Unlike the third-person observer keeping the objective time while sitting outside a clock, the second-person negotiators participate in forming the E-series time by punctuating and updating the interface through which different tenses meet at the moment of “now.” Although physics allows physicists to be the only interpreters, the semiotic perspective upends the physical perspective by letting local participants be involved in the interpretation of their mutual negotiations to precipitate that which is called time. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...) and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

The idea about this special issue came from a paper published as an updated and upridged version of an older memorial lecture given by Brian D. Josephson and Michael Conrad at the Gujarat Vidyapith University in Ahmedabad, India on March 2, 1984. The title of this paper was “Uniting Eastern Philosophy and Western Science” (1992). We thought that this topic deserves to be revisited after 25 years to demonstrate to the scientific community which new insights and achievements were attained in (...) this fairly broad field during this period. (shrink)

This is the editorial to the special edition of Progress in Biophysics and Molecular Biology on the role engagement with Eastern traditions of thought could play in the advancement of science generally and biology and the science of mind in particular.