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)

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 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)

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)

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)

Translation with notes of Ammonius' Commentary on Aristotle's Categories.

In 1896 William James published an essay entitled The Will to Believe, in which he defended the legitimacy of religious faith against the attacks of such champions of scientific method as W.K. Clifford and Thomas Huxley. James's work quickly became one of the most important writings in the philosophy of religious belief. James Wernham analyses James's arguments, discusses his relation to Pascal and Renouvier, and considers the interpretations, and misinterpretations, of James's major critics. Wernham shows convincingly that James was unaware (...) of many destructive ambiguitities in his own doctrines and arguments, although clear and consistent in his view that our obligation to believe in theism is not a moral but a prudential obligation -- a foolish-not-to-believe doctrine, rather than a not-immoral-to-believe one. Wernham also shows that the doctrine is best read as affirming the wisdom of gambling that God exists, a notion which James failed to distinguish from believing and which, among other things, he explicitly identified with faith. James's pragmatism, a theory concerning the meaning of truth, is shown to be quite distinct from the doctrine of The Will to Believe. In concentrating on a careful analysis of this doctrine of the will-to-believe, Wernham not only makes a major contribution to understanding James's philosophy, but also clarifies issues in the philosophy of religion and in the analysis of belief and faith. (shrink)

Papers delivered at the joint meeting of the Hegel Society of America and the Hegel Society of Great Britain held at Merton College, Oxford, Sept. 1-4, 1981, to mark the 150th anniversary of Hegel's death. Includes bibliographical references and index.

A t first glance you might not noorder, which afflicts about 0.5 percent of tice anything odd on meeting a American children. Neither researcher young boy with autism. But if had any knowledge of the other’s work, you try to talk to him, it will and yet by an uncanny coincidence each quickly become obvious that gave the syndrome the same name: autism, something is seriously wrong. He may not which derives from the Greek word autos, make eye contact with (...) you; instead he may meaning “self.” The name is apt, because avoid your gaze and fidget, rock his body the most conspicuous feature of the disorto and fro, or bang his head against the der is a withdrawal from social interacwall. More disconcerting, he may not be tion. More recently, doctors have adopted able to conduct anything remotely resemthe term “autism spectrum disorder” to bling a normal conversation. Even though make it clear that the illness has many rehe can experience emotions such as fear, lated variants that range widely in severity rage and pleasure, he may lack genuine but share some characteristic symptoms. empathy for other people and be oblivious Ever since autism was identified, reto subtle social cues that most children searchers have struggled to determine would pick up effortlessly. what causes it. Scientists know that sus- In the 1940s two physicians—Americeptibility to autism is inherited, although.. (shrink)

Gilligan’s (1982) refinement of Kohlberg’s theory on moral development operates on two theses: (1) females, more so than males, reach moral decisions based on the personalities of the relevant individuals; and (2) female behaviors stemming from moral decisions are based upon “care” and “responsibility for others.” This article accepts the first thesis but argues that the second is incorrect. That is, self-interest—i.e., aiding “blood” kin and/or carefully monitoring reciprocity—rather than “altruism” is argued to be the operant dynamic in forging distaff (...) morality and resultant behavior. Six empirical examples are presented as contraindicative of Gilligan’s second thesis. Finally, it is suggested that selection for the psychological traits of independence and the mastery of subtle social chess yielded ancestral females who had more descendants—us—than did females with alternative profiles. (shrink)

This article delineates the core concerns and motivations of the ontological work of Gilles Deleuze, and is intended as a programmatic statement for a general philosophical audience. The article consists of two main parts. In the first, two early writings by Deleuze are analysed in order to clarify his understanding of ontology broadly, and to specify the precise aim of his understanding of being in terms of difference. The second part of the article looks at the work of Heidegger and (...) Derrida in order to distinguish Deleuze's conceptions of ontology and difference from theirs. A final section clarifies Deleuze's efforts to undertake the construction of an ontology divergent from the dominant tradition and in contrast to the emphasis on the closure of metaphysics in the thought of Heidegger and Derrida. (shrink)

1. Hoi dialektikes morphes tēs pousias ston synchrono kosmo -- 2. Skepseis panō stēn agōnia, ston phovo, kai ston chrono ston Kierkegaard.

Upshot: In this response, I address the points raised in the commentaries, in particular those related to the scalability and robustness of the mechanism CALM, to its relation with the CAES architecture, and to the transition from sensorimotor to symbolic.

A.P. Martinich's interpretation that in Leviathan Thomas Hobbes believed that the laws of nature are the commands of God and that he did not rely on the Bible to prove this has been criticized by Greg Forster in this journal (2003). Forster uses these criticisms to develop his own view that Hobbes was insincere when he professed religious beliefs. We argue that Forster misrepresents Martinich's view, is mistaken about what evidence is relevant to interpreting whether Hobbes was sincere or not, (...) and is mistaken about some of Hobbes's central doctrines. Forster's criticisms are worth discussing at length for at least three reasons. He takes the debate about Hobbes's sincerity to a new level of sophistication; his misinterpretations of Hobbes may become accepted as correct; and his criticisms raise issues about the proper method of interpreting historical texts. (shrink)