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 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.

The causes of prehistoric inter-group violence have been a subject of long-standing debate in archaeology, an- thropology, and other disciplines. Although population pressure has been considered as a major factor, due to the lack of available prehistoric data, few studies have directly examined its effect so far. In the present study, we used data on skeletal remains from the middle Yayoi period of the Japanese archipelago, where archaeologists argued that an increase of inter-group violence in this period could be explained (...) by a population-pressure hy- pothesis. We quantitatively examine the effect of population pressure on the frequency of inter-group violence by compiling an exhaustive data set. We collected demographic information based on burial jars (kamekan) and the frequency of violence based on the ratio of injured individuals. The results are consistent with the hypothesis, i. e., high population density can promote inter-group violence. (shrink)

It has been commonly claimed that prehistoric warfare in Japan began in the Yayoi period. Population increases due to the introduction of agriculture from the Korean Peninsula to Japan resulted in the lack of land for cultivation and resources for the population, eventually triggering competition over land. This hypothesis has been supported by the demographic data inferred from historical changes in Kamekan, a burial system used especially in the Kyushu area in the Yayoi period. The present study aims to examine (...) the previous claim by using an expanded dataset of human skeletal remains and Kamekan. First, in order to quantify the intensity of warfare, we developed a database of injured individuals found in the middle phase of the Yayoi period in two large populations in the northern Kyushu area, the Fukuoka plain and the upperand middle-stream of the Homan River. Second, we collected Kamekan data from site reports published after 1990 and constructed a comprehensive database to infer the demography in these areas. Finally, we compared the frequency of injured individuals and the inferred demography. The results suggest that the frequency of injured individuals and the population increase tended to be higher at the upper- and middle-stream of the Homan River than on the Fukuoka plain. Different assumptions of the lifetime of each type of Kamekan can produce mixed results on the relationship between demography and the frequency of injured individuals. They were positively correlated under the traditional assumption of constant time intervals, while there was no correlation using time intervals based on carbon dating by the National Museum of Japanese History. Thus, our results are partially consistent with the previous claim that the population increase and the lack of land and resources due to the introduction of agriculture were causes of warfare in the northern Kyushu area in the middle phase of the Yayoi period. (shrink)