The prospects for mathematical logic in the twenty-first century

The four authors present their speculations about the future developments of mathematical logic in the twenty-first century. The areas of recursion theory, proof theory and logic for computer science, model theory, and set theory are discussed independently.Comment: Association for Symbolic Logi

Complexity, BioComplexity, the Connectionist Conjecture and Ontology of Complexity\ud

This paper develops and integrates major ideas and concepts on complexity and biocomplexity - the connectionist conjecture, universal ontology of complexity, irreducible complexity of totality & inherent randomness, perpetual evolution of information, emergence of criticality and equivalence of symmetry & complexity. This paper introduces the Connectionist Conjecture which states that the one and only representation of Totality is the connectionist one i.e. in terms of nodes and edges. This paper also introduces an idea of Universal Ontology of Complexity and develops concepts in that direction. The paper also develops ideas and concepts on the perpetual evolution of information, irreducibility and computability of totality, all in the context of the Connectionist Conjecture. The paper indicates that the control and communication are the prime functionals that are responsible for the symmetry and complexity of complex phenomenon. The paper takes the stand that the phenomenon of life (including its evolution) is probably the nearest to what we can describe with the term “complexity”. The paper also assumes that signaling and communication within the living world and of the living world with the environment creates the connectionist structure of the biocomplexity. With life and its evolution as the substrate, the paper develops ideas towards the ontology of complexity. The paper introduces new complexity theoretic interpretations of fundamental biomolecular parameters. The paper also develops ideas on the methodology to determine the complexity of “true” complex phenomena.\u

Termination of rewrite relations on λ\lambda-terms based on Girard's notion of reducibility

In this paper, we show how to extend the notion of reducibility introduced by Girard for proving the termination of $\beta$-reduction in the polymorphic $\lambda$-calculus, to prove the termination of various kinds of rewrite relations on $\lambda$-terms, including rewriting modulo some equational theory and rewriting with matching modulo $\beta$$\eta$, by using the notion of computability closure. This provides a powerful termination criterion for various higher-order rewriting frameworks, including Klop's Combinatory Reductions Systems with simple types and Nipkow's Higher-order Rewrite Systems

Towards a Coherent Theory of Physics and Mathematics

As an approach to a Theory of Everything a framework for developing a coherent theory of mathematics and physics together is described. The main characteristic of such a theory is discussed: the theory must be valid and and sufficiently strong, and it must maximally describe its own validity and sufficient strength. The mathematical logical definition of validity is used, and sufficient strength is seen to be a necessary and useful concept. The requirement of maximal description of its own validity and sufficient strength may be useful to reject candidate coherent theories for which the description is less than maximal. Other aspects of a coherent theory discussed include universal applicability, the relation to the anthropic principle, and possible uniqueness. It is suggested that the basic properties of the physical and mathematical universes are entwined with and emerge with a coherent theory. Support for this includes the indirect reality status of properties of very small or very large far away systems compared to moderate sized nearby systems. Discussion of the necessary physical nature of language includes physical models of language and a proof that the meaning content of expressions of any axiomatizable theory seems to be independent of the algorithmic complexity of the theory. G\"{o}del maps seem to be less useful for a coherent theory than for purely mathematical theories because all symbols and words of any language musthave representations as states of physical systems already in the domain of a coherent theory.Comment: 38 pages, earlier version extensively revised and clarified. Accepted for publication in Foundations of Physic

Inductive Definition and Domain Theoretic Properties of Fully Abstract

A construction of fully abstract typed models for PCF and PCF^+ (i.e., PCF + "parallel conditional function"), respectively, is presented. It is based on general notions of sequential computational strategies and wittingly consistent non-deterministic strategies introduced by the author in the seventies. Although these notions of strategies are old, the definition of the fully abstract models is new, in that it is given level-by-level in the finite type hierarchy. To prove full abstraction and non-dcpo domain theoretic properties of these models, a theory of computational strategies is developed. This is also an alternative and, in a sense, an analogue to the later game strategy semantics approaches of Abramsky, Jagadeesan, and Malacaria; Hyland and Ong; and Nickau. In both cases of PCF and PCF^+ there are definable universal (surjective) functionals from numerical functions to any given type, respectively, which also makes each of these models unique up to isomorphism. Although such models are non-omega-complete and therefore not continuous in the traditional terminology, they are also proved to be sequentially complete (a weakened form of omega-completeness), "naturally" continuous (with respect to existing directed "pointwise", or "natural" lubs) and also "naturally" omega-algebraic and "naturally" bounded complete -- appropriate generalisation of the ordinary notions of domain theory to the case of non-dcpos.Comment: 50 page

Protein folding using contact maps

We present the development of the idea to use dynamics in the space of contact maps as a computational approach to the protein folding problem. We first introduce two important technical ingredients, the reconstruction of a three dimensional conformation from a contact map and the Monte Carlo dynamics in contact map space. We then discuss two approximations to the free energy of the contact maps and a method to derive energy parameters based on perceptron learning. Finally we present results, first for predictions based on threading and then for energy minimization of crambin and of a set of 6 immunoglobulins. The main result is that we proved that the two simple approximations we studied for the free energy are not suitable for protein folding. Perspectives are discussed in the last section.Comment: 29 pages, 10 figure

Stepping Beyond the Newtonian Paradigm in Biology. Towards an Integrable Model of Life: Accelerating Discovery in the Biological Foundations of Science

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

Lambda theories of effective lambda models

A longstanding open problem is whether there exists a non-syntactical model of untyped lambda-calculus whose theory is exactly the least equational lambda-theory (=Lb). In this paper we make use of the Visser topology for investigating the more general question of whether the equational (resp. order) theory of a non syntactical model M, say Eq(M) (resp. Ord(M)) can be recursively enumerable (= r.e. below). We conjecture that no such model exists and prove the conjecture for several large classes of models. In particular we introduce a notion of effective lambda-model and show that for all effective models M, Eq(M) is different from Lb, and Ord(M) is not r.e. If moreover M belongs to the stable or strongly stable semantics, then Eq(M) is not r.e. Concerning Scott's continuous semantics we explore the class of (all) graph models, show that it satisfies Lowenheim Skolem theorem, that there exists a minimum order/equational graph theory, and that both are the order/equ theories of an effective graph model. We deduce that no graph model can have an r.e. order theory, and also show that for some large subclasses, the same is true for Eq(M).Comment: 15 pages, accepted CSL'0