The building of a global model of carcinogenesis is one of modern biology’s greatest challenges. The traditional somatic mutation theory is now supplemented by a new approach, called the Tissue Organization Field Theory. According to TOFT, the original source of cancer is loss of tissue organization rather than genetic mutations. In this paper, we study the argumentative strategy used by the advocates of TOFT to impose their view. In particular, we criticize their claim of incompatibility used to justify the necessity (...) to definitively reject SMT. First, we note that since it is difficult to build a non-ambiguous experimental demonstration of the superiority of TOFT, its partisans add epistemological and metaphysical arguments to the debate. This argumentative strategy allows them to defend the necessity of a paradigm shift, with TOFT superseding SMT. To do so, they introduce a notion of incompatibility, which they actually use as the Kuhnian notion of incommensurability. To justify this so-called incompatibility between the two theories of cancer, they move the debate to a metaphysical ground by assimilating the controversy to a fundamental opposition between reductionism and organicism. We show here that this argumentative strategy is specious, because it does not demonstrate clearly that TOFT is an organicist theory. Since it shares with SMT its vocabulary, its ontology and its methodology, it appears that a claim of incompatibility based on this metaphysical plan is not fully justified in the present state of the debate. We conclude that it is more cogent to argue that the two theories are compatible, both biologically and metaphysically. We propose to consider that TOFT and SMT describe two distinct and compatible causal pathways to carcinogenesis. This view is coherent with the existence of integrative approaches, and suggests that they have a higher epistemic value than the two theories taken separately. (shrink)

This paper is devoted to computer modelling of the development and regeneration of multicellular biological structures. Some species are able to regenerate parts of their body after amputation damage, but the global rules governing cooperative cell behaviour during morphogenesis are not known. Here, we consider a simplified model organism, which consists of tissues formed around special cells that can be interpreted as stem cells. We assume that stem cells communicate with each other by a set of signals, and that the (...) values of these signals depend on the distance between cells. Thus the signal distribution characterizes location of stem cells. If the signal distribution is changed, then the difference between the initial and the current signal distribution affects the behaviour of stem cells—e.g. as a result of an amputation of a part of tissue the signal distribution changes which stimulates stem cells to migrate to new locations, appropriate for regeneration of the proper pattern. Moreover, as stem cells divide and form tissues around them, they control the form and the size of regenerating tissues. This two-level organization of the model organism, with global regulation of stem cells and local regulation of tissues, allows its reproducible development and regeneration. (shrink)

In this paper the language of first-order modal logic is enriched with an operator @ ('actually') such that, in any model, the evaluation of a formula @A at a possible world depends on the evaluation of A at the actual world. The models have world-variable domains. All the logics that are discussed extend the classical predicate calculus, with or without identity, and conform to the philosophical principle known as serious actualism. The basic logic relies on the system K, whereas others (...) correspond to various properties that the actual world may have. All the logics are axiomatized. (shrink)

The field of synthetic biology is looking forward engineering framework for safely designing reliable de-novo biological functions. In this undertaking, Computer-Aided-Design environments should play a central role for facilitating the design. Although, CAD environment is widely used to engineer artificial systems the application in synthetic biology is still in its infancy. In this article we address the problem of the design of a high level language which at the core of CAD environment. More specifically the Gubs language is a specification (...) language used to describe the observations of the expected behaviour. The compiler appropriately selects components such that the observation of the synthetic biological function resulting to their assembly complies to the programmed behaviour. (shrink)

The paradoxes about truth are the subject of extensive research. Developing an original approach, this book argues that we should diverge from classical logic and presents a number of formal theories of truth. Also included is a beginner-friendly introduction to semantic paradoxes, and a discussion of alternative non-classical theories.

The classic model of blood pressure regulation by Guyton et al. set a new standard for quantitative exploration of physiological function and led to important new insights, some of which still remain the focus of debate, such as whether the kidney plays the primary role in the genesis of hypertension. Key to the success of this model was the fact that the authors made the computer code freely available and eventually provided a convivial user interface for exploration of model behavior (...) on early microcomputers. Ikeda et al. developed an offshoot of the Guyton model targeting especially the regulation of body fluids and acid–base balance; their model provides extended renal and respiratory functions and would be a good basis for further extensions. In the interest of providing a simple, useable version of Ikeda et al.’s model and to facilitate further such extensions, we present a practical implementation of the model of Ikeda et al., using the ODE solver Berkeley Madonna. (shrink)

In this paper, I investigate a system of quantified modal logic, due in many respects to Bressan (see [2]), from several perspectives -- both semantic and proof-theoretic. As Anderson and Belnap note in [1]: "It seems to be generally conceded that formal systems are natural or substantial if they can be looked at from several points of view. We tend to think of systems as artificial or ad hoc if most of their formal properties arise from some one notational system (...) in terms of which they are described." My efforts in this paper will be in part to lend substantiality to the system in question. Several formulation of the system are given and proved equivalent in appropriate senses. Also, some comments are made concerning possible alternative formulations. (shrink)

In this article we present a new kind of computing device that uses biochemical reactions networks as building blocks to implement logic gates. The architecture of a computing machine relies on these generic and composable building blocks, computation units, that can be used in multiple instances to perform complex boolean functions. Standard logical operations are implemented by biochemical networks, encapsulated and insulated within synthetic vesicles called protocells. These protocells are capable of exchanging energy and information with each other through transmembrane (...) electron transfer. In the paradigm of computation we propose, protoputing, a machine can solve only one problem and therefore has to be built specifically. Thus, the programming phase in the standard computing paradigm is represented in our approach by the set of assembly instructions that directs the wiring of the protocells that constitute the machine itself. To demonstrate the computing power of protocellular machines, we apply it to solve a NP-complete problem, known to be very demanding in computing power, the 3-SAT problem. We show how to program the assembly of a machine that can verify the satisfiability of a given boolean formula. Then we show how to use the massive parallelism of these machines to verify in less than 20 min all the valuations of the input variables and output a fluorescent signal when the formula is satisfiable or no signal at all otherwise. (shrink)

The Enzymatic control reactions model was presented within the scope of fractional calculus. In order to accommodate the usual initial conditions, the fractional derivative used is in Caputo sense. The methodologies of the three analytical methods were used to derive approximate solution of the fractional nonlinear system of differential equations. Two methods use integral operator and the other one uses just an integral. Numerical results obtained exhibit biological behavior of real world problem.

The growth of information acquisition, storage and retrieval capacity has led to the development of the practice of lifelogging, the undiscriminating collection of information concerning one’s life and behaviour. There are potential problems in this practice, but equally it could be empowering for the individual, and provide a new locus for the construction of an online identity. In this paper we look at the technological possibilities and constraints for lifelogging tools, and set out some of the most important privacy, identity (...) and empowerment-related issues. We argue that some of the privacy concerns are overblown, and that much research and commentary on lifelogging has made the unrealistic assumption that the information gathered is for private use, whereas, in a more socially-networked online world, much of it will have public functions and will be voluntarily released into the public domain. (shrink)

The joy of intimacy--with yourself, with others, and with the whole universe. The long-awaited first book from a prominent modern American Zen teacher. For Roshi Pat Enkyo O'Hara, intimacy is what Zen practice is all about: the realization of the essential lack of distinction between self and other that inevitably leads to wisdom and compassionate action. She approaches the practice of intimacy beginning at its most basic level--the intimacy with ourselves that is the essential first step. She then shows (...) how to bring intimacy into our relationships with others, starting with those dearest to us and moving on to those who don't seem dear at all. She then shows how to grow in intimacy so that we include everyone around us, all of society, the whole world and all the beings it contains. Each chapter is accompanied by practices she uses with her students at the Village Zendo for manifesting intimacy in our lives. (shrink)

本書は、2013年4月1日から2015年3月31日までの2年間、『みすず』誌に連載された「日記」を一書にしたものである。大学人としての仕事や作家として執筆に追われながら、政治学者として世の動向を分析し 、皇室の動きを観察し、鉄道旅行をする。日常から時代を解読する試み。.

In recent work MacPherson argues that the standard method of modeling belief logically, as a necessity operator in a modal logic, is doomed to fail. The problem with normal modal logics as logics of belief is that they treat believers as "ideal" in unrealistic ways (i.e., as omnidoxastic); however, similar problems re-emerge for candidate non-normal logics. The authors argue that logics used to model belief in artificial intelligence (AI) are also flawed in this way. But for AI systems, omnidoxasticity is (...) impossible because of their finite nature, and this fact can be exploited to produce operational models of fallible belief. The relevance of this point to various philosophical views about belief is discussed. (shrink)

The word 'actually' often refers to what is in fact the case, but it also often points to what would have been the case in a possible situation that is being envisaged. To capture such nuances, the formal languages discussed in the paper add subscripts to modal operators; in the model theory the subscripts allow an actuality operator to turn the evaluation of a formula to a world introduced by a preceding possibility or necessity operator having the same subscript. The (...) paper covers both propositional and predicate logic and proves the completeness of axiomatizations that extend standard modal systems beginning with K. (shrink)

Shōwashi e no renketsu -- Higashi Ajia kara no me -- Tennō to iu jiba -- Watashi no kaikōki -- Jikokuhyō katate ni ekisoba o.