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)

New concepts may prove necessary to profit from the avalanche of sequence data on the genome, transcriptome, proteome and interactome and to relate this information to cell physiology. Here, we focus on the concept of large activity-based structures, or hyperstructures, in which a variety of types of molecules are brought together to perform a function. We review the evidence for the existence of hyperstructures responsible for the initiation of DNA replication, the sequestration of newly replicated origins of replication, cell division (...) and for metabolism. The processes responsible for hyperstructure formation include changes in enzyme affinities due to metabolite-induction, lipid-protein affinities, elevated local concentrations of proteins and their binding sites on DNA and RNA, and transertion. Experimental techniques exist that can be used to study hyperstructures and we review some of the ones less familiar to biologists. Finally, we speculate on how a variety of in silico approaches involving cellular automata and multi-agent systems could be combined to develop new concepts in the form of an Integrated cell (I-cell) which would undergo selection for growth and survival in a world of artificial microbiology. (shrink)

Following a previous article published in Biological Theory, in this study we present a mathematical theory for a science of qualities as directly perceived by living organisms, and based on morphological patterns. We address a range of qualitative phenomena as observables of a psychological system seen as an impredicative system. The starting point of our study is the notion that perceptual phenomena are projections of underlying invariants, objects that remain unchanged when transformations of a certain class under consideration are applied. (...) The study develops with the observables, the entailed total order and metric, whence the algebra and the geometry of such a science, presenting a formal phenomenological model for phenomena that are not rigidly Euclidean. We show how non-Euclidean perception can have many useful Euclidean formalizations, as well as locally-homeomorphic-to-Euclidean-space models. The mathematical models we provide are tested on the basis of results from experimental psychology, in particular from the field of color, time, and space perception. (shrink)

This paper offers a new concept of the firm that aims at balancing the corporate economic, social, and environmental responsibilities and goes beyond the stakeholder approach. It intends to provide a conceptual and operationalizable basis to fairly assess corporate conduct from both inside and outside the companies. To a large extent these different responsibilities may overlap and reinforce each other. However, if they conflict, they should be clearly evaluated for their own sake and in terms of wealth creation. Only then (...) can a balanced approach be realized. Section 1 briefly discusses some general aspects of the relationship between concepts and measurement. In Section 2, a concept of the firm is developed that is based on the notion of responsibility and balances economic, social and environmental responsibilities. According to these concepts, different ways of measuring corporate planning and performance are examined in Section 3, followed up by a summary and conclusions. (shrink)

I have enjoyed my six years as editor of this journal. I was pleased to be able to bring the journal to Purdue University Press and learn how to produce a first-rate academic journal. From the early days of choosing a cover design, to supervising my graduate assistant Jiwon Kim as she expertly sought indexing services, to acquiring an ISSN number, to being lucky to convince David Granger to become the book review editor and, with the next issue, editor, I (...) have been fortunate to work with excellent colleagues. I particularly want to thank the staff at Purdue University Press, especially its former director, Thomas Bacher, who agreed to publish the journal in 2004. Tom later moved the management of the journal's .. (shrink)

This article focuses on the legal and organisational regulation of human cells in the United Kingdom and France. French Bioethics Law regulates human cells for health according to European Union law where it is enforceable. But products unregulated by EU law and based on human cells are never considered as medicinal products, given the strict implementation of the principle of “nonpatrimonialité” of the human body and its elements. By comparison, in the UK such products can be qualified as medicinal products. (...) Moreover, the setting up of the UK stem cell bank gives rise to the development of policies which expand the stem cell as a legal object. The paper discusses how these societies’ ethical and legal commitments underlie organisational practices in order to analyse the relationship between the existence (or not) of a national stem cell bank and the broader regulation of human cells. (shrink)

Background: Only data of published study results are available to the scientific community for further use such as informing future research and synthesis of available evidence. If study results are reported selectively, reporting bias and distortion of summarised estimates of effect or harm of treatments can occur. The publication and citation of results of clinical research conducted in Germany was studied.Methods: The protocols of clinical research projects submitted to the research ethics committee of the University of Freiburg in 2000 were (...) analysed. Published full articles in several databases were searched and investigators contacted. Data on study and publication characteristics were extracted from protocols and corresponding publications.Results: 299 study protocols were included. The most frequent study design was randomised controlled trial , followed by uncontrolled studies , laboratory studies and non-randomised studies . 182 were multicentre studies including 97 international collaborations. 152 of 299 had commercial funding and 46 non-commercial funding. 109 of the 225 completed protocols corresponded to at least one full publication ; the publication rate was 48%. 168 of 210 identified publications were cited in articles indexed in the ISI Web of Science. The median was 11 citations per publication .Conclusions: Results of German clinical research projects conducted are largely underreported. Barriers to successful publication need to be identified and appropriate measures taken. Close monitoring of projects until publication and adequate support provided to investigators may help remedy the prevailing underreporting of research. (shrink)