Grounding knowledge and normative valuation in agent-based action and scientific commitment

Philosophical investigation in synthetic biology has focused on the knowledge-seeking questions pursued, the kind of engineering techniques used, and on the ethical impact of the products produced. However, little work has been done to investigate the processes by which these epistemological, metaphysical, and ethical forms of inquiry arise in the course of synthetic biology research. An attempt at this work relying on a particular area of synthetic biology will be the aim of this chapter. I focus on the reengineering of metabolic pathways through the manipulation and construction of small DNA-based devices and systems synthetic biology. Rather than focusing on the engineered products or ethical principles that result, I will investigate the processes by which these arise. As such, the attention will be directed to the activities of practitioners, their manipulation of tools, and the use they make of techniques to construct new metabolic devices. Using a science-in-practice approach, I investigate problems at the intersection of science, philosophy of science, and sociology of science. I consider how practitioners within this area of synthetic biology reconfigure biological understanding and ethical categories through active modelling and manipulation of known functional parts, biological pathways for use in the design of microbial machines to solve problems in medicine, technology, and the environment. We might describe this kind of problem-solving as relying on what Helen Longino referred to as “social cognition” or the type of scientific work done within what Hasok Chang calls “systems of practice”. My aim in this chapter will be to investigate the relationship that holds between systems of practice within metabolic engineering research and social cognition. I will attempt to show how knowledge and normative valuation are generated from this particular network of practitioners. In doing so, I suggest that the social nature of scientific inquiry is ineliminable to both knowledge acquisition and ethical evaluations

Ocean Governance

There are a range of legal instruments, institutions, and organizations that collectively establish rules and policies for managing, conserving, and using the ocean. The United Nations Convention on the Law of the Sea (UNCLOS) provides the overarching legal framework for ocean governance and management on a global scale, but there are a number of other important ocean governance-related institutions, instruments and processes. This document provides a brief overview of those institutions and processes that are most relevant to multi-sectoral business and industry interests, with a particular emphasis on opportunities for industry to get involved in the policy-making process. It does not include policies, institutions, and processes that are primarily relevant to a single sector. After first reviewing key aspects of UNCLOS, this document discusses other key ocean policy and governance processes and bodies

The city of future: biourbanism and constructural law

Nowadays dynamic elements in urban fabric are often concealed by the insertion of stylish new architecture; real patterns of social life (‘bios’), have been replaced by rigid geometric grids and compact building blocks. New Urbanism and Biourbanism affirm that cities are now risking to be unstable and deprived of healthy social interactions. As an expansion of older historical urban fabric patterns, harmonious architecture can have a positive impact on the fitness of both human body and mind. Not only Biourbanism attempts to reinstate balance and lost values in the urban fabric, but also reinforces human-oriented design emergences in micro and macro scales. As a multifaceted discipline, it embraces laws of physics, such as Constructal Law and acknowledges its noticeable and unremitting influence to urban human behaviours. Urban life and behaviours are based upon systems of human communication formed by dynamic patterns; we are now talking about negotiating boundaries between human activities, changes in geographic mapping and mainly about sustainable systems to support uninterrupted growth of communities worldwide. Therefore, as a vital shift in architectural education, not only Biourbanism offers the opportunity to explore patterns and linguistics deeply imbedded into the built environment, but also enables scholars and communities to come together and participate actively into fast and innovative urban interventions. Projects developed during educational and professional training aim at reinstating memorable and preferential paths of communication, favouring everyday life rituals of the body and mind. Hence, by following everlasting laws of physics and formulas inherited from nature, architectural forms can be considered as the real innovation in urban design and planning of the City of the Future.Conference presentation funded by Department of Engineering

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie

Neural Mechanisms for Information Compression by Multiple Alignment, Unification and Search

This article describes how an abstract framework for perception and cognition may be realised in terms of neural mechanisms and neural processing. This framework — called information compression by multiple alignment, unification and search (ICMAUS) — has been developed in previous research as a generalized model of any system for processing information, either natural or artificial. It has a range of applications including the analysis and production of natural language, unsupervised inductive learning, recognition of objects and patterns, probabilistic reasoning, and others. The proposals in this article may be seen as an extension and development of Hebb’s (1949) concept of a ‘cell assembly’. The article describes how the concept of ‘pattern’ in the ICMAUS framework may be mapped onto a version of the cell assembly concept and the way in which neural mechanisms may achieve the effect of ‘multiple alignment’ in the ICMAUS framework. By contrast with the Hebbian concept of a cell assembly, it is proposed here that any one neuron can belong in one assembly and only one assembly. A key feature of present proposals, which is not part of the Hebbian concept, is that any cell assembly may contain ‘references’ or ‘codes’ that serve to identify one or more other cell assemblies. This mechanism allows information to be stored in a compressed form, it provides a robust mechanism by which assemblies may be connected to form hierarchies and other kinds of structure, it means that assemblies can express abstract concepts, and it provides solutions to some of the other problems associated with cell assemblies. Drawing on insights derived from the ICMAUS framework, the article also describes how learning may be achieved with neural mechanisms. This concept of learning is significantly different from the Hebbian concept and appears to provide a better account of what we know about human learning