Towards Understanding the Origin of Genetic Languages

Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from viruses and bacteria to human beings. Advances in genetics and experience in designing computers have taken us to a stage where we can understand the optimisation principles at the root of this system, from the availability of basic building blocks to the execution of tasks. The languages of DNA and proteins are argued to be the optimal solutions to the information processing tasks they carry out. The analysis also suggests simpler predecessors to these languages, and provides fascinating clues about their origin. Obviously, a comprehensive unraveling of the puzzle of life would have a lot to say about what we may design or convert ourselves into.Comment: (v1) 33 pages, contributed chapter to "Quantum Aspects of Life", edited by D. Abbott, P. Davies and A. Pati, (v2) published version with some editin

Synthetic biology—putting engineering into biology

Synthetic biology is interpreted as the engineering-driven building of increasingly complex biological entities for novel applications. Encouraged by progress in the design of artificial gene networks, de novo DNA synthesis and protein engineering, we review the case for this emerging discipline. Key aspects of an engineering approach are purpose-orientation, deep insight into the underlying scientific principles, a hierarchy of abstraction including suitable interfaces between and within the levels of the hierarchy, standardization and the separation of design and fabrication. Synthetic biology investigates possibilities to implement these requirements into the process of engineering biological systems. This is illustrated on the DNA level by the implementation of engineering-inspired artificial operations such as toggle switching, oscillating or production of spatial patterns. On the protein level, the functionally self-contained domain structure of a number of proteins suggests possibilities for essentially Lego-like recombination which can be exploited for reprogramming DNA binding domain specificities or signaling pathways. Alternatively, computational design emerges to rationally reprogram enzyme function. Finally, the increasing facility of de novo DNA synthesis—synthetic biology’s system fabrication process—supplies the possibility to implement novel designs for ever more complex systems. Some of these elements have merged to realize the first tangible synthetic biology applications in the area of manufacturing of pharmaceutical compounds.

Systematic evaluation of design choices for software development tools

[Abstract]: Most design and evaluation of software tools is based on the intuition and experience of the designers. Software tool designers consider themselves typical users of the tools that they build and tend to subjectively evaluate their products rather than objectively evaluate them using established usability methods. This subjective approach is inadequate if the quality of software tools is to improve and the use of more systematic methods is advocated. This paper summarises a sequence of studies that show how user interface design choices for software development tools can be evaluated using established usability engineering techniques. The techniques used included guideline review, predictive modelling and experimental studies with users

Intellectual property rights in a knowledge-based economy

Intellectual property rights (IPR) have been created as economic mechanisms to facilitate ongoing innovation by granting inventors a temporary monopoly in return for disclosure of technical know-how. Since the beginning of 1980s, IPR have come under scrutiny as new technological paradigms appeared with the emergence of knowledge-based industries. Knowledge-based products are intangible, non-excludable and non-rivalrous goods. Consequently, it is difficult for their creators to control their dissemination and use. In particular, many information goods are based on network externalities and on the creation of market standards. At the same time, information technologies are generic in the sense of being useful in many places in the economy. Hence, policy makers often define current IPR regimes in the context of new technologies as both over- and under-protective. They are over-protective in the sense that they prevent the dissemination of information which has a very high social value; they are under-protective in the sense that they do not provide strong control over the appropriation of rents from their invention and thus may not provide strong incentives to innovate. During the 1980s, attempts to assess the role of IPR in the process of technological learning have found that even though firms in high-tech sectors do use patents as part of their strategy for intellectual property protection, the reliance of these sectors on patents as an information source for innovation is lower than in traditional industries. Intellectual property rights are based mainly on patents for technical inventions and on copyrights for artistic works. Patents are granted only if inventions display minimal levels of utility, novelty and non-obviousness of technical know-how. By contrast, copyrights protect only final works and their derivatives, but guarantee protection for longer periods, according to the Berne Convention. Licensing is a legal aid that allows the use of patented technology by other firms, in return for royalty fees paid to the inventor. Licensing can be contracted on an exclusive or non-exclusive basis, but in most countries patented knowledge can be exclusively held by its inventors, as legal provisions for compulsory licensing of technologies do not exist. The fair use doctrine aims to prevent formation of perfect monopolies over technological fields and copyrighted artefacts as a result of IPR application. Hence, the use of patented and copyrighted works is permissible in academic research, education and the development of technologies that are complimentary to core technologies. Trade secrecy is meant to prevent inadvertent technology transfer to rival firms and is based on contracts between companies and employees. However, as trade secrets prohibit transfer of knowledge within industries, regulators have attempted to foster disclosure of technical know-how by institutional means of patents, copyrights and sui-generis laws. And indeed, following the provisions formed by IPR regulation, firms have shifted from methods of trade secrecy towards patenting strategies to achieve improved protection of intellectual property, as well as means to acquire competitive advantages in the market by monopolization of technological advances.economics of technology ;

Integration of BPM systems

New technologies have emerged to support the global economy where for instance suppliers, manufactures and retailers are working together in order to minimise the cost and maximise efficiency. One of the technologies that has become a buzz word for many businesses is business process management or BPM. A business process comprises activities and tasks, the resources required to perform each task, and the business rules linking these activities and tasks. The tasks may be performed by human and/or machine actors. Workflow provides a way of describing the order of execution and the dependent relationships between the constituting activities of short or long running processes. Workflow allows businesses to capture not only the information but also the processes that transform the information - the process asset (Koulopoulos, T. M., 1995). Applications which involve automated, human-centric and collaborative processes across organisations are inherently different from one organisation to another. Even within the same organisation but over time, applications are adapted as ongoing change to the business processes is seen as the norm in today’s dynamic business environment. The major difference lies in the specifics of business processes which are changing rapidly in order to match the way in which businesses operate. In this chapter we introduce and discuss Business Process Management (BPM) with a focus on the integration of heterogeneous BPM systems across multiple organisations. We identify the problems and the main challenges not only with regards to technologies but also in the social and cultural context. We also discuss the issues that have arisen in our bid to find the solutions

Concurrentie, innovatie en intellectuele eigendomsrechten in software markten

This study analyzes under which circumstances it may be desirable for the government to stimulate open source software as a response to market failures in software markets. To consider whether policy intervention can increase dynamic efficiency, we discuss the differences between proprietary software and open source software with respect to the incentives to innovate and market failures that may occur. The document proposes guidelines to determine which types of policy intervention may be suitable. Our most important finding is that directly stimulating open source software, e.g. by acting as a lead customer, can improve dynamic efficiency if (i) there is a serious customer lock-in problem, while (ii) to develop the software, there is no need to purchase specific, complementary inputs at a substantial cost, and (iii) follow-on innovations are socially valuable but there are impediments to contractual agreements between developers that aim at realizing such innovations. This publication is in Dutch.