Silencing trust: confidence and familiarity in re-engineering knowledge infrastructures.

In this paper, we tell the story of efforts currently underway, on diverse fronts, to build digital knowledge repositories ('knowledge-bases') to support research in the life sciences. If successful, knowledge bases will be part of a new knowledge infrastructure-capable of facilitating ever-more comprehensive, computational models of biological systems. Such an infrastructure would, however, represent a sea-change in the technological management and manipulation of complex data, inducing a generational shift in how questions are asked and answered and results published and circulated. Integrating such knowledge bases into the daily workflow of the lab thus destabilizes a number of well-established habits which biologists rely on to ensure the quality of the knowledge they produce, evaluate, communicate and exploit. As the story we tell here shows, such destabilization introduces a situation of unfamiliarity, one that carries with it epistemic risks. It should elicit-to use Niklas Luhmann's terms-the question of trust: a shared recognition that the reliability of research practices is being risked, but that such a risk is worth taking in view of what may be gained. And yet, the problem of trust is being unexpectedly silenced. How that silencing has come about, why it matters, and what might yet be done forms the heart of this paper.

Quantitative estimation of activity and quality for collections of functional genetic elements.

The practice of engineering biology now depends on the ad hoc reuse of genetic elements whose precise activities vary across changing contexts. Methods are lacking for researchers to affordably coordinate the quantification and analysis of part performance across varied environments, as needed to identify, evaluate and improve problematic part types. We developed an easy-to-use analysis of variance (ANOVA) framework for quantifying the performance of genetic elements. For proof of concept, we assembled and analyzed combinations of prokaryotic transcription and translation initiation elements in Escherichia coli. We determined how estimation of part activity relates to the number of unique element combinations tested, and we show how to estimate expected ensemble-wide part activity from just one or two measurements. We propose a new statistic, biomolecular part 'quality', for tracking quantitative variation in part performance across changing contexts.

Building Capacity for a Global Genome Editing Observatory: Conceptual Challenges.

A new infrastructure is urgently needed at the global level to facilitate exchange on key issues concerning genome editing. We advocate the establishment of a global observatory to serve as a center for international, interdisciplinary, and cosmopolitan reflection. This article is the first of a two-part series.

Building Capacity for a Global Genome Editing Observatory: Institutional Design.

A new infrastructure is urgently needed at the global level to facilitate exchange on key issues concerning genome editing. We advocate the establishment of a global observatory to serve as a center for international, interdisciplinary, and cosmopolitan reflection. This article is the second of a two-part series.

Synthetic biology: ethical ramifications 2009.

During 2007 and 2008 synthetic biology moved from the manifesto stage to research programs. As of 2009, synthetic biology is ramifying; to ramify means to produce differentiated trajectories from previous determinations. From its inception, most of the players in synthetic biology agreed on the need for (a) rationalized design and construction of new biological parts, devices, and systems as well as (b) the re-design of natural biological systems for specified purposes, and that (c) the versatility of designed biological systems makes them suitable to address such challenges as renewable energy, the production of inexpensive drugs, and environmental remediation, as well as providing a catalyst for further growth of biotechnology. What is understood by these goals, however, is diverse. Those assorted understandings are currently contributing to different ramifications of synthetic biology. The Berkeley Human Practices Lab, led by Paul Rabinow, is currently devoting its efforts to documenting and analyzing these ramifications as they emerge.