Archive by category | Synthetic

SB 3.0 day 3”

The Synthetic Biology 3.0 meeting ended yesterday with a closing keynote lecture by Tom Knight. In his lecture, Tom Knight explained how engineering principles can or could be applied in synthetic biology to facilitate assembly of “new systems that never existed in nature in a productive and safe way”. Key notions are the principles of hierarchical abstraction, modularity, standardization and flexibility. Defining appropriate levels of abstraction in the description and design of biological objects is essential to cope with the otherwise daunting complexity, says Tom Knight. The power of these concepts was illustrated by showing the many levels of abstraction used in electronics and computer science: at the top of the hierarchy are concepts as used at the level of application software, operating system and programming languages while the lowest levels of abstraction go progressively down to the levels of processing unit, logic gates, semiconductor physics and ultimately quantum mechanics at the very bottom of the hiearchy.  Read more

SB 3.0 day 3′

Ron Weiss just gave his talk at SB 3.0 on the application of synthetic circuits to control stem cell differentiation. Ron Weiss has already elegantly shown how synthetic circuits coupled to cell-cell communication can generate pattern forming multicellular systems (Basu et al, 2005). This previous work was performed in yeast and Ron now plans to port it to mamamlian stem cells. Pattern formation is crucial in developmental processes and the hope is that the synthetic approach will not only help to control and use stem cell differentiation and patterning but will also provide insight into the endogenous specification/differentiation mechanisms. One of the application envisioned is to develop a system regulating differentiation of pancreatic beta cells in function of cell density to enable a kind of “synthetic” homeostasis able to compensate autoimmune attacks in type I diabetes.  Read more

SB 3.0 day 3

How to develop organisms with modified and extended genetic codes? Can bacteria be evolved to replace given metabolic pathways by “exotic” alternative ones or eliminate altogether given amino acids from the entire proteome? These were the topics of a few talks presented at the third Synthetic Biology conference, Zurich, Switzerland.  Read more

SB 3.0 day 2

“Life, like a machine, cannot be understood simply by studying it and its parts; it must also be put together from its parts. Along the way to synthesizing a cell, we might discover new biochemical functions essential for replication, unsuspected macromolecular modifications or previously unrecognized patterns of coordinated expression.” (Forster and Church, 2006) .  Read more

SB3.0 day 1

Today was the first day of the Synthetic Biology 3.0 conference, held this year in Zurich and organized by Sven Panke, Matthias Heinemann, Jörg Stelling and Martin Fussenegger. For those who would like to have a definition of what Synthetic Biology is, there are very instructive explanations here by Drew Endy.  Read more

Oversight framework for the DNA-synthesis industry

Oversight framework for the DNA-synthesis industry

Last April, the US National Science Advisory Board for Biosecurity issued a draft report on Biosecurity (see post below). One point of criticism expressed with regard to this report was that it did not address explicitly concerns specific to synthetic biology. In a Commentary published in Nature Biotechnology (Bügl et al, 2007), a panel of scientists, executives from the DNA-synthesis industry and members of the US FBI present now their views and concrete recommendations on measures required for an efficient and practical oversight of DNA-synthesis activities. Rapid progresses in DNA-synthesis technologies are increasingly challenging the current safety measures and oversight  … Read more

Open Source Synthetic Biology

Open Source Synthetic Biology

In a News&Views just published in Molecular Systems Biology, Joachim Henkel & Stephen Maurer expose their views on the economics of synthetic biology (Henkel and Maurer, 2007): Synthetic biology contains almost all of the same ingredients that make embedded Linux successful. First, synthetic biology’s parts approach emphasizes strong modularity. This allows the work of creating a parts library to be spread over many companies. It also makes it possible for companies to earn profits by patenting some parts while making others openly available. Second, we expect companies to have fairly idiosyncratic parts needs. This means that they cannot simply ‘free  … Read more

Systems biology & global warming

Systems biology & global warming

Observations suggest that current climatic models may underestimate how quickly the climate system is changing (in particular for sea level), according to a report in Science a few weeks ago (Rahmstorf et al, 2007). Another Science paper published last week shows that the capacity of the Southern Ocean CO2 sink is weakening, which may result in increased atmospheric CO2 levels in the long run (Le Quere et al, 2007). I remember Hiroaki Kitano calling the systems biology community, in his talk at the ICSB meeting last October in Yokohama, for ideas on how system-level approaches could contribute to address the  … Read more

Wikification: will 2007 be a good “millésime”?

Wikification: will 2007 be a good "millésime"?

Literature reviews invariably get outdated. Could reviews benefit from being hosted within a wiki environment (be “wikified”) and kept up-to-date by the community? This is the experiment the Openwetware community has just started on the OWWReviews page (see also post on Public Rambling). One of the first articles selected for this interesting project is Ron Weiss’ review on synthetic biology (Andrianantoandro et al, 2006, Mol Syst Biol 2:2006.0028) published in Molecular Systems Biology last year. It will be interesting to follow the evolution of this derivative work and see how new knowledge is incorporated but also how the community deals  … Read more