ABSTRACT

One of the motivations behind computing with molecules is to "computerize" living systems, for example to prevent disease or control artificial tissues. Biology, however, is already very good at computing - the human brain being one example. Even on a single cell level information is constantly being processed, and the development of a functional organism from a single fertilized cells is controlled by an ingenious if only partially understood program encoded in DNA. Does this mean that the efforts to "write" new molecular programs are redundant? Not at all - natural programs have taken three billion years to evolve and, despite their beauty, are very difficult to alter in any way.

In my view the optimal approach is to balance the engineering principles inspired by computer science and engineering such as universal models, reprogrammability, modularity, etc., with the harsh reality of cell and organismal biology. The simple fact is that we do not know yet, even at the theory level, whether it is possible to perform reliable information processing in actual living cells as opposed to idealized "well-mixed reactors". Despite these limitations, the field of molecular computing in cells, or biological computing, has made significant steps forward with new design principles, new architectures, and new exciting experimental results. These developments also inform basic biological research.

In my talk I will address the challenges of computing in cells and use examples from our work and work of others in the field to highlight the progress but also point out what yet needs to be solved. I will also address the need for new computational tools and design frameworks to support this engineering effort.

BIOGRAPHY

Yaakov (Kobi) Benenson early work focused on molecular-scale computing systems. He co-developed a prototype biomolecular computing device made of DNA and enzymes, and later upgraded the device to perform diagnostics using molecular disease markers. This work was recognized by the Feinberg Graduate School's Kennedy Award and the Wolf Foundation. Dr. Benenson was also selected by the MIT Technology review magazine as one the world's top 100 young innovators for the year 2004.
In 2005 Kobi Benenson moved to Harvard University to take an independent position as a Bauer Fellow at the FAS Center for Systems Biology. In collaboration with the Weiss lab (MIT), Benenson lab pioneered an RNA interference-based approach to molecular computing in mammalian cells. Nowadays this method is successfully being used to construct increasingly complex synthetic circuits for the benefit of basic science as well as biotechnology and biomedicine. Benenson joined ETH in 2010 to establish a Synthetic Biology group at the Department of Biosystems Science and Engineering in Basel. The group will continue to pursue cutting edge research in synthetic biology and focus on applying the concepts of biological computing to problems in medicine.