I'm posting for Dave Ardell: 

Dear Colleagues,

I tried to email everyone who was there yesterday, but I may have forgotten someone. if so, please forward this to them.

Thanks for a lively discussion yesterday. I think I am starting to wrap my head around this pillar. I like it. I would like to suggest some additional application areas of what we discussed, and also introduce a well-motivated suggestion for how to extend our pillar to be more inclusive of current biology faculty and synergize with nascent interdisciplinary collaborations on campus. An example of the latter is the recent NSF CREST proposal headed up by Ajay and Victor for a Center for Cellular and Biomolecular Machines (CCBM).  A large and interdisciplinary network of faculty is on that proposal, showing that we have a critical mass in this area of molecular machines across bylaw units and schools.

Additional bullet list items on the materials side:

"smart" materials

regenerative materials

programmable materials

I suggest extending this pillar towards "materials and machines." In our discussion today, I mentioned "agents." Agents are automata, useful models of computers and other artificial machines, but also natural biomolecular machines, cells and whole organisms.

Synthetic biologists program organisms. Not just to synthesize materials within industrial plants. The confluence of SynBio with Biofuels/Bioremediation that we discussed today implies a scaling up in how much we expose substantially engineered Genetically Modified Organisms (GMOs), and the engineered genes that they contain, to the environment and to natural populations. This kind of thing happens already today with headline-grabbing consequences (google "The Frankenfish GM super salmon"). UC Merced can and should lead in this area of how to make synthetic organisms/GMOs/engineered biomaterials *environmentally safe* — safe to the environment and to natural populations. This motivates that we need to include the biology of organisms, populations and communities, as well as environmental science — not just suborganismal biological systems like cells, molecules and materials — in this pillar.

Attending to this directly addresses the pillar of sustainability, because... you can't program a pesticide to stop from diffusing to the north pole. But you can program a frankenfish, a bioremediating agent or biofuel-producing agent to die if it escapes a cage, tank or bounded area.

Since synthetic biologists program organisms, to do SynBio better we must better understand high-dimensional automata. But it isn't only SynBio in our bullet list that motivates the study of automata. Automata, particularly cellular automata, are useful for modeling materials and other complex physical systems. Automata and materials complement each other. This provides a triangulation of our theme and "closes" our research interests.

On the machines/automata side, and crossing to the materials side, I have some additional suggestions:

liquid and cellular automata

molecular machines

macromolecular interactions

network biology

natural computation

quantum computers

physics of computation

automata theory

It was a telling moment when the taboo word "biomedical" came up. Let us please not shy away from biomedical applications in this pillar. We have excellent MCB faculty who would be valuable partners in bringing innovations in materials and machines to new and improved biomedical interventions. Also, current synthetic biology faculty in MCB and Engineering address biomedical applications in their research. We should extend the benefits of our pillars of excellence as broadly as possible to have the greatest impact.

Thanks and Cheers,

Dave

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David H. Ardell

Chair, Graduate Group in Quantitative and Systems Biology

5200 North Lake Road, School of Natural Sciences, University of California, Merced CA 95343

office: SE 228 // (209) 228-2953 // fax: (209) 228-4675 // http://compbio.ucmerced.edu/ardell