Endy:Who rules the forest?

Synbiotic: Social Study of Synthetic Biology

This page is dedicated to the anthropology study of synthetic biology

Sophia Roosth is driving this project.

Questions for open discussion

These are just to get everyone started—feel free to add whatever you like...

• What does it mean to standardize biological parts? What is the metric with which to measure standards?
  • The motivation for standardization is to enable biological parts to be used in composition with eachother. So if I design a part at MIT and someone else designs a part at UT-Austin, a third person from somewhere else can combine those parts and make use of them because they adhere to some standard. Thus one metric for a standard is how easily it facilitates this goal of interoperability. Note that there are several classes of standards that one could imagine would be useful: fabrication standards (i.e. BioBricks assembly) and performance standards to name a couple. --Reshma

• What is the disciplinary genealogy of synthetic biology? Which fields did it arise out of, and how does it differ from those previous fields?
  • The beginnings of an answer to this question are now online here.
  • In some sense synthetic biology currently is the application of engineering ideas (like abstraction, decoupling, standardization) to the science of biology. Thus, it has its roots in both engineering disciplines (in terms of ideas and approach) and in biology (in terms of substrate and many techniques). --Reshma

• What made it necessary for synthetic biology to become its own field, and what circumstances (technological advances, scientific goals, etc) made it possible to do synthetic biology?
  • Cheap and fast sequencing and synthesis of DNA are a couple of the critical technologies for synthetic biology. --Reshma

• How did you come to study synthetic biology? How did you first hear or come to think of what you’re doing as synthetic biology?
  • Frustration with unpredictability and limitations of 'normal' recombinant DNA work led me to start doing more modeling-type stuff. Frustration with the lack of tangible outcomes in modeling led me to synthetic biology. The idea of starting with simple systems and trying to get a toehold where biology was designable and predictable was very appealing. -- JK

• How useful is it to differentiate between living and non-living systems? Are there any problems or benefits specific to engineering living systems which do not arise in conventional engineering?
  • I think it's useful to differentiate self-replicating systems from those that don't self-replicate. ('living' might be defined as self-replication with errors, you can get more information about that here.) There are many problems/benefits to engineering self-replicating systems:
  1. Usually piggy-backing a system onto a cellular host - need to deal with engineering interactions between designed system and a very complicated, poorly-understood chassis .
  2. Errors in replication need to be controlled/predicted to determine expected failure rates
  3. Can presumably use evolution as a design tool
  4. others?

--JK

• How do you take into account evolution and mutation when designing living systems?
  • Right now we don't very much, although we are beginning to think about it. For most applications we would likely want to suppress mutation to ensure long-term reliable performance. However, you could imagine situations where you might want to increase the mutation rate as well - to break a system after a certain period of time for instance. We are also looking into using 'directed' evolution as a design tool. --JK

• Why is T7.x a model, and what is it a model of?

• Your lab organizes itself around the ethos of Creative Commons (BioBricks, OpenWetWare, etc.). How do you see this open approach to research as related to synthetic biology—is there anything specific about synthetic biology which lends itself to the Open Source philosophy?
  • There are three aspects of synthetic biology that ties it to an open approach to research. 1) Synthetic biology has a tremendous potential application space. However, like any technology, there is the possibility of abuse/misuse whether by intention or by accident. Thus, in my mind the most responsible thing synthetic biologists can do is carry out the work in as open as environment as possible. Such an environment enables more rapid detection of issues in the work and more rapid mobilization of resources in response to risks. 2) Since synthetic biology is still a relatively new field, we have some choice over the direction the culture of the field takes. Thus, we're trying to foster a field in which people feel comfortable sharing their work and ideas as early and as much as possible. 3) Another contributing factor is that synthetic biology at MIT has ties with people like Gerry Sussman and Hal Abelson who were key players in the Free Software Foundation. The involvement of these people has also had an impact on the group's thinking. --Reshma

• What is the difference between a part, a device, and a system?
  • The beginnings of an answer to this question are posted here.

• When discussions about the ethical and social implications of synthetic biology come up in the lab, what sorts of issues or concerns are voiced?

• What are the questions you think I should be asking?

From Seed Magazine

Synthetic biology is this month's entry for the column 'Nomenclature--Term On the Tipping Point'...

"Synthetic biology--the discipline devoted to the study and creation of artificial life.

In June 2004, a small group of biologists gathered at MIT for a conference with an intriguing title: Synthetic Biology 1.0. The juxtaposition of "synthetic" with "biology"--which, at its simplest, means "the science of life"--seems an oxymoron. But for scientists, the term was perfectly accurate. It defined a nascent discipline that aims to synthesize life from the existing pieces of a biological system.

The term 'synthetic biology' first appeared in scientific literature in 1980, but it wasn't until the millennium that it took on its current meaning. By then, biologists had begun to modify living organisms through genetic engineering. For some, its cut-and-paste technique fell short. These researchers believed that the best way to understand a complex structure was to try to create it from scratch. So, using functional bits of DNA as their raw building blocks, they began to design organisms from the bottom up.

These 'synthetic biologists' have claimed that they may produce new life in a lab and, in so doing, better comprehend how life evolved. Maverick geneticist J. Craig Venter is convinced that, by harnessing a cell's energy-producing mechanism, he can create organisms that manufacture alternative fuels. His institute is hoping to program artificial bacteria to combat disease. It remains to be seen whether synthetic biologists will succeed, but if they do, they may radically redefine life as we know it."

Below the column is a strange little cartoon that looks like a computer attached to someone's liver? Right.

So, I was curious to hear everyone's take on this definition...thoughts?

Life Engineering Symposium--Rabinow talk

and if anyone is interested in Paul Rabinow's talk at the Life Engineering Symposium last August, but doesn't want to sit down and listen to the whole recording, i condensed the lecture into 4 pages of notes. the cost of reading these notes is giving me your opinion of his talk...

Lab Wildlife

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