Berkeley Engineering Blogs

CNN reported briefly on a conference which took place at Oxford University from July 16 to July 20 called the Global Catastrophic Risk Conference.  The focus of the article, entitled “Scientists:  Humans and machines will merge in future,” was mostly on the viewpoints of two participants of the conference, Drs. Nick Bolstrom and Ray Kurzweil, whose perspectives were distinctly geared towards the inevitability of this human-technology merger and provoked fear in the reader about a foreseeable possibility of “the extinction of the human species” if something goes catastrophically wrong as we get closer to being “posthuman”–or “beings that possess qualities and skills so exceedingly advanced [as a result of technology] they no longer can be classified simply as humans.”  Bolstrom and Kurzweil describe themselves as “transhumanists“–part of “a movement that advocates not only the study of the potential threats and promises that future technologies could pose to human life but also the ways in which emergent technologies could be used to make the very act of living better.”  Transhumanists, Bolstrom tells us, “want to preserve the best of what it is to be human and maybe even amplify that.”

But what is the “best of what it is to be human?”  Who decides what this “best” is?  According to Bolstrom and Kurzweil, this isolation and amplification of the best of being human includes a longer lifespan and superintelligence which “could be capable of solving many of our biggest threats, like environmental destruction, poverty and disease.”  But, as can be observed in readers’ commentary at the bottom of the page, this is not everyone’s “best.”  One reader remarked that “with our world in such rapid demise due to overpopulation, environmental over-extension and human self-interest, we need to focus on restoring the natural balance, not escalating the technological divide between ourselves and nature.”

Additionally, Kurzweil’s emphasis on eventual and inevitable human superintelligence in parallel with the advancement of technology as the solution to all of our current problems (ie:  environmental destruction, poverty, and disease) highlights a frequently and strongly held belief:  that science will solve all of our problems.  But what happens when we call environmental destruction, poverty, and disease “solvable problems?”  Are such problems really “solvable,” like a mathematical equation is solvable?  These human and geological realities have infinite externalities and particularities in a world of more than 6 billion people, with different cultural norms, political systems, and environmental perspectives.  Describing them as solvable problems creates a frame around them which implicitly decides unthinkable parameters:  What would these “solutions” look like?  What would the world look like after such “solutions” were implemented and when could we say that the problems are solved?  Who would decide on these solutions?  Who would benefit?  Who would be overlooked?

For example, tying this to the “best of” question, aiming for increased life expectancy of populations in Namibia certainly avoids the question of what the quality of those lives would be–another “problem” (quality of life) not even approached by Kurzweil in his assessment of the main problems of humanity.  Or perhaps he is tying quality of life to the “solvable problem” (that is, with our superintelligence) of poverty.  It is here that we see the biggest fault with this argument:  the technologies that he and other transhumanists see as inevitable are born into a world with established power structures–with those who choose which problems will be “solved” being those who will find those “solutions.”

We can see parallels of this in the world of synthetic biology, a field which is mandated to “solve real-world problems through the design of novel organisms and biologically-inspired systems.”  There is no separation between the research done under the banner of synthetic biology and the “problems” in the “real world” its leaders and funders have decided are approachable and “solvable.”  Sythetic biology forefather Drew Endy discussed what he saw as the foreseeable possibilities of catastrophic risks (framed as the only real problems involved with doing research in the synthetic biology field), which could be consequences of synthesizing DNA into novel or manipulated organisms, as the possibilities of “nefarious forces” getting a hold of the means to make dangerous organisms.  Overlooked are questions of accidental contamination or manipulation and questions of how these “solutions” will actually impact the populations they seek to impact.

Restricting the frame of problems and solutions is a direct result of writing proposals for funders, but mediating questions of consequences goes far and away beyond questions of how to keep “nefarious forces” from gaining access of tools of DNA manipulation.

Hey all,

Testing sessions were a mix between fun and some kind of crazy. I stayed up til about 5AM to prepare for the 1st testing session! Though I must admit, I’m normally up til about 3AM. Anyway, enjoy the visuals. I’ll be introducing my teammates along the way, and of course the software testers!

Left: Anne Van Devender, teammate. Right: Doug Densmore, advisor. We’re waiting for the testers, and it looks like we’re pretty excited to begin.

Left: Matthew L.E. Johnson, teammate. Middle: Anne. Right: Doug. I believe Matt’s starting up Clotho, and we’re all watching quietly.

Left: Matt. Right: Dirk VandePol, wetlab teammate. Dirk was the third tester of Clotho, and is a high school teacher, to my knowledge. Matt’s currently assisting him with the Clotho SequenceView.

Left: Doug, Right: Cici. Cici is one of the wetlab members as well. She’s a high school student, one of the only two on the wet team.

A bunch of people. Right now we’re gathering everyone’s final remarks from the very first testing session. Dr. Chris Anderson (leftmost) is explaining what he sees as the greatest asset behind Clotho, which is its eventual connectivity and seamlessness between different pre-existing tools.

The one and only picture I have so far posted of our second testing session. I was mostly busy this testing session, so I had less pictures to choose from. You can see we moved up to a conference room, as opposed to our student offices :).

Hello All,

My name is Nade Sritanyaratana and I’m one of the members of the 2008 Cal iGEM Computational Tools Team! Mouthful, I know. I’m a 3rd year undergraduate at Berkeley in Bioengineering, and (to those wondering about Cal life) it’s been an amazing three years. I’ve been holding back on posting on the blog, because during the time we gained access to the blog our team was mad crazy programming to prepare for our testing sessions (which have just passed).

A little bit about our project. For those techies that want to know about the infrastructure as well, you can go here: http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development

For everyone else, here’s the quick description :). Synthetic biology is getting large. Very large. There are now so many biological DNA parts in various databases that it’s getting very difficult to organize them all. And there are a growing number of computer programs out there that edit DNA sequences, provide different ways of looking at DNA (other than your standard ACTG), etc. Our project hopes to consolidate all these tools into one nice working environment, kind of the same way Adobe Photoshop brings together many tools for a consolidated imaging program.

What can you expect from my posts? Lots of pictures. And if coding doesn’t keep me busy (as it already does), then hopefully a balanced amount of writing. I won’t write as much as the two under me, and I’ve got to admit they’re more amazing with this blog than I. Keep tuned for my next post (which will probably come up in the next few minutes) for pictures of my team, and pictures of our first two testing sessions.

Signing out,

Nade Sritanyaratana

This year’s dual-sided iGEM project at UC Berkeley is headed by Chris Anderson, Terry Johnson, Megan Dueck, and Doug Densmore.  Whereas last year’s two Berkeley teams addressed specific problems in the medical world—one of which was the lack of low-cost and wide access to plasma for blood transfusions, whose project was affectionately called Bactoblood, the two teams under Berkeley’s header this year are attempting to ameliorate the actual processes used to do synthetic biology.

Lysophonix, the project belonging to the “wet team,” is looking at ways to make bacteria burst open in response to sound—not just specifically to ultrasound but to the sound of any full-length album that the lab researcher may want to blast that day—so that the process of part assembly may be more cleanly streamlined and efficient.  The idea would be that the correct amount of reagents needed to cut a plasmid at certain locations (here:  enzyme restriction sites) would be found within a bacteria, along with the part in a plasmid-to be mixed with a different bacteria that has reagents and the plasmid where the part is meant to be put.  This sound induced lysis would allow the assembly of parts to be less abrasive to the proteins involved and the process would allow for more efficient assembly.

Likewise, Berkeley’s “computational team” is working on a better version of ApE (A Plasmid Editor)-the DNA sequencing program that most manipulators of DNA are dependent upon-called Clotho, cleverly named after the youngest of the fates of Greek mythology.  Their goal is to make a more user-friendly and comprehensive software program that would interface with BioBricks or a similar parts registry, making the research done in the lab and access to standardized parts more streamlined.

The lab team leaders are branding this kind of research the inquiry into “foundational technologies”-it is meant to help define the protocols of doing synthetic biology (which is still an emerging science and engineering discipline) and at the same time provide a more fleshed-out definition of what synthetic biology is.

So, what does this mean to make a process more streamlined and more standard?  These projects at UC Berkeley, as well as many others involved in the iGEM competition (one of the “special prizes” portion of the judging process at the Jamboree includes the “Best New Standard”-perfecting the craft of doing synthetic biology is extremely important to the actual doing of the science), are working at how to work on the efficiency of synthetic biology, as if—as the name “Genetically Engineered Machines” implies—the entire research process were a sort of assembly line at a factory.  How do you confront questions of trouble-shooting this kind of “trial and error” science, as it has been coined, when so much biological life (though the E. coli or yeast organisms are argued to have been greatly mapped out and understood by biologists) is still uncharted and beyond our scientific knowledge?

Welcome to a blog devoted to all things relating to synthetic biology and the international Genetically Engineered Machines (iGEM) competition at the University of California-Berkeley!!

Well, the obvious first question is:  What is synthetic biology?

As an emerging field of scientific research being designed as an academic discipline, synthetic biology has many definitions, depending on who is doing the defining.  Essentially, as an offshoot of the vast field of bioengineering, it aims to engineer novel organisms “from the ground up”—relying on technologies that allow for the standardization of strings of DNA as “parts” (functioning like electrical engineering’s parts for constructing circuits and signal processing) which are known to have certain functions.  Synthetic biologists then use these standardized parts to form “devices” (and, much more complexly, “systems” constructed from a series of these parts and devices, housed in, usually, a bacterium shell referred to as a “chassis“) that will produce a desired output.  For example, the goal of one project under the synthetic biology banner on the Berkeley campus, headed by bioengineer J. Chris Anderson (who is also the assistant professor that spearheads the Berkeley iGEM team) is to create “tumor-killing bacteria,” a system that is designed to produce a certain output (ie: “tumor-killing toxin”) only after it receives certain inputs from its environment.  According to MIT’s Technology Review,

“…to build a cancer-killing bacterium, biologists must create organisms that can perform a series of complicated functions — namely, when in the bloodstream, they have to sense and respond to the tumor environment. Once inside the tumor, the bacteria must infiltrate the cancer cell, and then — and only then — start producing a tumor-killing toxin. The researchers plan to engineer such super-organisms by co-opting parts from different types of bacteria and inserting them into Escherichia coli, a bacterium commonly used in research.”  (Singer 2006) (Full article here:  “Tumor-Killing Bacteria: Scientists are synthetically engineering E. coli that can target and kill cancer cells”)

It is this “ground up approach” that is often pointed at to distinguish this sort of research from genetic engineering and other closely aligned fields.  Other major synthetic biology projects happening on campus include the designed manufacture of the malarial drug artemisinin through adding “new genes and engineering a new metabolic pathway in Escherichia coli bacteria” in Jay Keasling’s lab (Yarris 2004) (Full article here:  “Synthetic Biology Offers New Hope for Malaria Victims”) and the various projects surrounding cellulosic biofuels at the Joint BioEnergy Institute (JBEI) and the Energy Biosciences Institute (EBI) (EBI’s proposal found here:  “Energy Biosciences Institute proposal summary”).

For more information on what is involved with synthetic biology, look here:  OpenWetWare Main Page.  One of the main objectives of synthetic biology is to be opensource, which includes providing tutorials and elaborate explanation of its procedures to a wide public.

Question number two:  What is iGEM?

Officially (according to its main wiki page), “iGEM addresses the question:  Can simple biological systems be built from standard, interchangeable parts and operated in living cells?  Or is biology simply too complicated to be engineered in this way?”  Started as purely a workshop involving only MIT students in 2003, iGEM earned its “i” after it became an international competition in 2005.  It now connects dozens of teams from around the globe, who create projects ranging from “engineering probiotic bacterium to improve its medical applications” (Caltech) to engineering “a common yogurt bacteria, Lactobacillus bulgaricus, so that it will express the 20aa peptide p1025,” which has been seen to improve dental health (MIT) to creating “E. coli that lyse [or burst open] in response to a sound stimulus,” which could make protein purification (an essential process for research in synthetic biology) less abrasive (UC Berkeley).

For more information on iGEM, look here:  OpenWetWare: iGEM.

Third question of my introductory blog entry:  Who am I?

Unlike the other members of the Berkeley iGEM team, my main research objective is to contextualize synthetic biology (whether anthropologically, politically, economically, philosophically, or ethically) and the research done under its heading.  As a “human practices” researcher, a part of the fourth “thrust” or branch of the Synthetic Biology Engineering Research Center (SynBERC, which is one of the funders of iGEM), my goal is to both learn the science involved in doing synthetic biology but mainly to conduct a continual second-order investigation of synthetic biology:  allowing for the comparison and alignment of relationships with other scientific research, observing the culture of learning synthetic biology and of conducting the research, and discussing controversial issues surrounding synthetic biology research.  For example, looking at the introductory information offered above, information widely available and rhetorically formulated by the scientists designing their projects, we can ask an infinite number of second-order questions:  What process is involved with standardizing genetic information and overlaying an electrical engineering structure on biological systems?  What assumptions and generalizations are established with such standardization and how do processes adhering to such standardization actually function?  What does it mean to “engineer novel organisms,” ie:  create life?  What are the limits to what you can create?  Who decides?  What does it mean that everyone has a different definition of “parts” or “devices” or even “synthetic biology?”  As the months wear on, I will use this blog to confront these and many other questions relating to the design and function of synthetic biology.

And for more information on SynBERC’s human practices, look here:  Anthropology of the Contemporary Research Collaboratory.

I am excited that we have finally got this blog going! It seems to be just one more way that we are all making headway on our projects. Right now in the wet lab, we have finished making our initial set of basic parts (we had slightly over 100 of them) and we have set the stage for composite part assembly. We should be beginning our large scale operation to create about 1300 composite parts tomorrow!

In the meantime, I am glad that we have also gotten a decent start on our wiki and our animated logo. We seem to be making slow progress on our animations, our model, and establishing reaction conditions for a gateway buffer, but I am sure things will pick up. At the moment, I am super excited and relieved that I finally cloned all of my BamHI parts (some of them required eight transformations to get the right thing) and the DNA ligase (which required 7 PCR reactions to get to the product). I am also a bit scared of the massive assembly operations that will be taking place over the next few weeks. I think everyone is ancy about this, including Jin, because there appear to be so many places where things can go wrong and one wrong move has the potential to mess up all of the reactions because they will mostly be done in parallel in 96 well plates. I am especially worried about the special attention and changes in design that will be required for the BamHI and BglII parts because they are toxic to regular cells and we will have to work in strains where either one site or the other is blocked by methylation. Since our assembly requires digestion with these enzymes to put parts together, the subset of parts that involve these two parts will be complicated and tough to deal with.

Hopefully, everything will come through just fine and the assembly-line style production will facilitate all of us working together more as a team (although we seem to be doing a pretty good job already). I guess we all just need to hope for the best at the moment. Whatever happens, we know that lysophonix rocks!