Template:Team:UC Berkeley/Notebook/MT notes

From 2008.igem.org

Latest revision as of 02:44, 30 October 2008

Marleejot Week 1: 16 June 2008 - 20 June 2008

18 June 2008

My first wiki journal entry! As the SynBERC human practices member on the team, I have studied synthetic biology from a contextualizing and encompassing point of view for two semesters and am now trying the opposite way: from the ground up. My research has been focused on the discussion of rhetoric of eudaimonia, or conditions for flourishing, claimed by the different stakeholders involved with the biofuels research associated with the UC Berkeley campus, and this coming experience is a departure from this form of inquiry.

Catch-up Orientation: Today was my first day meeting with Chris, Terry, Kate, and the Wet Team--in other words, my first day in the lab. My role as the human practices member of the team (including the Wet Team and the Computational Team) has been molded to focus on the production of a blog maintained by UC Berkeley's College of Engineering (along with Madhvi and Nade). In an attempt to find my feet in the lab (the rest of the team started in the lab two weeks ago), I have been going through the orientation materials they received. Not having touched math or science in three years, other than some orientation when first studying synthetic biology with Professor Rabinow in the fall of 2007, this has been quite an adventure.

Demand for a Deliverable: During my first meeting with Chris, he explained that his view on the important aspects of iGEM are in the following order: (1) to provide an educational experience for those involved on the team, (2) to investigate and further research in the field if possible, (3--"much further down the line") to win at the Jamboree in November. He focused on the importance of my producing a deliverable that was both useful and educational, but which did not need to be completely coherent with the product of the rest of the group. My goal is to produce something that is useful to the students themselves--even if what I am producing is in a different form than their product--and also to provide a convenient outlet for their own thoughts. Also, thankfully, I will be allowed the space to discuss both the work the iGemmers are doing and larger ramifications of synthetic biology as an emerging discipline.

iGEM's Math Modeling Requirement: After giving me a tour of Stanley Hall and the lab spaces, Terry gave a presentation on the math modeling project the team is required to design and produce for the competition. It is important that the team not only do extensive experimentation, but that they produce a coherent model of possibilities within certain parameters. The model is approaching the question of holin and anti-holin production (two parts to be spliced into the DNA of the E Coli, of possible additional parts) which will form pores on the membrane between the cytoplasm and the periplasm of the cell in a roughly measurable way--6 holin join together to form a hexagon with space in the middle which will allow for the passage of both enzymes and ions into the periplasm--enzymes which will lyse the cell and ions which will allow for a depolarization of the periplasm and the cytoplasm (the antiholin will not act like holin--and form pores--unless there is a depolarization). The students must form a model of how this process will unfold.

From Madhvi and Terry, I understand that, as part of their project, the students must explain the applications of the technology they are engineering--cells that lyse in response to sound--and that the main objective is to gently distribute product (such as insulin) into the blood stream. Normally, cells are lysed from the outside and the process can destroy some of the product or the process cannot be mediated at all--allowing for too much product being produced among other possibilities. With the multiple changes of the system, it is hard to predict how they would interact. Two other applications involve the amelioration of current technology involved in the splicing of DNA. (edit: I found out much later that the team was also simultaneously working on in vivo parts assembly processes--this would become the main focus of the project later on. Both products of research are in the pursuit of formalizing foundational technologies for the discipline.)

In the orientating world, I am learning about the basics of the definition of synthetic biology, cloning, and the assembly of basic parts.

19 June 2008

Second day of orientating. Spent the morning going over my notes from yesterday and continuing through the tutorials, and I went into the lab in the afternoon. Chris gave a presentation on Adobe Illustrator and its differences from Adobe Photoshop--it is very important that the team create innovative, attention-grabbing, and attractively created graphics for their presentation and poster in November.

The Formation of a Blog: Susanna, the moderator and technical producer of the COE blog for the team, came to take a group picture of the team and to discuss with Nade, Madhvi, and me the technicalities and utility of the blog. I expressed my desire that there be a large amount of videos of the students talking about what they are doing, as well as space for excerpts of lectures and the space for a portrayal of the dynamics of their day. I had a discussion about the blog and the culture of the College of Engineering with Susanna after the meeting. The other blog ideas the college had were to follow around a handful of engineers who are doing work abroad relating to installing cell phone networks in Uganda or installing water filtration systems to remove naturally occurring arsenic from water resources that are harming people in the region.

Terry continued his tutorial on the math modeling, focusing on the computing of a "transfer function" of an experiment at steady state and the creation of a range of kinetics parameters.

A few of the students were quite happy with the video idea and proposed that we post videos of shenanigans. I must say I agree.

Marleejot Week 2: 23 June 2008 - 27 June 2008

23 June 2008

Worked in the student offices, trying to find the fine line between understanding the research going on in the lab versus all the chemistry and biology upholding it, ie: trying not to balloon out to far in understanding the mechanics of cloning. Moderately succeeding. Also, Jin gave me a tutorial, along with Cici and Sherene, about using the ApE program to find the genetic code for a specific part that the team wants synthesized for their project.

Presentation of Ideas and Abstraction: While going through the tutorials, I began thinking about how the presentation of ideas was an extremely important aspect of spreading knowledge. Simple example: Watson and Crick's large-scale double helix version as an illustration to a wider audience of the abstractly small reality. The students are constantly reminded that they have to present their findings in a manageable, approachable, and simplified way; presentation being as important as the research itself. The question becomes: how much abstraction is involved in this tailoring of information and how much is it necessary?

24 June 2008

Met with Lizzy from OKAPI (Open Knowledge and the Public Interest) to show her around Stanley Hall for filming location options. She will be helping me a lot with recording interviews of the instructors and students for both the Berkeley College of Engineering blog and the Ars synthetica web project. Met with Professor Rabinow, Gaymon, and Noah about the technicalities of Ars synthetica as far as design and implementation are concerned. Brainstormed with Noah on topics and forms of depiction of the building of context surrounding the research going on in the Berkeley iGEM lab.

25 June 2008

This morning was the mini-meeting! Got to hear about the details of the research students have been doing in building their parts, and where their work fits in a grander scheme. Also, was egged out to describe what my role will be for the iGEM team: human practices on the scene will involve my second order observation of what is involved with doing synthetic biology, as well as participating in the science myself. Chris assured me that I would be able to make a part, as long as it was a less complicated one. Also important to me is that I involve the students themselves in engaging with their research in a different, and hopefully unexpected, manner (as previously mentioned).

I found particularly interesting the emphasis on the fact that the chance for "catastrophic failure" is higher than we would hope--and Terry, Chris, and Megan were quite descriptive with their "Christmas Tree" analogy: these Christmas lights (parts) are independently strung together, and the whole batch will only work if the lights are in a certain order, and only if paired with only certain other lights, only if placed in certain spots on the tree... and then the tree catches fire------and what about the cats??

Did a preliminary interview with Chris and Lizzy, which will be quite useful on Ars synthetica both in bits and as a whole description on what is involved with synthetic biology. Extremely interesting to me are the distinctions between descriptions and explanations of what synthetic biology aims to achieve.

Question of the day: What does it mean to be a part of a field that designs itself to make things instead of study things?

26 June 2008

Terry sent out a blurb from Seed Magazine on synthetic biology, which emphasized the fact that the field aims to build organisms from scratch and the problem of dual-use in the democratization of biotechnology. What does democracy mean in this context? What assumptions are made when the focus is on making microscopic changes that have macroscopic impact?

I ran a gel electrophoresis, using invitrogen's e-gel, with lots of help (and mostly just assisting) Madhvi! Yay pipetting!

Continued reading Rabinow's Anthropos Today to continue to build my own equipment for meditation on synthetic biology.

27 June 2008

Interviewed Terry with Lizzy. He had very interesting things to say about synthetic biology with a chemical engineering perspective on the "system" mentality of doing such research, pointing to the fact that he can be a big help with the modeling project of the team because modeling in that way has always been a part of his technical development.

Marleejot Week 3: 30 June 2008 - 3 July 2008

30 June 2008

Met with Prof. Rabinow, Gaymon, and Noah to discuss what progress we have made in defining the web project and the structure around it. Kate and Kevin later came to help brainstorm and discuss what progress has been made--main goal: make participation in the web project enjoyable and useful for the scientists and SynBERC team members themselves.

Synthetic biology is more than what happens in the lab itself.

Reading: Anthropos Today

1 July 2008

Met with Kevin this morning. He has some amazing perspective on what is needed for synthetic biology to function and what its connection and its relationship are with SynBERC at UC Berkeley and other institutions in the US. The constellation of synthetic biology, iGEM, and SynBERC is more complicated than earlier assumed. Will be interviewing him on film on the 3rd.

Met with Prof. Rabinow and Gaymon for brainstorming what my posts will be like on the COE blog, which will have a threefold perspective: (1) Putting the iGEM research project into relationship with other projects (whether synthetic biology projects or not, other iGEM projects or not), (2) Second order interpretation of materials and descriptions, (3) Introduction of discussion of topics surrounding synthetic biology (eg: biofuels, questions of governance, 'dual-use,' etc.)

E-mailed Susanna about the COE blog, and it is now up, though final touches not completed.

Reading: Anthropos Today, James Clifford's Writing Culture (rereading- for questions of representation of subject, and for avoiding portraying complete objectivity), "Synthetic Biology Primer" by Scott Mohr (second order observation of what defines synthetic biology)

2 July 2008

Putting up the final version of the first post of human practices viewpoint on the COE blog. Helping Christie with growing her cultures for her basic parts tomorrow.

Reading: Anthropos Today, Stephen A. Tyler's "Post-Modern Ethnography," "Synthetic Biology Primer," Aristotle's Politics

3 July 2008

I got an explanation from Christie on the parts that she has been working on--her microray data still has not gotten in and she's decided to go with the ultrasound sound promoters while waiting for that data (as a backup--the team really wants to use different sound promoters). She also explained that the microray allows for many genes to be tested at once--if the genes respond to sound they will form a certain protein, which can be distinguished from the other genes, and the sound promoter can be found and cloned out of the sequence later. I will be helping her tomorrow with some real lab stuff (yay for being in the lab on the 4th of July!).

Tried to interview Kevin Costa, the administrative director of SynBERC, today, but we had some technical difficulties. Like our first conversation, though, his commentary was quite an interesting perspective on what synthetic biology is. One discussion point was his interest in the way that BioFabs have evolved from an idea to an idea in process in the US (which would change drastically the way that synthetic biology is done and what it would mean). But what is a biofab? That is an excellent question with an answer still being formulated. I planned to go down to the new JBEI building on Monday to see what's going down.

One thing happening at the JBEI building this summer is what is being affectionately called "iCLEM," after Clem Fortman, the post-doc running the lab--it is a group of 6 high school students who are involved in a summer biotech program, who were accepted from different areas of the Bay Area. Generally, Kevin said, the students are working at finding organisms that break down plant mass.

There was also another modeling meeting today in the lab, trying to deal with the complexities that are inherent in the modeling problem with holin and anti-holin. Questions must be asked about whether we need to keep track of each partial pore (and how does this happen on a molecular level?), is pore formation reversible, and do we need to keep track of degradation at least of anti-holin? Depolarization must be taken into account, eventually. Terry said that we make assumptions and use information that we cannot necessarily back up, because if we did not we could not begin the work that can be later altered.

4 July 2008

Ya! Helped Christie do some minipreps today and to grow up some colonies. With the amount of miniprepping that normally goes on in the lab, the 5 minipreps that I helped with pale in comparison.

Marleejot Week 4: 7 July 2008 - 11 July 2008

7 July 2008

Biked down to the new JBEI building today! Was a labyrinth of security to get in and most people have not yet figured out how to get around the building themselves (it has only been open for about a month now). Found myself locked in the staircase and had to exit in the basement and start all over again on the ground floor (what happens if people don't want to use the elevator?). Met with Kevin and he showed me around the top floor of EmeryEast Station that JBEI occupies. The iCLEM team was in the middle of their photo shoot (we will have ours tomorrow), so I couldn't talk to the students, but I did meet Clem and he explained to me the basics of this specific research group (touching on the research he does elsewhere on the building) and what he is trying to get out of the summer biotech program for the students involved. The students involved in this lab, he says, are not doing synthetic biology--they're doing old fashioned microbiology. Clem would like me to be involved as a human practices person with this lab, which means in one way he would like me to be in communication with how the students are understanding their experience.

I also met with Leonard Katz, the industry liaison and research director of SynBERC, for a brief conversation about SynBERC and our respective roles in research and with synthetic biology. He remarked on the drastic difference between what sort of experience iGEM provides for those involved and what getting your PhD looks like--teamwork is often focused on with the iGEM world but a hindrance in the PhD world. More than anyone else, Katz has emphasized the separation of the lab/lab workers and the society outside the lab, and wanted me to be really careful to not overemphasize the security problem often associated with synthetic biology. He has agreed to meet next Tuesday for a filmed interview.

Reading: The Politics

8 July 2008

Photo shoot in the lab! Woooo. Also met with Paul, Gaymon, Noah, and Kevin to discuss Ars synthetica. For the next meeting, it was suggested that I create some prototype examples for the site with the content I have been gathering. I'm looking forward to learn how to edit videos and figure out how to make what I have been learning accessible and engaging. I tried out vuvox.com with some great success and interest, creating photo essays of sorts.

Reading: Rabinow's "Assembling Ethics in an Ecology of Ignorance"

9 July 2008

Found out that Terry Johnson writes for a science fiction online mag! io9! ([http://www.io9.com]) They have a lifeform contest that is associated with synthetic biology!

Read about Leonard Katz's participation in the European TESSY organization, which is hoping to create an EU-wide organization similar to SynBERC, but the effort is coming up against some interesting organizational and academic problems in the process. In the report, Katz explained that one of SynBERC's immediate missions "is to reach out to industry and promote the field's potential both for the discovery of novel drugs and production methods."

The modeling meeting that was supposed to happen yesterday happened today, and it was discussed that perhaps a simplifying of externalities should be underway--as well as a great research effort in reading scientific papers on the holin-anti-holin arena. Main questions discussed in the meeting: (1) What is the significance of dimer? (2) How do we want to deal with the cascade of events?

My questions: how do you model something for which you have very few numbers to populate and what use does such a model serve? Terry has been giving lot of support in the model arena, which he says derives from his background in chemical engineering--which often depends on rough models to define a space for implementation.

Reading: The Politics

10 July 2008

Tried to generate my second blog entry today, but distracted by the many different topics that are overlapping and smudging the issues.

Had the minimeeting, but needed to leave early because it was moved later and I had a scheduled interview with Kevin. And the interview with Kevin happened! Tried out the "tougher" questions on him, and on the whole it went quite well.

11 July 2008

Met with Lizzy and Noah to brainstorm ways to express the information we've been gathering. Video vignettes here we come! Then, Lizzy and I went into the lab to do some filming of the students doing synthetic biology and did an interview with Dirk about the research he was doing and his opinions and understandings of synthetic biology. It was quite hilarious.

Marleejot Week 5: 14 July 2008 - 16 July 2008

14 July 2008

Had made an appointment with Lizzy to get together today to create some material to show in the Ars synthetica meeting tomorrow. Was unfortunately unable to go to the kayaking trip nor the Clotho meeting this morning. Spent a good long while editing 4 videos into one, it being the first time I have edited (so exciting!). I focused on the question of "what is synthetic biology" as a first frame to look at this whole kit and kaboodle, and I was quite happy with my final project.

Also generated a photo slide project with some photos we got from the lab. I really wanted to make a collage and I finally figured out how to--that will be my next attempt in producing content for AS.

15 July 2008

Lizzy and I went down to the new JBEI building (after some hilarious mishaps) and interviewed Leonard Katz, who had some extremely interesting and alternative perspective on synthetic biology and SynBERC, coming at it from an industry angle. He encouraged me to interview Kate Spohr, because he finds the education aspect of synthetic biology and SynBERC the most interesting to AS--last year at iGEM, SynBERC received many questions from media sources about the novel education process involved in training new synthetic biologists.

Had our glorious AS meeting and we're getting closer to a clear understanding of the time line of the project, its content, the design of its content, and the door for communication and collaboration on the site.

Tomorrow, I will be going back to the JBEI building to talk to the iCLEM students!

16 July 2008

Attended the Clotho testing session this morning. Although I do not use ApE on a regular basis, it was interesting to see how the students interacted with the software (which is how Doug described my role: as the observer of human-computer interactions; "closest thing to human practices in computer science.")

Went down to JBEI and talked with Clem Fortman, Saber Kahn, and the high school biotech kids (the iClemmers). It is interesting to me to see how the same object is presented in many different ways, as the iGEM group and the iCLEM group are working with similar ideas, but they are understood as different. Alternately, "metabolic engineering" and "directed evolution" are sometimes called "subtopics" of synthetic biology, and other times referred to as entirely separate from the discipline.

Marleejot Week 6: 24 July 2008 - 25 July 2008

24 July 2008

Learned a bit about cybernetics, meaning the "study of feedback, black boxes, and derived concepts such as communication and control in living organisms, machines, and organizations including self-organization." The concept seems quite apt for studying synthetic biology, studying how synthetic biology is done, and studying how people do human practices.

Had our mini-meeting today, and there has been some difficulty with how things have been going in the lab because of the high throughput methods the students have been utilizing.

Met with the iCLEM students again today, and observed and helped with their lab work. The students had broken up into groups, and they were learning how to read articles comprehensively and make powerpoints from the information--technology to be used forever in the field of science. The instructors on the team are constantly asking the students questions to make connections between what they have been told and what they are doing. The instructors on the team joined as a result of IISME (the Industry Initiatives for Science and Math Education program), which is what Dirk on the iGEM team did as well. They are required to take bits of what they have learned back to their own classrooms.

The students went to see the UCSF iGEM team, which is made up primarily of high school students. They described what they saw and what they were told there by saying that the UCSF team was "building a tool for other scientists to use to make stuff." Meaning that team is also working on foundational technologies for synthetic biology and affiliated fields.

25 July 2008

Wrote on the blog about biosecurity issues.

I also talked to Madhvi about the programs she is working on right now in outreach and college prep, as one of the head people of a women bioengineering organization on campus.

Marleejot Week 7: 28 July 2008 - 1 August 2008

29 July 2008

Decided the blog needed a biography section on the team members, and so I built a list of questions that I found interesting to get people on a human level online (tricky business). Hopefully people will get them back soon.

Surveying Questions: The act of "summarizing" people in this way is an interesting one--and a topic for a huge tangential debate, which I will only hint at here. Our generation, growing up almost completely without a memory of the world before the internet and certainly without even the faintest informed memory of the world before corporate capitalism, has learned how to define individual identity with little hand-picked quips about our likes and dislikes (rounding down, essentially, to what we do or do not consume--music, books, film, tv, food, etc--especially in the world with social networks like facebook and myspace), though there are definite exceptions to this rule. Compiling a list of biographical questions for the blog and the wiki means framing how others can present themselves--a task that should always be avoided if at all possible. Standards, however, of what information to give and how to give it are the norm in how we package and process ourselves and knowledge, and I would say that this formation of American privileged youth predisposes us for standards in packaging and processing (and black boxing)--yes, you saw it coming--genetic information.

Met with Paul and Gaymon about biofuels research and the rhetoric of different stakeholders.

30 July 2008

Learned about bacteriophages today. They are one model being used to create the Berkeley iGEM project. The levels of abstraction and discussion on multiple levels of scientific discovery and research is quite interesting to see when Berkeley iGemmers describe their experiences and understanding of their own research. What they are doing also involves a changing of protocol for synthetic biology in general, although the protocol is also strictly applied in other instances.

Went down to the JBEI building to hang out with the iCLEM students. Most of what they were doing today had to do with preparing themselves for applying to college. I talked with Rowan Driscoll for a long time about his opinion on science education in high schools, and California's emphasis on preparing for the Star Test, which now leans heavily towards microbiology, rather than integrative biology, in biology education. Complexities of chemistry vocabulary often restricts what he feels is his efficacy in addressing the "big concepts" of molecular biology.

The instructors present a piece that is skeptic of ethanol's ability to solve our "energy problem," but the students did not respond about how it was related to their own research (they are searching for enzymes that efficiently break down cellulose for JBEI).

31 July 2008

Read up on Craig Venter and his definitions of life and species. Continuously searching for a way to define life, according to Carol Cleland, means that we avoid understanding life. Scientists, she says, should be looking for a theory on life, not definitions, which are only concerned with language and concepts. I'm not sure how much a agree.

1 August 2008

Bad karma in the lab! Everyone's moving upstairs!

Read Arkin's and Endy's new articles on standardization in synthetic biology. Met with Paul, Gaymon, Noah, Kevin, and Adrian about Ars synthetica. Web design is getting closer!

Marleejot Week 8: 4 August 2008 - 8 August 2008

4 August 2008

Sick, worked from home. Wrote a blog entry to provoke thought on biofuels. Where does cellulosic biofuels fit in our solution? And to what problem?

George Church and Identity: Read up on George Church's Personal Genome project--he asks the question: what defines our identity? We hold on so dearly to these dates and facts (like birth dates, bank account numbers, height, etc), but do they really mean all that much? Are they merely phenotypes? He published all these little bits of "trivia" about himself on-line for all to see, using it as a way to engage in a "philosophic exercise in what identity is and why we should care about that." This is extremely interesting, considering how much "identity" and "life" and "happiness" are tied up together in the American culture. This desire to distinguish--to be unique and innovative, a carver of one's own space in the world--is part of the American individualistic ethos that Church shows here is at the foundation of biology and its offshoots. To clarify, manipulation of genetic information is dependent on the understanding of how that genetic information affects and shapes "life"--but the definition of "life" is culturally and philosophically situated. Adrian Van Allen, the web designer for Ars Synthetica,

Church's Personal Genome Project is an effort to make correlations between what is present in the human genome and what human traits are expressed after "the environment has had its say," using the genetic data of volunteers. Church is associated with SynBERC, but his approach is wildly different from the MIT/Drew Endy foundational technologies and biobrick standardization approach. This desire to discern and understand also associates him more closely with the science of synthetic biology than its engineering aspect. One can ask the question: to what extent can C.P. Snow's arguments about "Two Cultures" (his being about the differences in language between the scientists and the social scientists) be mapped onto the cultural divide between scientists and engineers?

5 August 2008

Went down to JBEI today with Lizzy and interviewed Clem today about his opinions on synthetic biology and his biography. Adventures all around. The iCLEM students were preparing their presentations for August 14th.

6 August 2008

Barbecuing in Golden Gate Park! Talked with Chris, Clem, Kevin, and others about biology and politics.

Chris said that it took him a long time to get used to the looseness of rules (that are generally associated with academia that is somewhat distanced from industry or governmental oversight) at Stanley Hall on the Berkeley campus--where the large part of bioengineering is now housed. Also related to policies surrounding the discipline, Molly brought up the excellent question of why industry would want to patent findings in academic labs, when that information could be used to help others.

7 August 2008

Biofuels Research and Science Fairs: Had a nice long conversation with Cici about the biofuels project she did last year and her interests in synthetic biology. She designed and researched, during her sophomore and junior years in high school, how to convert cellulose into ethanol. Working under a mentor at the Joint Genome Institute at Walnut Creek during her junior year, she has already learned some of the procedures that are required of her in the lab here, such as PCRs and transformations. This project won her the 3rd place prize at the International Science Fair this past May. These experiences, she say, has helped her feel like an undergraduate herself. The difference lies in the independent nature of those research projects of her past two years and the collaborative nature of the iGEM experience--where, it is actually true, the project is "more than the sum of its parts"--in the sense that the whole picture is dependent on details controlled by many different actors in the lab.

She really wants to continue working on her biofuels project, which is entirely unrelated to the work she is doing in the lab here, and she has heard about the program that Madhvi has developed for high school students to get the funding for a mentorship with local academics in their fields (one of the reasons that Cici applied to do iGEM this summer is because there was not funding at the Joint Genome Institute for her to continue research there this summer). Since her work with biofuels and iGEM, she had been more interested in clinical biology, but she has since been leaning more heavily to the synthetic biology side. Time restraints with the necessary hurdles for applying to universities this fall are going to restrict her time for lab work, which she is extremely disappointed to acknowledge.

When I asked her why biofuels were more interesting for her as a topic of research (as she asserted), she said, "because you can feel it, you can feel how serious it is, how hard gas is to get, how expensive, how it has become a global problem."

Because of last week's decision that something was contaminated in the lower lab room (bad karma, too!), everyone has moved up to Chris' lab upstairs. With the other undergraduate and graduate researchers in Chris' lab, the room can get a bit crowded.

Foundations for Engineering Biology: Read Drew Endy's "Foundations for Engineering Biology" (Nature 438, 449-453 (24 November 2005)). He makes the assertion that engineered biological systems have had great impact, but reminds the reader that our ability to do this "quickly and reliably" is extremely limited (it is up to you to determine how much the processes have been improved since mid 2005 when the article was written--Chris Anderson, when I interviewed him a few weeks ago, said that the tool kit needed to do synthetic biology effectively is still in dire need of innovation, which is why he is so interested in foundational technologies "these days"). Endy tells us, in 2005, that "vibrant, open research communities" and "strategic leadership" are necessary. He goes on to show how, historically, it has been more efficient for an engineer to approach a problem and find a solution (his example: the amount of time it would have theoretically taken to create a genetically encoded ring oscillator) in comparison with how long it takes a scientist to do the same. The reason, he argues, that synthetic biology had not become a viable, inexpensive, and reliable field by 2005 (a full 27 years after Szybalski and Skalka coined the term), is that engineering has not had its chance with it. Despite this assertion, he does concede that "it is possible that the designs of natural biological systems are not optimized by evolution for the purposes of human understanding and engineering" (a concession which is nonetheless strangely worded--that somehow nature faulted at engineering itself for our (necessarily) rational understanding and manipulation). This is the first possibility for the unreliable nature of synthetic biology. The second, and the one he focuses on, is that we have purely and simply not yet invented the tools to do what he knows we are capable of performing. And the term "foundational technologies" was born. The take-home message he wishes to impart on the reader is that "engineering of biology remains complex because we never made it simple."

8 August 2008

Interviewed Christie and Madhvi in the lab with Lizzy. They connected some of the material for explaining synthetic biology that is widely available with what happens daily in the lab.

I also went down to JBEI to see Jay Keasling present his artemisinin and biofuels research to the biotech students. "It's typical of biology," he said, "to run into problems with engineering." But to make the research narrative tangible, he used analogies comparing synthetic biology to computer systems. He mentioned the Joint Genome Institute (Walnut Creek), where Cici had done some work last summer, and where there is a project to figure out how ruminants from cows could be used to break down cellulose. At the JBEI, though, it's focused more "on looking at the forest floors"--which the students can give meaning to with the experiments they have been doing in the lab. They have been studying termites and bacteria that grows on rotting plant mass. "Biology," Jay (a chemical engineer) explained to the kids, "is good at creating complex systems and can give you a configuration that you exactly want. This is better than chemistry in some respects." Jay told the students that it is "some people's dream" that there will be a chassis that has a minimal number of complexities. Although we do not know enough about biology at the present to design chassis to such simplicity, he is confident that we will one day be able to simplify complexities in the way at the moment.

Specialization: Jay also recommended to the students that they not be "quick to specialize--be a generalist as long as you can and don't worry too much about what you want to do when you grow up."

Scientific Education in America and Certainty in Scientific Discovery: Talked with Terry about the modeling requirement for iGEM, his opinions, and his role as "cheerleader" of this summer's team. He had quite a lot to say about science education in America, as well. Undergraduates, he said, are a very interesting group to work with--they're ready academically, but not emotionally, for this sort of research--which is a failure of our school system. Scientific development through an undergraduate career, unless the student takes the initiative to do research under a professor (and even in these conditions, as a required contributor to the furthering of the professor's research interests, there is a specific outcome sought for from them), exists within the frame of a search for the "RIGHT ANSWER," to which scientific discovery is diametrically opposed in the world outside of problem sets and well structured (and oft-performed) experiments. When things fail in the iGEM lab, as failures are sure to occur at some point in scientific research, the students felt it more poignantly--they have had some level of control over the creative aspect of their research in design and implementation, but most of them have not had experience before this (other than tutorials and lectures) on how to design experiments. King of analogies, Terry explained that "science is like art, you abandon it, you don't finish it"--the students have, until this point, been told to find a conclusion, a sum-up. Interestingly enough, although scientific discovery is, indeed, not founded on certainty, iGEM and its practical framework require that the students present such a conclusion and sum-up at the presentation.

More generally, Terry discussed the anthrocentrism and narrowed view of global environmental issues which are ever present in the media now--humans have been "fiddling with life," he said, for thousands of years. From the moment we started farming and domesticating animals (note: what is the line between humanity and nature? is there one?), life has been fiddled with by humans. His analogy for this: "Whereas we were fiddling with life with hammers and saws, now we have a set of screwdrivers." (Analogies, he says, do not need you to have a complete understanding, but just need to be mildly clever.)

Marleejot Week 9: 11 August 2008 - 15 August 2008

11 August 2008

Design and implementation: Had a very intense meeting about design for the Ars Synthetica website. How do we design it in a way that will be user friendly but will avoid hierarchical and guided movement through the material? I tried to lay out a sort of graph of Design, Ontology, & Ethics vs iGEM, Artemisinin, & Biofuels (as case studies in which to discuss within each theme). I think the idea of presenting material through "pathways" on the website is an interesting one, but does not really eliminate the guided nature of providing information in a particular form. Perhaps I am just so embedded in iGEM and the formation of synthetic biology at the moment (as is Ars Synthetica, really), but I cannot but help to see parallels between the discrepancies between the design philosophies and pragmatic implementations of Ars Synthetica and those of synthetic biology as a whole (edit: Anthony, a graduate human practices research assistant at Berkeley, warned me later about mixing together the "usefulness" of Ars Synthetica and the "utility" of the foundational technologies of synthetic biology. However, I believe the parallels of processes of formation still hold). But, on the other hand, anything emergent is by definition undefined by known parameters and will require compromises. Chronicling such compromises within the study of synthetic biology (which includes all of us) seems extremely pertinent to more complex understanding of synbio's abilities and limits.

Whose Synthetic Biology?: I had an awesome conversation with Dirk and Chris today about the differences between different strains of synthetic biology. Drew Endy would say that synthetic biology is "not [about] what you make, it's how you make it." There is constantly the desire to distinguish synthetic biology from genetic engineering, even though lessons could be learned from this (questionably) more established field. And, perhaps more importantly, bioengineering could, theoretically, be seen as an umbrella discipline to allow the productive interaction of many different forms of biological engineering. This ever present "public relations" rap about the separation of synthetic biology from other versions of biology and chemistry differs a little from what happens in the lab, however, as much of the research the students have been using as a resource is from multiple disciplines. And as right it should be.

Interestingly, bloggers talking about Endy's move from MIT to Stanford speculated about what drama led to this transition, to which another replied: "I wouldn't speculate too much about his position at MIT--synthetic biology does not need a Perez Hilton." True words, indeed.

Standards: Chris has been developing a Biobrick b (BBb) standard and a Biobrick c (BBc) standard for the BioBrick framework encasing part of synthetic biology. iGEM still mostly functions in BBa--these different standards are defined by which restriction enzymes are encoded at the edges of the "part"--and Chris says that BBa could be manipulated to be much more flexible and efficient. This brings up the question of establishing standards and seeking standards within synthetic biology.

12 August 2008

Sound Promotion: Sound promoter testing happened in the lab today. I posted two blog entries about it with pictures. The team is extremely hopeful that the experiments will work as expected. Christie has set up an experiment with two test tubes--one filled with LB and bacteria that have been transformed with plasmids with the sound promoter attached to GFP and one without—and has submerged waterproof earbuds into both of them. After I left, the team believed that the experiment worked-as the pellet of the sound promoter-attached batch glowed green under a UV light. Great happiness in the lab! Also, confessions come out that some never believed it would actually work-general feeling of relief abounds.

13 August 2008

Read an article by Greg Pahl, "Can Communities Generate Their Own Local Power?” ([http://www.alternet.org/environment/93347/can_communities_generate_their_own_power/ link]), in which he makes the argument that our energy challenge does not end at what kind of energy we use, but also how we receive that energy, outlining problems in using the national electrical grid--most importantly being that it is big and slow to adapt.

Paul said today that biotechnology is an extremely important threshold of how human beings think about themselves and how they are going to change themselves.

Emerging is hard: Wrote an entry about changing habits in relation to energy usage and the search for an energy solution. Emergence, whether that of an entire scientific field or in adjusting to new environmental conditions, seeks to find the common denominator and a stable foundation for its innovation. Infrastructure and the production of mass manufacture are often pointed to as the reasons for not departing too far from current habits surrounding consumerism. When and how does one decide when the standards being used are not useful or are even detrimental to "flourishing?" In other words, how quickly can standards change and who is allowed to change them? This is related once again to the differences and uses of BBa/BBb/BBc standards in synthetic biology, as Madhvi pointed out today. There are restrictions to the uses of BBa and even BBb standards, but how will a shift happen toward a more fitting standard, when the discipline is trying so hard to establish and build infrastructure on the standards it has already built? Scientific thought, in its most orthodox of forms, sought to question everything, even its own assumptions--how does this idea of scientific discovery mesh with the contemporary mainstream scientific desire to make the uncertain certain?

14 August 2008

In the iGEM lab for a short while--the sound promoters tested a few days ago are not exactly what the team thought they were, and a second round of experimentation shows that there are complications they were not expecting. Christie is going to grow up a new batch and sequence the DNA of the plasmids she has been testing to see what's up.

High School Biotech Presentation: Went down to JBEI because the High School Biotech Kids had their presentation today. They composed, with the help of their instructors, a powerpoint and presentation for friends and family to learn about the research they have been doing over the past eight weeks in relation to biofuels. The students discussed the material from different angles, presenting information on JBEI as a whole and the pitfalls of corn ethanol. Analogies were in full swing, as one student compared bacteria that normally eat starch but which researchers are trying to get to eat cellulose to "vegetarians in a room full of meat--they've got to eat the meat to survive!" The question session after the presentation was very interesting, and while some parents and friends asked for specifics like "when will cellulosic biofuels be ready for commercial use?", others asked about how the experience changed the way students think about research and their opinion on energy problems and solutions. Although it has at this point been largely shaped by their instructors, the experience has been extremely fruitful in helping the students develop a critical eye on the world around them.

15 August 2008

Cost Reduction Impetus: Lab equipment and chemicals are expensive--this is a reality of the academic scientific world. Reducing the price and amount of products needed to buy in order to do the basics of synthetic biology are an enormous part of the drive for innovation within the field (to lead to more innovation in application later).

Chris and I had a conversation about the politics involved with the politics of representation and actuality of labor of faculty and staff on campus.

Question: How do you troubleshoot in an experiment that is as intricate as sound promoted self-lysis?

Marleejot Week 10: 19 August 2008 - 22 August 2008

19 August 2008

Reboot: We found out today that the results associated with the sound promoter we got in the lab last week are unreproducible, not for the ultrasound promoter nor for the white noise sound promoter. "Lysophonix" no longer exists (Molly: "Lysophonix is no more?"), and the idea of trying to find another sort of promoter to induce lysis is severely restricted by time. The students now have to figure out what aspect of their research to present at the Jamboree and how to present it. Jin believes that presenting on a project that "failed" (it did not work as expected, and there is not enough time to troubleshoot the project before November) would be a wrong move at the Jamboree and has encouraged the other students to look to the other side of their efforts, working on processes of in vivo parts assembly, to be the focus of their presentation in November. This movement is like a large rewrite and reformat of what the project was to focus on in the beginning, perhaps becoming even more important when the name was chosen and graphics were devised. Science experiments often do not go to plan, and I understand that new evidence should shape and that time restraints do shape what data and conclusions are emphasized. I am, however, curious as to what happens to the information gained from the trials and errors of trying to find a sound promoter, if not incorporated into the final product of the team's research presentation. This seems to be an issue embedded in the fact that iGEM is, at heart, a competition--failures or unpredicted aspects, if not easy explainable, are cut away. The alternative does seem tedious: a careful explanation of what the process of experimentation, an investigation of why the results showed something different, what could be pointed out to change in the experiment to get the "right" results, and what those right results could actually look like (an exercise that would, nonetheless, be quite enlightening, considering the students would be explaining their protocol and projections now with some training in and understanding of what synthetic biology is actually all about--the students themselves had decided on the sound promoted lysis device back in the spring).

20 August 2008

Worked in the media lab to do some editing. Trying to create a pathway for Adrian and AS surrounding iGEM and provoking questions. Going through video footage, I found a theme that was constantly used in distinguishing synthetic biology: the distinction between artisanal and assembly line processes in approaching the manipulation DNA and the necessities to make apply the analogy--e.g. black boxing, simplifying, standardizing. Taking a moment to expand out from the particular case of iGEM, research that has used "synthetic biology" as a label has not always necessarily tied itself to this idea of "plug and play" parts. Certainly, the work of Jay Keasling (artemisinin and biofuels projects) and even Chris Anderson's work with tumor killing bacteria have utilized "artisanal" methods of manipulating DNA. However, streamlining the process of transformation and plasmid assembly within biological systems would certainly benefit more than a "plug and play parts" kind of synthetic biology.

21 August 2008

More talk about the existential crisis of Lysophonix. What is going to be the new name? The focus will definitely be on the streamlining of processes.

Chris is already designing a BBc standard, he verified today--he has the two enzymes with compatible sticky ends and possibilities for a stable scar sequence sitting around. Standards have a hard time being standardized.

Innovation Policy: Read an article about "innovation policy" in Nature magazine ("Innovation policy: not just jumbo shrimp" by David Guston--who is at Arizona State's Center for Nanotechnology in Society--a sort of more fully developed Human Practices division for nanotechnology, which has been around longer than synthetic biology). His question is simple: how do you predict something that is by nature unpredictable. This is a question that has synthetic biologists scratching their heads as well. "Policies," Guston points out, "are made too late to change the past that necessitated them and too early to understand the future they are meant to shape." It is perceived that while policies are made incrementally and bureaucratically, innovation is revolutionary. It is also generally believed in the scientific community that scientific discovery can not be shaped, only "killed or mutilated." He makes the important point that nations often invest in research for "social progress" which is restricted by the nature of the research itself (his example: scientific papers outlining a new discovery of creating a revolutionary drug or revolutionarily creating a drug do little to improve accessible health care). His solution is what he calls "anticipatory governance," focusing on the need for interdisciplinary focus and suitable administrative oversight--a way to incorporate values within the deliberation. Scientists needs to be "more reflective about practices and choices within the laboratory, and if necessary change their practices."

22 August 2008

Today is the last official day of iGEM. I will continue to work on the media work for the website, to read articles relating to the discipline, and to come into the lab (which will still be working away feverishly in the next two months) until November.

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