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Template:Team:UC Berkeley/Notebook/MT notes
From 2008.igem.org
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.
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.
During my first meeting with Chris, he focused on the importance of my producing a deliverable that was both relevant 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 relevant 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 implications of synthetic biology as an emerging discipline.
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.
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 in November and their poster.
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 killing people.
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.
Jin gave me a tutorial, along with Cici and Sherene, about for using the ApE program to find the genetic code for a specific part that the team wants synthesized for their project.
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 cat??
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 tools for meditation on synthetic biology.
27 June 2008
Interviewed Terry with Lizzy, who had very interesting things to say about synthetic biology with a chemical engineering perspective on the "system" mentality of doing such research.
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! (io9.com) Lifeform contest! 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 is coming up against some interesting organizational and academic problems in the process. In is, 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: (1) What is the significance of dimer? (2) how do we want to deal with the cascade of events?
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. Wasn't able to go to the kayaking trip nor the Clotho meeting this morning, on account of one of my other jobs. 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.
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 (a group which is affectionately called "iCLEM"). 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. Alternatively, "metabolic engineering" and "directed evolution" are sometimes called "subtopics" of synthetic biology, and other times referred to as entirely separate.
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.
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 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. Read up on George Church's Personal Genome project. Wrote a blog entry to provoke thought on biofuels. Where does cellulosic biofuels fit in our solution? And to what problem?
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.
7 August 2008
Had a nice long conversation with Cici about the biofuels project she did last year and her interests in synthetic biology. Everyone has moved up to Chris' lab upstairs and the lab's a bit crowded.
8 August 2008
Interviewed Christie and Madhvi in the lab with Lizzy. And also went down to JBEI to see Jay Keasling present his biofuels research to the biotech students. He used analogies comparing synthetic biology to computer systems.
Talked with Terry about the modeling requirement for iGEM and his opinions. He had quite a lot to say about science education in America, as well.
Marleejot Week 9: 11 August 2008 - 15 August 2008
11 August 2008
Had a very intense meeting about design for the Ars Synthetica website. How do we design it in a way that will be both user friendly but 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 get rid of the guided nature of providing information. 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 design philosophies and pragmatic implementations of Ars Synthetica and synthetic biology as a whole. 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.
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 genetic engineering. And that bioengineering could, theoretically, be seen as an umbrella discipline to allow the productive interaction of many different forms of biological engineering. This ever present PR 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 are from multiple disciplines. And as right it should be.
Interestingly, bloggers talking about his 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.
12 August 2008
13 August 2008
14 August 2008
15 August 2008
Marleejot Week 10: 18 August 2008 - 22 August 2008
18 August 2008
19 August 2008
20 August 2008
21 August 2008
22 August 2008
