"
Template:Team:UC Berkeley/Notebook/MT notes
From 2008.igem.org
Contents |
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 Mahdvi 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 Mahdvi 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, Mahdvi, 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) Mahdvi! 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 Christine 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.
