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2017 July 12

UCSC iGEM crowd-funding 2017

Filed under: Uncategorized — gasstationwithoutpumps @ 18:30
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Each year a group of UCSC bioengineering engages in a summer research project in synthetic biology as part of the iGEM synthetic biology competition.  Although they get some support from the University, they have to raise the money for going to the iGEM jamboree (the conference where every team presents its results) by crowd-funding.

The UCSC iGEM team has opened their crowd-funding site for this summer:
UC Santa Cruz | UCSC iGEM 2017: Bugs without Borders

UCSC iGEM 2017: Bugs without Borders

What is iGEM?

The iGEM (International Genetically Engineered Machine) competition is an international symposium dedicated to the advancement of synthetic biology. For over 10 years, iGEM has been encouraging students to work together to solve real-world challenges by building genetically engineered biological systems with standard, interchangeable parts. Student teams design, build and test their projects over the summer and gather to present their work and compete at the annual Jamboree.

The epitome of undergraduate research, iGEM provides an unparalleled opportunity for talented students to administer their own projects, advocate for their research and procure resources for funding. In doing so, the competition promotes creativity, collaboration and curiosity as students develop the critical, analytical, and independent real-world problem solving skills that are difficult to cultivate within the classroom.

Our Project: Bugs Without Borders

UCSC’s 2017 iGEM team is focused on the shortage of supplements and essential vitamins in third world countries. Affectionately dubbed “Bugs without Borders”, this year’s project aims to engineer a Generally Regarded As Safe (GRAS) microorganism capable of producing a target supplement or essential vitamin in a safe and efficient manner.

Go to their crowd-funding site and watch their video to see what they are planning for this year.

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2016 November 13

BioTreks—a specialized research journal for high-school students

Filed under: Uncategorized — gasstationwithoutpumps @ 18:09
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Five and half years ago, I published a blog post, Journals for high school researchers, which listed the tiny number of venues I knew of that were open to high-school researchers.

At iGem this year, I heard about a new peer-reviewed journal for high-school students: BioTreks.  Currently the journal is planning on one issue a year, and solely on the subject of synthetic biology, which seems a bit narrow to me:

In 2016, BioTreks will begin publishing open access, peer-reviewed articles related to the implementation and outcome of high school student-driven synthetic biology research. We’re currently accepting original articles that present perspectives, methodologies, and outcomes related to the study and practice of synthetic biology in high schools. Students, educators, and biologists from around the world are invited to contribute content that promotes and describes synthetic biology education and research at the high school level. Authors who are interested in contributing original research articles, methods papers, literature reviews, editorial perspectives to the journal are encouraged to contact us for more information. We look forward to hearing more about your experiences in synthetic biology and discussing ways in which you can share your insights in our journal. Please contact us to learn more about publishing in the journal.

I chatted with one of the originators of the idea for a while at the iGEM Jamboree, and they may be open to expanding the journal to be “synthetic biology and bioengineering”, which is a considerably wider scope, and which may open up opportunities for a lot more high school students.

I don’t know whether this would require them to rewrite their description of their goals:

Ars Biotechnica is a 501(c)3 public charity whose mission is to support science education by introducing high school students to the emerging field of synthetic biology. We do so by awarding grants for schools to use in obtaining laboratory supplies, coordinating local and regional symposia on synthetic biology, and administering a peer-reviewed journal. Our organization has been providing financial and technical support to iGEM-bound synthetic biology teams since 2013 and supporting high school focused synthetic biology symposia since late last year. We’re now excited to announce the launch of BioTreks, a peer-reviewed journal just for high school synthetic biology.

The organization has a very small budget and relies mainly on volunteers:

BioTreks is maintained by a volunteer staff of dedicated biologists, students, and educators. If you have a background in biology, education, peer-reviewed publication, or graphics design and would like to help us develop and maintain the journal, then we would like to hear from you. Volunteers can work remotely and on their own time to coach students on writing scientific papers, serve as section editors, copy editors, and peer-reviewers, and contribute to the journal’s overall presentation and design. Please contact us to learn more about volunteer opportunities at the journal.

They don’t charge anything to students for publication—they aren’t a vanity press that makes money off of selling overpriced printing to suckers students.

If anyone knows of other journals interested in high-school submissions (not vanity presses), let me know, and I’ll blog about them!

2016 October 29

iGEM age rules

Filed under: Uncategorized — gasstationwithoutpumps @ 05:12
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I’m currently attending the iGEM synthetic biology competition’s “Jamboree”, where all the teams present their results.  It is a big conference (about 3000 attendees this year, representing about 300 teams), so a bit overwhelming.

One thing that surprised me was that the UCSC team of 17 undergraduates was listed as an “overgrad” team, rather than an “undergrad” one.    It turns out that the classification has nothing to do with student status or education:

There are 3 sections in iGEM 2016:

  1. Undergraduate: all student team members are age 23 or younger on March 31, 2016
  2. Overgraduate: one or more student team members are older than 23 on March 31, 2016
  3. High School: all student team members are high school students on March 31, 2016; includes students who graduate from high school spring 2016

http://2016.igem.org/Requirements/Sections

The age constraint seems like a very strange way to divide undergraduates from graduate students.  It does not work well in countries where there is mandatory military or civil service before college, and it does not work well for minorities and the poor in the USA.  I think that the problem is that the people defining the sections have a very narrow view of what it means to be an undergraduate—one that is colored by their teaching at elite private universities in the US.

The Common Data Set that each college in the US has to publish provides information about the percent of undergrad students age 25 and older at different institutions (question F1 on the form).  For example, UCSC reports  4% of undergrads are 25 and older, UCLA reports 5.1%, UC Berkeley and University of Illinois report 6%, Cal Poly reports 3%, San Jose State reports 20%, while Stanford and  MIT report only 1%.  I have not looked at many colleges, but there seems to be a clear trend that elite private schools are much less likely to be familiar with older undergraduates than public schools, and that higher status public schools have (like UC) have fewer older students than good, but slightly lesser status schools like San Jose State.  (I’ve not found a site that allows rapid summaries of the Common Data Set across many institutions—colleges are required to report the information, but no one seems to be making it accessible other that by one-college-at-a-time lookup—if someone knows of a good site for exploring the data, please let me know.)

Looking at the schools most attended by minorities and poor students in the US—the average age of a community college student is 29 [http://www.aacc.nche.edu/AboutCC/Trends/Pages/studentsatcommunitycolleges.aspx].

By using age as a cutoff, iGEM is being quite elitist—their definition of “undergraduate” only matches the demographics at elite private schools.

I asked about the reasons for the age cutoff, and it seems like some teams were complaining about having to compete against teams that had 35-year-old students on them, and that this was somehow unfair.  I find this mystifying.  How is it that a student who worked in a warehouse or tending bar for 15 years before finally being able to afford college has an unfair advantage over a student whose parents had the money to send them to college immediately?

I’m a bit more sensitive about re-entry students than many college professors, perhaps because of my mother.  Her college education was interrupted by World War II, and she did not get an opportunity to go back to college until her 50s. I am very grateful to the US system of community colleges that allowed her to return to college at that age and earn an AA degree. Being told that she would not have qualified as a “real undergrad” is personally offensive.

Coming up with a simple rule that can be applied uniformly around the world to distinguish undergraduate from graduate students is not easy, but I think that a simple age cutoff is one of the poorer choices that could have been made.  Years of education since age 5 (to avoid cultural differences in when schooling starts) might be a better choice.  Certainly the reasons given for the age criterion (to make the competition fair to undergrads) reveals a real misunderstanding of who undergraduates are outside the elite US colleges.

2016 July 30

UCSC iGem 2016: Sugar Slugs

Filed under: Uncategorized — gasstationwithoutpumps @ 19:46
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UCSC’s 2016 iGEM team has finally had their crowd-funding site go live at https://crowdfund.ucsc.edu/project/2548.  They have an interesting project this year:

Engineering a Better Future

The world of crop production is laden with agricultural co-products that are unfit for human consumption. The vision of the UCSC iGEM team is to develop a novel process for converting these co-products into the high-value sweetener, Erythritol. It’s simple, sweet, and best of all, zero-calorie.

Ever wanted a bioreactor you can control at the click of a button? Our team is also designing and building our very own autonomous bioreactor, the Taris V1. Whether its temperature, pH, nutrient uptake, or beyond, our bioreactor will also monitor and feed its internal conditions into an online interface where users can seamlessly track their data and change conditions as they see fit. Talk about convenience.

With its low cost and ease-of-use, we hope our Taris V1 bioreactor can serve as a platform for other teams across the globe to create innovative solutions to real-world problems.

Source: UC Santa Cruz | UCSC iGem 2016: Sugar Slugs

I don’t know much about what they are doing for the metabolic engineering to make the erythritol, but the bioreactor project is a rather fun “maker” project.

They have posted their budget on-line, and by far the largest cost is getting to the iGEM “Jamboree” in Boston in October. All the lab equipment is provided by UCSC (except the bioreactor they are designing and building), and all the student labor is free (in fact, they are paying summer tuition in order to take the iGEM course). So they have about $1000 for hardware, <$200 for reagents, and $31,300 for travel to the conference.  I think that they’ve over-estimated the price of flying to Boston, though, as Southwest flights are currently about $320 round-trip, and ground transportation at each end would probably add only about $200 to that, so 21 people  (20 undergrads and 1 instructor) should be able to do the travel part for under $11,000.  They’ve probably underestimated the lodging costs though, unless they are planning to pack like sardines into an AirBNB rental.

I’ve been thinking of going to the iGEM conference myself this year (on my own money, not crowd-funded), as I’ll be on sabbatical in October, and not teaching. I’ll have to make up my mind soon, though, as the cheap flight prices will probably go away.

I’ll be giving the iGEM team some money for their crowd-funding campaign, as it would be valuable for all of them to be able to attend the conference after the work they’ve put in—I know many of the students on the team this year, and they are the hard-working students that teachers love to have in their classes.

I urge others to make at least a token donation, to let them know that the hard work they are doing is recognized by the community.  Donations can be made through the UCSC crowd-funding site.

Disclaimer: I’m officially the “2nd PI” for the iGEM team this year, because the iGEM organization insisted on there being two faculty involved. I’ve done some advising on the bioreactor project also, though only through a few conversations with the lead designer on that team (who was also my group tutor for my applied electronics course in the spring).

2014 July 7

Crowdfunding for UCSC iGEM project

Filed under: Uncategorized — gasstationwithoutpumps @ 19:34
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The UCSC undergraduate team for the iGEM synthetic biology competition have put up a crowd-funding web site to try to raise the money they need for their contest entry.

https://experiment.com/projects/sustainable-next-generation-biofuel-production

Their design project is to engineer a bacterial strain for cellulosic alcohol production—not ethanol, but butanol, whose energy density is more compatible with the existing gasoline infrastructure and that does not absorb so much water.  Conventional ways of creating butanol are too expensive, so recombinant bacteria are a promising approach.  Using cellulose as a feedstock avoids competing with food production, as waste paper and other non-food sources can be used.

They are not trying to do everything at once—they are working this summer on getting butanol production from glucose engineered into Haloferax volcanii, a halophile that their mentor has worked with a fair amount.  I’m not sure what their reasoning is for using a halophile—perhaps they just wanted to work in an archeon, and H. volcanii is one of the best-established model organisms for Archaea.

Their mentor for the project is donating his time, so all the costs are unavoidable reagent, equipment time, or registration fee costs.

The team description (including membership) is at http://igem.org/Team.cgi?id=1560, and the wiki where you can follow their progress is at http://2014.igem.org/Team:UCSC (though they’ve nothing there yet but an introduction to the project).

I gave a token amount, and I urge others to do so also (or more if you are feeling generous).  They’re currently about halfway to their goal.

https://experiment.com/projects/sustainable-next-generation-biofuel-production

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