Archive for December, 2009
Many of us in the DIY realm rely on the open publications of the Public Library of Science at plos.org. 
You may feel surprised to know that PLoS has web icons which you can display on your own web page! Check it out, make your science blog or web notebooks “PLoS inside” to raise awareness of their efforts. Here’s how:
Great work by 2 DNA explorers — it seems high school students are kicking ass all over the place, first in sushi, now this! Check out this big DNA species identification project, about 200 samples from around the neighborhood and lots of cool findings. Even one that suggests they found a new species of cockroach!
From their website: “We identified 95 different animal species.”
You probably wouldn’t believe me if I told you that all of the species displayed above were found in local supermarkets and homes in New York City. A feather from a duster yielded Ostrich DNA. A delicacy labeled “sturgeon caviar” instead turned out to be from the strange-looking Paddlefish. A popular Asian snack was revealed as Giant flying squid. Bison DNA was found in a dog biscuit.
>
We found DNA evidence all around us. We found DNA “name tags” in all kinds of human and pet foods including raw, cooked, dried, and processed items. We obtained DNA from dried soup mix, scrambled eggs, dog food, chicken McNuggets, hamburger, beef jerky, bologna, yogurt, cheese and even butter. By analyzing DNA, we traced tiny, unrecognizable bits of once-living things to their source.
We could identify animals from what they left behind in the environment. We found tell-tale DNA in dried-out horse manure in Central Park, a pigeon feather on the sidewalk and a shed snakeskin.
Good work!
Website: http://phe.rockefeller.edu/barcode/dnahouse.html
PDF of samples and results: http://phe.rockefeller.edu/barcode/DNAHouse%20specimens,%20results.pdf
Cathal has designed a simple centrifuge using open source hardware technology, and you can order one yourself! (For use as entertainment purposes only, of course; wouldn’t want anyone to save nearly a thousand dollars by not buying real centrifuge now would we?)
Dremelfuge is a rotor designed to fit standard lab microcentrifuge tubes and miniprep/purification columns, to be spun by either a powerdrill or other
chuck-loading machine or by a popular rotary tool.
Dremelfuge features an easy click-in loading system which holds tubes
parallel to the plane of rotation for optimum pelleting and delivery of
force.
Do-it-yourself biology on the rise - 20 Dec 2009 - SF Chronicle (pdf)
SF Chronicle reporter Juliane Guthrie interviews Tito Jankowski, Phil Ross, Jason Bobe, and Raymond McCauley about the DIYbio projects they are working on. They also interviewed Drew Endy about safety and regulatory concerns. The article is online at SFgate.com.
One of the article’s main thrusts is concerned with safety and regulation, or the lack thereof. I know diybio-nyc has been thinking about it and is organizing a round-table in a month or so, and I’ve been throwing a couple of ideas around with people here in boston. Maybe it’s time to set up a safety working group to synthesize the community’s thoughts on the issue with pointers to relevant resources. Is anyone doing this already (there’s some info in the faq).
Happy holidays,
Mac
Shaunalynn Duffy, Alec Resnick, and David Thompson lean closer as the ucam's image comes into focus. The camera cost $10 and took 5 minutes to hack.
We hacked $10 webcams into microscopes, a la Hackteria.org at the bosslab + sprout. Yashas Shetty, Jason Bobe, Rich Pell, Myself, and others are planning a worldwide webcam hacking day on January 30th, in conjunction with the UCLA “Outlaw Bio” symposium.
@molecularist (Charlie Schick) posted a great writeup with some photos on his blog.
hello world, ucam style
@jasonbobe was the first to have a cam connected to his laptop and the lens unscrewed and inverted.
Jason testing the ucam: lens unscrewed and inverted, clipped to laptop screen, with an alligator clamp holding a microscope slide above the camera (consider vibration and focal point).
A droplet of saliva dripped onto a microscope slide held above the webcam/microscope (microcam? u-cam? ucam?) showed up as amorphous blobs: Hello World! The inverted lens resting on top of the camera chasis seemed to have a focal plane somewhere inside the lens body. This is when we realized we should screw the lens into the chasis in reverse.
detail of Jason Bobe's laptop w/ skype; soon this ucam will be broadcasting microscopic images all across the world...
@jayunit & David Thompson built an ad-hoc microscope slide holder out of a block of insulator foam, a pencil, two black binder clips, a bolt, a nut, and a washer. By rotating the nut (or holding the nut and rotating the bolt), we could raise and lower the height of the microscope slide.
the nut on the bolt controls the height of the slide above the camera. Unscrew the lens from this particular $10 usb webcam, open the camera body, reverse the lens and screw it back through the camera body inside out, and voila, instant microscope.
I hacked together some rudimentary processing code to access the usb microscope. It seemed to be more reliable than quicktime (or skype) and I was excited about using my favorite blob-detection library on the microscope feed.
You can grab the source here: ucam.
To get the focal plane outside of the lens assembly, we unscrewed the 2 small machine screws holding the camera body together to open the camera then and screwed the camera lens back into the housing from the inside-out such that the the lens was reversed. The part of the lens that had originally been closest to the CCD was now outside the camera body. Then screwed the housing back together.
By rotating the lens and and the nut on the slide holder, we were able to intersect the focal plane of the ucam with the microscope slide. it works!
ucam hello world: looking at streetwater and blood from mac cowell on Vimeo.
12 Dec 2009 – wiki notes.
U.S. Office of Science and Technology Policy soliciting YOUR feedback on "Improving Public Access to Results of Federally Funded Research" until Dec 20, 2009
December 12, 2009
Jonathan Cline
The U.S. Office of Science and Technology Policy, under directives from the President Obama administration, is soliciting public feedback. Note the deadline! (Dec. 10th-20th for this phase)
Policy Forum on Public Access to Federally Funded Research: Implementation
Thursday, December 10th, 2009 at 7:25 pm by Public Interest Declassification Forum
By Diane DiEuliis and Robynn Sturm
Yesterday we announced the launch of the Public Access Forum, sponsored by the White House Office of Science and Technology Policy. Beginning with today’s post, we look forward to a productive online discussion.
One of our nation’s most important assets is the trove of data produced by federally funded scientists and published in scholarly journals. The question that this Forum will address is: To what extent and under what circumstances should such research articles—funded by taxpayers but with value added by scholarly publishers—be made freely available on the Internet?
The Forum is set to run through Jan. 7, 2010, during which time we will focus sequentially on three broad themes (you can access the full schedule here). In the first phase of this forum (Dec. 10th-20th) we want to focus on the topic of Implementation. Among the questions we’d like to have you, the public and various stakeholders, consider are:
- Who should enact public access policies? Many agencies fund research the results of which ultimately appear in scholarly journals. The National Institutes of Health requires that research funded by its grants be made available to the public online at no charge within 12 months after publication. Which other Federal agencies may be good candidates to adopt public access policies? Are there objective reasons why some should promulgate public access policies and others not? What criteria are appropriate to consider when an agency weighs the potential costs (including administrative and management burdens) and benefits of increased public access?
- How should a public access policy be designed?
- Timing. At what point in time should peer-reviewed papers be made public via a public access policy relative to the date a publisher releases the final version? Are there empirical data to support an optimal length of time? Different fields of science advance at different rates—a factor that can influence the short- and long-term value of new findings to scientists, publishers and others. Should the delay period be the same or vary across disciplines? If it should vary, what should be the minimum or maximum length of time between publication and public release for various disciplines? Should the delay period be the same or vary for levels of access (e.g. final peer reviewed manuscript or final published article, access under fair use versus alternative license)?
- Version. What version of the paper should be made public under a public access policy (e.g., the author’s peer-reviewed manuscript or the final published version)? What are the relative advantages and disadvantages of different versions of a scientific paper?
- Mandatory v. Voluntary. The NIH mandatory policy was enacted after a voluntary policy at the agency failed to generate high levels of participation. Are there other approaches to increasing participation that would have advantages over mandatory participation?
- Other. What other structural characteristics of a public access policy ought to be taken into account to best accommodate the needs and interests of authors, primary and secondary publishers, libraries, universities, the federal government, users of scientific literature and the public?
We invite your comments [...]
Give government your feedback on how to release data and publications from publicly funded research.
- Register for an account on the U.S. Office of Science and Technology Policy site here: http://blog.ostp.gov/wp-login.php?action=register
- Leave your policy comments on their WordPress blog!
More information is in the U.S. Office of Science and Technology Policy video:
Last week I hired Micah & Caroline from WeAreaGoodCompany.com to design an extensible diybio logo and related illustrations. I gave them a quick intro to diybio and synthetic biology (see a lot of design notes here) and asked them to create artwork that could be used by diybio.org and built apon by regional groups + related organizations (diybio-nyc, bosslab, etc.). I stressed extensibility – the final design should support remixing by all interested parties.
Micah & Caroline are about halfway done and I want to show you their work so far and solicit comments and suggestions. Above all the graphics are intended to be a community resource, so they need to be built with community feedback.
They have worked on two things: an extensible diybio logo and diybio themed icons.
logo
Micah & Caroline modified a typeface called “the mix” for the diybio logo to make it look hand-cut. When they are done they will provide the typeface for the community so that any group name can be written with it. As you can see, their current idea has been to cut out illustrations from the “golden days” of amateur science in the pattern of the typeface.
black-filled diybio text & icons
They have garnished this design with a rich wood background which I think goes far in dispelling the typical clinical, clean ethos of science imagery. But it’s also pretty “loud.”
diybio logo cut out of old science diagrams & engravings
icons
I also asked the team to design a set of reusable icons and illustrations that represent things common to diybio activities. I wasn’t very specific.
diybio logo and icons grayscale
What 10 icons should I ask them to design? This is really where feedback would be helpful. For instance, we could ask them to design:
A pipet; dsDNA; a microscope; a waste container; a falcon tube; e. coli; yeast; a petri dish; a generic chemical bottle; DNA sequence.
In this version they incorporated the icons into little bottle-cap pins to emphasize DIY approaches. (note: when they are finished they will provide the source illustrator files to maximize these kinds of reuse.)
diybio logo cutout of science diagrams with bottlecap logos
diybio logo variations
feedback
Please please please mail your feedback to this thread on the diybio google group or in the comments below. In particular, consider these two questions:
- what 10 icons should be designed?
- what graphical concepts should comprise the diybio logo?
Go check out my notes for my thoughts. I hope the artwork will be a graphical synthesis of (playfulness + art + DIY) + (science + engineering + biotechnology).
(I’m still thinking about a retro-arcade-game theme…)
Also see these other handy links:
- OpenWetWare went through an involved feedback process when they created their logo. They paid a lot of attention to technical details, like the handedness of DNA.
- Science Creative Quarterly’s merit badges – they designed a TON.
I’ll include my feedback in the comments with everyone else.
All this stuff is licensed CC-BY.
Here I go. Start off with something like “Bryan got to speak at H+ Summit 2009 and spotted some neat numbers.” Maybe this will end up in GBM or H+ magazine as a small blurb?
Bryan Bishop presented at the 2009 H+ Summit onopen source hardware and took copious notes. Here he presents some of his favorites:
Patri Friedman. Meeting him in person is like meeting with a living legend. Hell, he wrote the book on seasteading. His talk was short and to the point: let’s make startups for governments and ways of organizing people. You know how everyone says let a thousand flowers bloom? Same thing going on here, except he’s serious about it. The Seasteading Institute is a 501c3 non-profit organization dedicated to living on the high seas and promoting a diversity of ways of living and organizing groups of people. At the end of the talk he gave a shout-out to the DIY scene: 12 miles off the coast, there is no FDA. The talk was recorded and is somewhere here, and here’s the transcript. I didn’t catch the Q&A because I was up next! What a talk to follow.
Todd Huffman also talked (transcript). Todd organized BIL, the simple and free alternative to TEDtalks. Todd spoke about whole brain emulation and his startup, 3Scan. He showed some really amazing videos collected from his team back at TAMU running off of a knife-edge microscope. His plan is to slice and dice brain tissue so as to scan in details all the way down to mitochondrial positions in order to parameterize and seed emulations and simulations of brains.
Gregory Benford (transcript) also showed up and talked about personal genomics, or what he calls “nutrigenomics”. It turns out that he bought the original Methuselah flies. The Methuselah flies were super-longevity flies living well beyond average lifespans. With these flies he sequenced their genome and found particular up-promoted and down-regulated genes that might be causing the flies to live longer. The idea is to then synthesize custom pharmaceuticals that enable and disable gene regulation for different (but targeted) genes in the human body. Greg is really amazing in person, although maybe that’s just me being a fanboy for his scifi after all these years? At some point you go “wtf, I’m having a one-on-one with Gregory Benford!” (He was also at the Singularity Summit earlier this year.)
You should also check out Anselm Levskaya‘s talk on brain input/output projects, Dylan Morris, and Christine Peterson had some good suggestions for not dying.
And one final plug- there’s no transcript for me because I was presenting (!) on open source hardware (1, 2, 3).
hplusmag - winter 2009 - cover "Hi there, Ray"
Parijata Mackey wrote an article for the Winter 2009 h+ magazine about diybio titled “diybio: a growing movement takes on aging.” She provides an overview of diy -hardware, -software, and -wetware, and gives shoutouts to some of the projects listed at diybio.org/projects (man we gotta develop a better system for collecting projects). Overall she provides an overview of where diybio came from and where it’s going in an optimistic manner consistent with h+. She also provides tantalizing interview coverage with John Schloendorn concerning his DIY SENS lab and biotech co-working space in the Bay Area.
Andrew Hessel wrote another article called “Why DIY Bio” in which he explains his vision, based on open source & synthetic biology principles, for a distributed, open anti-cancer research collective. He calls it Pink Army.
UPDATE: slashdotted on 26 Jan 2010.
[@molecularist](http://twitter.com/@molecularist) [blogged](http://www.molecularist.com/lifeblog/2009/11/video-diybio-meetup-22nov09.html) about the 22 Nov 09 [diybio-boston meetup](http://diybio.org/boston/) at [sprout](http://thesprouts.org/) and recently posted a great little [video](http://www.youtube.com/watch?v=HcZtnT8mbaA&fmt=22) of the tour. You can see us setting up Sprout and touring through the mobile lab. Read Charlie’s [full post](http://www.molecularist.com/lifeblog/2009/11/video-diybio-meetup-22nov09.html) for more info.
