Hi all,
Thought I would share a DonorsChoose.org biology project that I donated to back in December — Our Ancestors’ DNA Roots

“I teach middle school math science and history for beginning ESL students. My students originate from all parts of the globe including Sudan, Peru, Mexico, Korea, and Japan. 80% of my students receive free or reduced lunches.
Students often see subjects such as history and science as unrelated. In the community where my students live they often do not see the practical application of scientific methods in the work force. Additionally, the rich diversity of cultures makes the idea of interconnectedness especially important.

Testing our mitochondrial DNA will allow my students to trace their haplogroups and trace their ancestors migrations out of Africa. We’ll be able to find common ancestors between us and tell the history of the human race. Using the lab equipment (the conical tubes, saline solution, and kit) students will process their own DNA using the same process anthropologists and forensic experts use, giving students a real connection to science in the work force. The DNA models and evolution charts will be used to explain the processes of population shifts and explain how we can use DNA to determine common ancestors.

Your help will fund a project that connects science (through genetics), history, and math. Students will get training in DNA testing that is used by real scientists everyday. This project makes the vital concept of DNA tangible and gives my students the tools needed to access higher science subjects in high school. You will make it possible for my students to describe our common heritage as humans.

My students need 9 pieces of DNA analysis equipment such as conical tubes, saline solution, DNA models, evolution charts, and a DNA Replication and Transcription Set.”

Check out some photos from the project:
http://www.donorschoose.org/donors/proposal.html?id=341067&pmaId=264576&pmaHash=-507759220

There is a whole range of biology, biotech, and DNA related projects that you can contribute to on the Donors Choose website: http://www.donorschoose.org/

Tito

This cowboy hat is acid-proof and recommended diybio safety-wear.

Chris Kelty just kicked out the Outlaw Biology Symposium here at the N(c)SI center at UCLA. “Outlaw is not the same thing as criminal,” he said.

Marcus Wohlson and I live-blogged it here, with help from Charles Fracchia.

There is a live stream.

Some of us are taking living notes here: http://ietherpad.com/ZxNM3bq5zh

Photos here: http://www.flickr.com/photos/macowell/sets/72157623185479749/.

Panelists

Each panelist gets 2 slides. Starting w/ Jason Bobe‘s 2nd, I’ll try to take a picture of each one.

Hugh Reinhoff – tons of sequencing and searching for the mutation causing his daughters’s disease, narrowing in on the target. May start biochemistry in mice models soon.

Philip Lukeman – made 100nm wide gear out of DNA origami. Working on nanoscale devices. Demoing open-source software tomorrow that takes in a drawing and spits out oligo strings that will self-assemble via the origami techniques into the shape. I’m thinking… we should fold some DNA into cool shapes and send the results to ASPEX for free electron microscopy.

Meredith Patterson – “work in linguistics, data mining, computer security, and biology all have something in common: finding patterns.” She shows a picture of Lactobacteria acidophilus. “Come to the demo tomorrow to get some of it’s plasmids.” She mentioned the crypto-crusade of the cypherpunks in the ’90s and read from an updated cypherpunk manifesto, roughly “biohackers are dedicated to putting the tools of scientific enquiry into the hands of everyone. Come, let us research together.”

Gaymon Bennett – an ethicist and theologian focused on synthetic biology, “how is biotechnology contributing to the good forms of life?” Bios Technika. “I think the kind of moral life we would be engaging in when doing diybio is very different from the kind of moral life one would engage in when doing big bio.”

Victoria Vesna – artist at UCLA. http://artsci.ucla.edu.
Visiting professor at Parson’s School of Design

Gravitated toward university setting because bioartists have had trouble finding a place in the gallery system. After arriving, she says she “started slowly moving toward the other side of campus [i.e. toward science labs].” Not only because there were “more money and toys there,” she said, but because it was “like walking into the most amazing sculpture studios.”

Shows a slide of piece she did called “Blue Morph”. The flashes of light were translated into sound, flashes from the metamorphasis of a blue morpho caterpillar into a butterfly.

She talked about her new HOX project. She’s thinking about turnining different animal’s homebox gene’s into sounds, or taking samples and making them into poker chips (since Chris is from Nevada). I think she should use our k12 E. coli button technique to make

The way art is done, taught, critiqued has also changed. Looking for public input for next HOX project: The best idea gets $1,000! Comment and suggest at http://artsci.ucla.edu/hox/.

Roger Brent – Badass Basic Scientist. Ran the Molecular Science Institute,/a>. Drew Endy and Rob Carlson were hanging out there in the early 2000s.

Patterson: Yeah! I love http://www.seedinglabs.org/.

Audience: ScienceShops, like in Europe!

Me: any tools that speed up the interaction with biological devices. Interactivity is key to play, and play is key to intuition, and intuition is key to innovation.

Lukeman: Doing stuff in silica versus doing stuff in the real world is different. “There will always be speed limits to doing stuff in the real world.” (Narrator: let’s make an xbox game of “the inner life of the cell” then)

Patterson: The hackerspace movement!

Narrator: Hackerspaces are becoming “centers of inquiry for anyone who just wants to walk in.

Discussion turns to the patient-driven research movement.

In the audience is Alice Wexler of the Hereditary Disease Foundation, which began four decades ago as a family effort to trace the genetic origins of Huntington’s disease.

Audience: Why are we interested in diybio? Is it for entertainment, or for survival? I started a small lab for artists at UCI. But in the end, we didn’t have the people power. I’m an artist. I didn’t have enough time to maintain the equipment and to figure everything out. So where are the situations where the Space and Equipment and People come together? I see a lot of really cool geeks here… but I see everyone alone. Working in isolation.

Brent: Well, I just want to say a person who wants to do art would be welcome in my lab.

Rienhoff: It might seem like a solitary activity, but I am connected to a very large community. I don’t feel like I am working in isolation.

Me: Roger, could you describe a page in a cloning manual and how much those publications cost?

Brent: Full subscription to “Current Protocols” used to run $1,200 a year. Anyone in UC system has access electroincally. Everyone knows someone.

Me: And there are torrents! But my point is that these protocols are often just a little too technical or telegraphic for the beginner to actually be able to use them. They are written for grad students. We need new manuals. We need books with the same technicality but written for high school students.

Bennett: The real test is to go home and boot up our Internet and see if we can learn how to do this. But why should you care about diybio? Find this essay: Weber’s Science as a Vocation. Science is hard and takes incredible enthusiasm and drive. We need to think about the why! It’s not just to do something cool. (Narrator: we might have missed the nuance of his discourse).

Audience: a sociologist, compares “outlaw biologists” to buffalo soldiers, i.e. outsiders who at the same time have connections to powerful institutions. Asks panelists to reflect on connection.

Rienhoff: When you’re outside the institution, you’re allowed to speculate and connect. The dots can be much farther apart. You can go way out and not take professional risks doing that. Being on the outside is “stretching the scientific method.”

Patterson: You have the freedom to look into questions that haven’t seen a lot of focus because projects would generally benefit marginal populations. Much of the resistance I’ve seen to my work comes from “upper-class liberal white people” who fear genetic engineering but lack sensitivity and awareness to its potential to benefit the poor and marginalized.

Lukeman: Who remembers “The Island of the Misfit Toys?” I think a bunch of the scientists you see here could be described as being from the island of the misfit toys. Scientists are not homogeneous, but often “deeply weird” people who have useful and not-so-useful ideas.

Bennett: A concrete example of the adjacencies between big bio and so-called diybio: consider the work of iGEM teams. It’s generating new kinds of participation, proliferating around the world. Getting some purchase on the movent among and across these places… should help us answer the question.

Audience: As exciting as outlaw projects are for lowering barriers to participation, how do you envision the work changing the interaction of the broader public with the science?

Meredith: If I could llive in my ideal world, it would be one in which people actively realized how much they use the scientific method every day.

Brent: Americans idolize the autodidact, the tinkerer, the Thomas Edisons. If biohacking captures the public imagination, regardless of technological achievement, a broader dialogue about science will be opened.

Bennett: The kinds of things we can do well in labs today can seem boring. What goes on at the bench every day is not the grand story about the human genome and the code of codes changing your life. A real problem: Combining a frank discussion of what we can and can’t do with fostering enthusiasm for trying.

Lukeman: Hard to convey to people what we’re doing without resorting to the five-minute montage. (a la CSI).

The conversation switches to citizen science

Audience: I want to point out http://scienceforcitizens.net/ (any maybe http://citizensforscience.org/ ?), and tell you that I’m going to a citizen science literacy conference later this year run by http://www.copusproject.org/. What messages do you want me to bring to that conference?

Kelty: I encourage you to just focus on enabling citizen science. The literacy will follow.

Audience: I am a gerontologist here at UCLA. Most citizens don’t have any science understanding at all… but I think it’s changing. Someday there will be science experts who are high school students. Freeman Dyson’s Domesticating Biotechnology.

Jankowski: I think we would all agree: biology is hard. We’ve talked about the available electronic resources, and the cheap ways at getting lab equipment. So let’s talk about how to develop access to experts who can teach us.

Fracchia: We’re running periodic classes at the bosslab in Boston.

Littrell: And tomorrow we’re starting DIYbio-SF here.

Audience: We’ve talked a lot about DIYbio practice, but I’m more interested in the theory. I’m a scholar who studies 19th century renegade scientists. I want to know what the big ideas are or will be coming out of this community and knocking on the door of orthodox science.

Lukeman: Outlaws don’t need your stinkin’ metaphysics.

THE END.

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Rob Carlson on synthetic biology: THE ECONOMIST

Rob Carlson states: innovators are necessary to create solutions to pressing problems – and these innovators often work with or come from interest groups such as DIYbio.

The Economist: “You can do a lot in your garage – A professor of biosynthesis on DIYbio / open-source biology, buying DNA online and the problem with patents”

Rob Carlson on synthetic biology

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:

Read more

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.

Read more

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!

http://vimeo.com/moogaloop.swf?clip_id=8182346&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=00ADEF&fullscreen=1

ucam hello world: looking at streetwater and blood from mac cowell on Vimeo.

12 Dec 2009 – wiki notes.

The U.S. Office of Science and Technology Policy, under directives from the President Obama administration, is soliciting public feedback. Note the deadline! (Dec. 10^th-20^th 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. 10^th-20^th) 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?

1. 1. 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)?
   2. 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?
   3. 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?
   4. 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:

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