Etech Liveblogging: Lessons from China for the World, Rebecca MacKinnon (Global Voices)

Rebecca explains the current viral anti-censorship protest video: The song of the grass mud horse. (In this case an alpaca)

It features videos of alpacas while child sing about the grass mud horse, but the difference in tones between "Grass mud horse" and "Fuck your mother" is just a subtle tonal change. Since song tones override speaking tones in Chinese, it's a sweet choir of children singing "Fuck your mother." They sound very sweet. The alpacas are fluffy, but slightly creepy.

Definitely best misheard lyrics since "wrapped up like a douche bag in the middle of the night"

This video is coming to represent the fight against censorship. If you type in obscene or politically sensitive words often the software or the server will bounce you to an error message, so people use puns and slight changes in language to defeat the software, but everyone knows what you're really talking about. This is very like how people got around filtering in Napster oh so long ago now.

There's another older meme about a rivercrab wearing three watches. (Ethan mentioned this last year.) It's another homonym pun. It's a play on two government mottos: the "harmonious society" and the "three represents." Harmonious becomes rivercrab, and three represents becomes wear three watches. A rivercrab wearing three watches seems to be a bit about going along with the government plans.

So now there's an intellectual discussion going on about the rivercrabs versus the alpacas.

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Etech liveblogging: Mobile Phones Reveal the Behaviors of Places and People (Tony Jebara)

(Tony is from Sense Networks, and also a prof at Columbia University in comp sci)

Starting out with what we have now:

Online data isn't disconnected documents, but a network, with links between docs and the key information is the links. Folks like Google have obviously exploited that network technology. Online social networks, networks of people, the relationships being the important part. - looking at Facebook, but also affinity networks like Amazon recommendations.

The issue is using some real world activity to build networks. What can you tell about a place by what it's connected to? They're using mobile location data passively - but it's messy and hard by comparison to online data. Should Facebook be able to build my friend network by seeing our phones cluster? (That will put a damper on my extramarital affairs.)

We already have smarts in online data: collaborative filtering, marketing, advertising, search, social recommendation - the next step is pulling that out of location data.

They've been collecting location data from taxis, blackberries and iphones

An example of what can be found:

In SF - commuting into the financial district for work. When people come into work correlated with the Dow Jones, when the stock market started going down people rolled into work later.

How much are people in SF going out at night? How late are people staying out? Night life goes way down with the economic downturn, in fact gps is down over 30% in general in San Francisco now.

The app: citysense.com: Where is everyone? How is sf right now? They can show you a heat map of iphone or blackberry to get a feeling how active the world out there is-
this brings the ability one has in a small community to tell if something is going on to a scaled up urban area. Go towards the red dots!

You can search for bars and restaurants in ranked order in how active they are. They have a buddy finder: kind of like a Google latitude.

In the next step, citysense 2.0 they are color coding the dots to find people like you. Each color represents a different 'tribe' - orange is the young edgies, light blue the business traveller, for instance. The citysense app determines what crowd you're in - this is the 'secret sauce' - tehy'ree going to try and build a social network out of the location data. It's honest in a way Facebook isn't, because you co-locate with your friends. Both actual colocation and behavioral colocation- if you go to the same kind of place at the same kind of time, that's a semantic relaitonship.

They start by building a network of places- like google meta data but for physical locations. For every possible place or street corner they're looking to find is place a similar to place b? Some of this can be got from gov databases, and some from flow analysis. Similar to page rank... if people come to a place from similar types of origins, then leave to similar places later, they can extract that as meta data about the place. eg bankers leave the Financial District, go to an Italian restaurant then go to a similar neighborhood for the night.

They color code bars by the similar inflow and outflow, so they make them semantically adjacent. They are working with an advertising company to change how they target their beer ads.

Then to the poeple: they translate the gps trails of users into flows. As in, what are the odds of finding person of demographic 2 in commercial sector 3, which is fine dining, at 6pm on saturdays: 52%

Measure them not where they live, but where they hang out on average as a probability. They then toss out the actual location data and only keep the matrix. The matrix light up quickly because we all follow very normal weekly routines. (The Dopplr crowd must look super strange to them)

They have 4 million users - with semantic data relationships being the social network.

They identify tribes based on advertising applications:
young and edgy: poor, more ethnically diverse
weekend mole- out occasionally on weekdays, Latino, middle income neighborhood
mature homebody - rarely goes out

This is to help companies better target their ads.

They've had to do interesting re-calibrations recently. Usually the season requires re-calibration, but the economy has caused massive changes.

They're interested in the next network: it's not the online network, it's the offline world.

Etech session liveblogging: Mr Hacker Goes to Washington (Greg Elin of Sunlight Foundation)

(Came in a few minutes late)

Greg was a firehose, forgive my errors and omissions.

DC is like a university with a really massive ROTC program. If the internet is ethernet, congress is token ring. One person speaks at a time, for instance. Once Greg saw more than 10 minutes for a roll call vote--no electronic anything. Congress paper based--so it's not exactly version managable the way people want to stick bills in Subversion, that kind of thing.

Important to realize that Legal code != Software code
Legal is intentionally fuzzy rather than rigorously logical--it's good that way.

It's really not like what programmers are used to. One of the bills going through the Senate during the banking crisis changed a medical benefits bill, turned it into the Emergency Economic Stabilization bill. It would be like a quick patch of your word processor that turned it into a database.

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Etech Session Liveblogging: Real Hackers Program DNA (Ginkgo Bioworks)

GB is "Making the process of engineering biology easier."

Synth bio is the idea that biology is a technology to engineer novel systems- say drugs, biofuels, other sexy sexy projects.

This is to be a flavor of what engineering biology is all about.

We will be installing a program into E coli to make it turn red, glow in the dark, or smell like bananas... We get to pick!

The DNA is stapled to the pages that describe them in the notebook.

Some of the tools of synth bio: biobricks, interchangeable components that can be strung together into programs. The parts registry lets you snap programs together.

iGem participants get a kit in the mail and pick out parts and mix and match them into new programs they want- much like the one we're holding. The Scottish team made and E coli that turned red in response to arsenic contamination.

Standardized interchangeable components are limited, but let a lot more people get involved and democratizes access to the tools. This is still biology- it can seem kind of scary- do you trust your neighbor to engineer biology?

Question from the audience: how do you prevent the terrorists from building smallpox?
Answer: You can't perfectly. "How do you prevent a car bomb from blowing up outside?" You don't, but you can limit it, and create a community that self polices.

Question from the audience: What about release? Would the arsenic detector be scattered on the ground?
Answer: We don't understand how manufactured organisms will interact with the environment. We work with safe organisms, and we don't release our stuff. These E coli are pretty innocuous, so we're going to wash our hands before lunch.

It's pretty unlikely that anyone is going to make anything in a lab that's dangerous right now, but we should think about that.

It's a bit legally gray, the guidelines everyone follows are only required for people receiving NIH funding, and there's some places with local laws (like Cambridge) ... There's no clear answer.

We're punching out our DNA and dropping it in cells. (Ben has returned our vial, #19 and #10 to ice, while the receptive cells take up our dna)

We're installing on a plasmid. "You're literally just mixing the plasmid DNA with the cells." These cells are competent, which means they can take up DNA easily. We cool the DNA, then do a heat shot- then shock it in a 42 degree water bath for 30 seconds, time it, put it back on ice for two minutes. We're disrupting the membrane of the cells and letting them recover. Then we're adding media, food for the cells. Then we're incubating them with our bodies. I'm going to keep mine in my armpit, I think.

Can't mix the three bit of dna, because they're the same plasmid - they are ampecillin resistance plasmid, so there's a space collision, things aren't likely to play well together.

DIYbio.org is a good place to learn about good lab practices.

I am now heading to lunch, incubating a tube of e coli in each armpit. (Will update with pictures after lunch)

Update: I've now transferred my E. coli to a petri dish and a vial, freeing my arms.

...and no, I was in a hurry, and I didn't wash my hands before lunch. Phear my bad lab skillz. (& Know your organisms.)

Synthetic Biology: The conclusion of the very beginning

Note: This ends Quinn Norton's five-part series on Drew Endy and synthetic biology. The earlier installments are Everything you needed to know about human-created life forms but were afraid to ask, The dummy's guide to engineering genes, Play God for fun and profit (mostly fun), and Managing the unmanagable future.

"Biology is a technology for manufacturing," says Drew Endy. Engineered genes could remake mass-production and materials. Cells are proven nanotechnology with a history of creating large-scale output. Look around the room, anything manufactured or grown could very well be produced more efficiently in a cell. From impact resistant plastics to water proof fabrics or moisturizing cosmetics -- it could very well make the most financial sense to design an organism that cooks up what you want in almost any existing manufacturing industry.

All of this is still a ways away. A genetic engineering job today requires a Ph.D in a subject like molecular biology. Often postdoc work is on the job description, experience working directly with genetic sequences, and amazingly comprehensive knowledge of a number of organisms ... and, of course, the ability to be a team player. Genetic engineering is a boutique field. High status, highly trained specialists create changes out of the ATGC's each time they are needed to serve specific business goals. "Imagine if you had to build a mechanical device, or a computer, and your work started with the refinining of ores to produce raw materials, and then next the processing of these materials into custom components, that you eventually assembled to produce a perhaps working system. That's what genetic engineering is like today," explains Endy.

Also: Dr. Endy wraps up on the impact of synthetic biology. (mp3, 5.1m)

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Managing the unimaginable future

Note: This is the fourth of Quinn Norton's five-part series on Drew Endy and synthetic biology. The earlier installments are Everything you needed to know about human-created life forms but were afraid to ask, The dummy's guide to engineering genes, and Play God for fun and profit (mostly fun).

Extraordinary opportunities for yet-unknowable creativity nearly always comes with the threat of catastrophic destruction. In biology, the downside comes up quickly. This is because un-engineered Nature has always been so good at catastrophic destruction on its own.

What happens when the bad guys start making microbes? Thoughts of malicious biology haunt the background of all the miraculous proposals. Indeed, with a little imagination, bioengineered threats could emerge from anywhere. From industrial espionage in the farming sector to massive production of illegal drugs, it's easy to see that a world of synthetic biology will offer challenges well beyond what we can imagine now. Much of our current worry is focused on lethal pathogens, like smallpox or the 1918 flu. The later created a stir in 2005 when a group of researchers published the genome, and then recreated the virus on their own. A bit of nearly all genetic engineers' minds seems to be chewing on the biosecurity problem. Some of the ideas being discussed are controlling access the production of genes, auditing manufactured genes for known pathogenic sequences, and creating comprehensive biosensing in the environment. All of these proposals have well understood flaws.

There is no comprehensive answer to the threats, and it's not likely there will be. While the best minds in bioengineering are thinking a lot about these dangers, it seems likely that management of human created malicious creatures could be its own full time industry, joining our existing war with natural disease. We know we have to go forward. The cat is out of the bag -- even if the good guys complete gave up genetic research, there's no way to stop the bad guys going forward.

Also: Dr. Endy on biotech security. (mp3, 3.2m)

Next: What's next for the microbe hackers.

Wheat Rust is courtesy stellarr on Flickr.

Play God for fun and profit (mostly fun)

Note: This is the third of Quinn Norton's five-part series on Drew Endy and synthetic biology. The earlier installments are Everything you needed to know about human-created life forms but were afraid to ask and The dummy's guide to engineering genes.

Three years after Tom Knight invented the first standard for hooking together genetic parts in a living programming language, the BioBricks standard, MIT put the idea to work. They started a contest for students around the world called the International Genetically Engineered Machines (iGEM) competition. Students began to make and put together parts of DNA code into repurposed organisms. Some were bacteria that smelled like bananas, some glowed red or green, one team even created a cell that built itself protein balloons. Every year the teams can build on the parts they and other students have created. Theoretically, this means next year's iGEM winner could be a balloon-building organism that glows green and fills a room with banana scent. Today, the parts database at MIT boasts an impressive 2,500 reusable snippets of public domain DNA -- all for the taking.

Stringing together many parts or devices, creates systems -- those are what can sniff arsenic or take light impression like a film emulsion. They are the complex forms of many connected devices. Being student work, the quality of iGEM systems is all over the place. But once one student group has put something in the archive, anyone can see how it was done and how it was used. They can contribute novel combinations back into the archive, creating systems of DNA that still others can expand on. It's not at a commercial level, but provides a proof of concept for a much more sophisticated archive. In the mean time Endy sees this open source genetic model as a vital key to getting people playing with DNA.

Endy refers to the students in iGem as "freeform teenage genetic poets." He points out that what they do for fun is still a bottom line business decision in the real world of biotech. It's clear that he's not just trying to create an academic or business model for synthetic biology, but a full culture. Genetic artists as well as students, hobbyists, activists, researchers, and businesses are part of Endy's future. Genetics will be social, political, mainstream, and constructive in an entirely new ways.

[Also: Dr. Endy on Biobricks, iGEM, and a new project that takes parts to the next level. (MP3 format, 3.9M)]

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The dummy's guide to engineering genes

Note: Yesterday we began Quinn Norton's five-part series on Drew Endy and synthetic biology with "Everything you needed to know about human-created life forms but were afraid to ask."

Photo courtesy of Mike & Amanda Knowles, via flickr.

Dr. Drew Endy's approach to the next generation of bio technology depends on engineers, programmers, hackers, social theorists, lawyers and so forth, to inform biology. He believes we can make genetic engineering, like computers, part of every facet of our lives, changing the way humans do their business.

He seeks to put synthetic biology into the hands of the interested, not merely the professional. The potential is to widen the range of goals, to extend this emerging tool to many disciplines.

The key, says Endy, is what computer scientists call abstraction.

Fundamental to what created modern software was that idea that no one should have to type in that monotonous stuff twice. Once something was there, it should just be reused, not re-created. More important, once it was done the programmer didn't have to know how it worked to do it again. The common wisdom became that no one should have to know how a computer worked to make it do entirely new things.

Also: Dr Endy explains Abstraction (mp3, 4.9mg) and Standards (mp3, 3.1mg) for synthetic biology.

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Everything you needed to know about human-created life forms but were afraid to ask

One of the great pleasures of being involved with O'Reilly Media is learning from the many fascinating people who get involved with the company on one level or another. They're Friends of O'Reilly, or Foos. We have occasional get-togethers with Foos, our own Nat Torkington has taken the concept to New Zealand, and we have one -- on the social graph (see coverage in the next Release 2.0) -- coming up this very weekend. While the Foo events are quite off-the-record, the work Foos do is very much public. So we'd like to share with you some of what we're learning. Over the next few days, we're going to use this blog to introduce you to one Foo in particular, synthetic biology pioneer Drew Endy. This multi-part profile of Drew and his work is, appropriately, written by another Foo, Quinn Norton, who will be talking about body hacking at ETech in March.--Jimmy Guterman

Dr. Drew Endy tends to fidget. He motions frantically when he's trying to get something across. "It's hard because we've never made it simple," he explains with exasperation. Endy, a professor at MIT until the end of the school year (he's headed to Stanford), engineers new life forms. He's spent his life doing the hard work of bending the complexity of DNA to his will.

And he's determined to make it simple for you.

Drew Endy is a leading star in a field that's emerging to be the biggest thing since Walter Brooke suggested to Dustin Hoffman he should think about plastics. He's a synthetic biologist, a group of scientists and engineers that take microbes with familiar names like E. coli and yeast and make them do previously unimagined things.

Also: Dr. Endy explains what synthetic biology is. (mp3, 5.7mg)

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