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"To formalize this idea, I designed a speculative definition of life named the “Cellularity Scale” which shows how five different living properties accumulate at each subsequent stage." [by @jamesking]
links for 2010-07-03
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"We ask filmmakers to share their cinematic visions of a future biotech society. "
links for 2010-06-29
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"In a lab at the American University of Sharjah, in the United Arab Emirates, Ginger Krieg Dosier, an assistant architecture professor, sprouts building blocks from sand, common bacteria, calcium chloride, and urea (yes, the stuff in your pee)."
Caveat: “The results show that working with natural processes is not necessarily equivalent to sustainable practices!” "
links for 2010-06-28
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"The good PhD programs are the ones that let you explore and change your mind and let you work in any lab that will take you. The good labs are the ones that let you explore and define your own path, support you through thick and thin while still allowing you to establish your own scientific independence. The good new fields are the ones that grow from collaborations between people with new ideas and different backgrounds."
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"As the first film about synthetic biology, Synbiosafe is a great introduction and hopefully the start to something bigger. Indeed, the filmmakers are now sponsoring a film festival for new films about synthetic biology called Bio:Fiction, with awards for best short fiction, best documentary, and best animation."
One more thing I missed by being too too slow. At least I've gone through this year marking things I need to remember for next year and can (slowly) put into motion.
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"It is possible to do everything in washable, reusable glass test tubes with reagents made from scratch, but kits with disposable tubes and pre-mixed chemicals can save hours a day, time that adds up when you're a grad student."
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"By defining arbitrary standards early on in our understanding of how these genetic elements work in their rich biological contexts, and early in our ability to engineer novel functions, we lose sight of much of the complexity of biology and get stuck in what could become difficult and useless technological cycles."
links for 2010-06-26
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I particularly liked this seminar because it was about a trend that challenges old notions of Statism. The 20th Century was the rise of the State (and nationalism and so forth). But I see the early 21st Century, with the dissolution of the Cold War empires, further break down of States into their representative cultures, the rise of potential City-States, the focus away from over-lording nations to smaller communities. Does this spell the end of the State? Gilman points out that deviant globalization is a challenge to notions of Statism (most pointedly said at around 1h03m of his talk). My thought, would "Failed States" be "Failed" if we didn't expect a "State"? Can we have a world where there is no State?
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"The term natural theology as used by Gifford means theology supported by science and not dependent on the miraculous."
A while back I listened to the In Our Time episode on the Gifford Lectures. The description of Gifford's theology ("awe") certainly reminds me of Magical Nihilism.
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"No external power is needed: the lift lock functions by gravity alone using the counterweight principle."
I saw this on TV and have been thinking about it since. It's a great example of electricity-free machines that do amazing things. I like examples that remind us of a time before electricity, because I think we've become lazy and can only think of electronic and digital computer-based machines these days.
This is why we need to take back the Cloud
Services like Twitter and Facebook have centralized our communications, such that we depend on their skills to keep their part of the network up (let alone, safeguarding all the data they collect from us). But, unlike electricity companies and telcos, who have their pseudo-monopolies highly regulated, we are stuck _trusting_ that Twitter and Facebook won't do us harm.
But how many times will we allow them to shut down their service or play games with our data?
Twitter this week seems unable to stay up. Or, maybe they are just spreading out failure rather than having a total melt-down (a micro-down?).
I think this would not be happening if all our communications and data lived in our hands rather than someone's servers in the Cloud.
How does this make you feel?
links for 2010-06-23
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The House voted 150-1 this afternoon to approve changes to state driving laws that ban texting while driving and allow doctors to alert the state that a patient might be a dangerous driver, among other provisions.
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"A 5.0-magnitude earthquake that struck the Ontario-Quebec border region in Canada this afternoon sent tremors throughout the Northeast, earthquake experts said. At least two buildings in the Boston area, more than 300 miles from the epicenter, were evacuated due to concerns about the shaking."
Everyone at work felt it. I was out and about and didn't notice it.
DIYBio meet-up – Folk Microbiology
It was a night of culture – yoghurt cultures. Vaughn Tan shared his passion for yoghurt with about two dozen captivated future yoghurt makers. He spoke about the biochemistry and microbial ecology of the process – ways to optimize the proteins in the milk, effects of inoculation temperatures, the activities of the different bacterial populations in the culture.
Complex systems
The coolest thing Vaughn explained was about the three key populations of bacteria in yoghurt, their optimum growth temperatures, and how he varied inoculation temperatures to encourage the right populations of bacteria to grow. He pointed out that the usual yoghurt recipes keep the yoghurt culture at a single temperature; this likely diminishes the cultural diversity, reducing the quality of the yoghurt. It was clear that Vaughn’s delicious yoghurt benefitted from a multi-organismal systems understanding.
Ancient cultures
Of course, he brought samples (tasty!) and encouraged everyone to take a bit home. The story around this strain was that Vaughn got it from the Google yoghurt three years ago, and the Google cook apparently got the strain from India, where it was already 500 years old, so we joked that the strain was 503 years old.
But Vaughn mentioned that these complex cultures are always changing, so they really are not the same culture when folks take samples to new places. Also, most cultures come from a previous one unless someone starts one from nature, so it’s highly likely this culture might be even older than we think.
Vaughn was also encouraging us to take some home as an insurance that this strain never dies out. That made me feel that I’ve become part of Vaughn’s network of apprentices, carrying the “flame” of this strain.
Here’s the culturing guide for download.
The cultured crowd
Vaughn led a great discussion, and the audience was quite engaged. Mac posed a great question regarding the copyright of strains, if there were legal ramifications to using strains taken from commercial yoghurts, such as from Vaughn’s favorites Stonyfield and Seven Sins (I think that’s what it was called). I joked that commercial strains could be fingerprinted for copyright protection.
In the spirit of Folk Microbiology, Keegan brought his microbial battery. It also uses a heterogeneous bacterial culture of aerobic and anaerobic bacteria to create a useful electric gradient.
Also, I brought a few bottles of my own home-brew (an IPA) for everyone to enjoy. Alas, my brew was started with commercial yeast, most likely mono-cultural, though, no doubt, itself an old strain. Vaughn urged me to experiment with lambic-style open-air inoculation of my beer, with the potential benefits of a heterogeneous culture. Heh. Could be interesting. And since sometimes I inoculate with a bottle from the previous batch, I could then start my own strain of beer yeast to hand down to future generations of home brewers.
Awesome experience
As an aside: I brought my 15 year old son along. My highlight of the evening was watching his wonder as he met with everyone, saw their demos, read some books off the shelves, and, basically, saw that there are many ways to express one’s curiosity and creativity. From dirt batteries, to electronic poi, to ancient bacterial cultures, his expanding world was pure joy for me.
links for 2010-06-21
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"As we return to the realties of our day jobs at the end of a brainstorm, we run into road blocks, inertia, committees and other hazards that can water down ideas or shut them down entirely. That's what organizations do well."
Can you say "Jell-O"?
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"The issue of unusually high phone charges is currently under review by the Federal Communications Commission, which is considering regulations that could include requiring carriers to notify customers of unusual activity on their accounts, much like credit card companies already do. According to a recent survey released by the agency, about 30 million US mobile phone customers have received exorbitant bills that are unwarranted, a problem the agency refers to as “bill shock.’’"
Do we need a DIYbio academy?
Among my many ideas I have lying around is some form of institute to support the DIYbio community. This is different from the meet-ups happening in places like Somerville, San Francisco, Houston, and New York. And this is a bit more than what DIYbio.org is providing (sharing of ideas within the community).
This idea adds some pieces that seem to me to be missing (please correct me, of course). I’ve been turning over these thoughts for some time, and since nothing has really materialized (remember, I have a high idea-execution quotient), here are my thoughts.
In my notes, I call it the Molecularist Academy (why? check out the URL above). But the name is inconsequential, what’s important is the mission – Funding, Education, and Outreach.
The mission supports seeding of money – to jump-start activities; legitimacy – practitioner education and safety (certification?); and advocacy – promotion and community education to communicate what DIYbio is about and what folks are up to.
Funding
There are a few interesting funding models out there, such as Kickstarter, Biocurious, and Awesome Foundation. My thought is to create a traditional funding system backed by large sponsors and donors to provide DIYbio-specific grants for exploration, seeding ideas, and to support activities. This funding system would have someone actually reaching out to sources such as biotech industry associations (around here, the Mass Biotech Council), leading biotech businesses (around here, Biogen, Genzyme, NEB, among others), the NIH and NSF, institutes like the Wyss and Venter Institutes, universities, and community organizations.
I do think there’s a bit of a local focus needed, as I feel the biggest contributions DIYbio can make is actually in the local communities the different groups have sprung up in.
And by creating a formalized fundraising and granting structure, the hope is to build an endowment that lasts as the DIYbio community grows. (and I've wondered about alternate ways to fund and legitimize practitioners, in an HHMI-sort of way – more in another post)
Which leads to the next mission focus.
Education
I carry a lot of baggage from my institutional science days, so I am always stuck between letting a thousand flowers bloom and hoping folks don't kill themselves or others while futzing with biotech tools.
The education part of the Academy would set up courses and seminars to teach techniques, science culture, and, most importantly, safety certification. The Academy would be vetted by existing safety organizations and provide legitimacy to the practitioners. And, there would be a structure of re-certification and continuing credits sort of education.
Safety is a big deal and my brief foray into how to communicate it made me realize that it’s much more than just putting up a bunch of pages of regulations and recommendations. Folks like the FBI and the local regulatory bodies likely want more structure.
As part of this Education mission, I’ve also been trying to gauge the need for a patent clearing system, to make sure DIYbiologists are working with the appropriate product licenses, which suggests the Academy should work with tools providers to create special DIYbio tinkering licenses.
And that leads to the third and final part of the mission.
Outreach
This is public outreach, outside the community.
I’ve spent less time thinking of this part as the folks from DIYbio.org already seem to be doing a good job of reaching out to the public and news groups to explain what DIYbio is and can do, and reaching out to agencies who should consider the implications of DIYbio.
And I know there’s been talk of extending this outreach to courses and seminars to engage schools, local communities, and influencers to make DIYbio part of public thinking.
Outreach should also include working with regulatory and policy agencies to take DIYbio into consideration when revising or creating regulations and policies. DIYbio.org has been very good here too.
And, finally, as part of outreach, would we need to have an Asilomar-type event, bringing stakeholders together to hash out the future of Natural Philosophy in the 21st Century, particularly as it pertains to Biology and non-institutional biologists?
There it is
So there’s my Academy, supporting funding, education, and outreach to promote DIYbio. Of course, this could be built upon the existing DIYbio.org structure. I just wanted to get these ideas out there.
What do you think?
Image from tiseb
As an aside, I was looking more into Biocurious and see they are thinking the same things, though still with a crowd-funded model.