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"The Center for PostNatural History is dedicated to the advancement of knowledge relating to the complex interplay between culture, nature and biotechnology. The PostNatural refers to living organisms that have been altered through processes such as selective breeding or genetic engineering. The mission of the Center for PostNatural History is to acquire, interpret and provide access to a collection of living, preserved and documented organisms of postnatural origin."
Video: DIYBio meetup 22nov09
We had a DIYbio Cambridge Boston Sommerville meetup this past weekend to get familiar with a nice new hackspace, The Sprouts, to come up with a project for the next few months, and to move and set up equipment in the current space.
The great folks at The Sprouts actually want a wet-space for DIYbiology. They gave us some space and they even had some equipment. We added to that the equipment Mac picked up from a failed biotech.
The whole moving, setting-up thing was quick. We had Kay, Mac, Manuel, Paul, Charles, Jason, and I there, so the "many hands" made the work lighter.
I was happy to see things happening, space being set up, projects being set. Of the things on my to-do list, a few have been now knocked off, allowing me to join existing set-ups.
I took some video of what we were up to.
One last thing: I am so pleased with The Sprouts. They only opened in August, but show great promise. I hope that our group can be part of their growth and give back as even more than they have already so generously given us.
links for 2009-11-23
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"“The level of ingenuity in the Third World to reuse things is so great. We send things that a lab here would say, it’s not worth the expense to fix it. But people in the Third World have this kind of MacGyver mentality where somehow or other you make it run again.’’"
links for 2009-11-21
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"Hey DIYbio-Boston peeps. I’ve been making progress on getting us a lab space here in the Boston area."
So full of awesomeness.
Mac, Sophia, and the philosophy of 21st-century Biology
Mac has written two short but deep posts, inspired by a talk by Sophia Roosth. What inspired Mac was Sophia's "anthropological insight" that DIYbio is "domesticating" Biology.
While I don't feel that it's an explicit doctrine, domestication of Biology is indeed the spirit of what DIYbiologists are up to. It's something that arises from the curiosity, openness, and tinkering that represents the DIYbiolgist "ethic." Sophia puts it in terms of "episteme" (Knowing) and "techne" (Doing).
Biology, as a discipline, is young in many ways – "science" itself is a product of the Enlightenment. And, as a focus of understanding, Biology is old – Aristotle was a biologist.
But domesticated Biology is at the core of civilization: thousands of years ago folks were breeding animals and plants, and brewing beer, bread, yogurt, and wine. These are the heart of Genetics and Microbiology and Biochemistry.
Mac made a recording of Sophia's talk. It's brilliant and really expresses DIYbio (and synthbio) as it is today and where it can lead. It's a must-listen for anyone interested in the future of Biology.
She makes a very nice story of the mind-sets of institutional and non-institutional scientists. And she pivots around the Homebrew Computer Club analogy as a way to think of the where DIYbio is going.
In many ways, she reminds me of the talks Dana Boyd gave, back in the day, as she watched the early evolution of social networking – Sophie brings together a range of threads from different disciplines to provide some coherence and understanding of the events and thinking unfolding right in front of us. Sophie has articulated what DIYbiologist just knew, just "did," in their hearts.
I think her insights just accelerate the nucleation of the "movement" at these early stages of exploration.
Go listen to it.
Image from pusgums
links for 2009-11-19
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Meh, I think that what they were measuring at the time needed a separate measurement – blogs. Now, all that is mainstream and mundane, and, as you say, mixed in with other forms of communication and engagement, so they are a bit irrelevant now.
We were using them to track the quality of Nokia Conversations and noticed that it was superseded by better metrics already in mid-2008.
links for 2009-11-18
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Brilliant analysis of choose-your-adventure books. [via @alfie]
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Layer upon layer.
“The Machinery of Life” – a great book for molecularly-minded folks
I've been meaning to share this for the longest time. I've had this book for ages and never tire of it.
"The Machinery of Life," by David Goodsell, is an illustrated journey through cells and proteins and macromolecules – at scale.
What I like about the book is that it attempts to show what it really looks like if you're the size of a molecule – the crowding, the relative sizes, and so on.
It's a really fascinating book for someone like me who has his head in the (molecular) clouds. 🙂
There is a review of the original edition (PDF). A nice phrase from that review was "cellular numeracy," referring to the way Goodsell places things in scales, making us realize the relative sizes of molecules and cells.
At the iGEM Jamboree I saw a color image from Goodsell. After searching a bit, I now know that there is a color edition of the book (just out in 2009?), updated with new molecules, too. You can see more on Goodsell's own pages at Scripps.*
I highly recommend this book for anyone messing with molecules, to get a good idea of what the macromolecular landscape truly looks like.
Enjoy!
*It's a shame that the Scripps pages are so 1999-ish. The site needs to be more visual and more up to date.
links for 2009-11-17
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While on the topic of logo evolution: Here's Morton's Salt
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I have a fascination for how brand logos evolve over time. Pertinent, as well, for my current employer…
Building a Minimal Airplane?
At the iGEM Jamboree there was a lot of discussion of Minimal Cells, cells that have the fewest number of components to function as a laboratory organism. One of the key benefits is that it's a defined organism that does only what it needs to do and gets out of the way of the main things someone wants to use them for, say, to create an engineered machine.*
From the discussions, a few said that the route to a Minimal Cell was to subtract components from a current cell and see which ones were essential for operation.
That didn't sit well with me. And it took a while for me to develop an analogy to explain why.
To me, removing components from an existing cell to create a Minimal Cell is like removing components from a Boeing Dreamliner to see what's essential for an airplane (a Minimal Airplane could be like a Wright Flyer).
The mistake is forgetting that even bacteria are highly complex and evolved organisms with complex multi-subunit enzymes and structures. That complexity causes a limit to what can be removed, simply due to the complexity-overhead the bacteria has accumulated over billions of years.
In the plane analogy, the Dreamliner has a ton of essential components, say fly-by-wire, that really were added in evolution, replacing a simpler version, such as manual flying. The function, "controlling the flaps," is what's important, not the component. And the fly-by-wire system makes a whole load of other systems essential (complexity overhead), but which could be dispensed with in a manual system.
Makes sense?
I suppose I am of the school of bottom-up rather than top-down construction of Minimal Cells. And I suppose these discussions have already happened. [Indeed, Foster and Church's 2006 paper "Towards synthesis of a minimal cell" is a good foundation paper.]
I'm not trying to knock on all those working on Minimal Cells. here is a benefit to top-down reductionism, teaching us which pathways and functions are essential, even if we are not finding out the ideal components.
I'm just trying to develop a metaphor for myself to help me think of how to build a Minimal Cell.
That's all.
Image from Boeing
*Heh, one interesting thing I noticed at the iGEM Jamboree was a vocabulary developing around synthbio – machine, quorum sensing, chassis – words I've never used before in biology and that come from engineer-speak. I like it. 🙂