Mac, Sophia, and the philosophy of 21st-century Biology

image from www.flickr.com 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

links for 2009-11-18

“The Machinery of Life” – a great book for molecularly-minded folks

MoL2-cover 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

Building a Minimal Airplane?

Dreamliner 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. 🙂

links for 2009-11-14

Is the interent killing storytelling?

Bard I'm always interested in storytelling in its many guises, so the recent article titled "The internet is killing storytelling" was sure to catch my eye [I got it via @stephanierieger].

The author claims that in the modern hyper-connected society the long-form narrative, commonly seen in books, is losing out to the bite-sized snacking culture of the Web.

I read all the comments, many pointing out that narrative was alive and well, the Web full of all sorts of texts and stories and fan-fiction and such (long tail-ish and thru democratized creation and distribution). While a decent rebuttal of the author's thesis, these comments still missed one key fact (below).

Also, this article isn't really saying anything new, but bringing up a recurring theme. We've heard all this before, so it's a bit odd to see this thesis in a modern 2009 article. Indeed, I claim that this article is even weaker now than it would have been 5 years ago.

Why?

What all the commentors missed was that this whole article and all the comments focused solely on text as the medium for narrative. Humans have had many forms with which to tell stories – dance, art, song, theater, radio, TV – all of which are used in some form on the Web.

I claim that the Web has caused a huge transformation in non-text forms of narrative (in oral culture, as it were). We now have easy to use and widely available audio and visual tools and the Web has become a strong discovery and distribution mechanism for these productions. A scan of iTunes, Jamendo, YouTube, or Flickr will reveal of treasure trove of stories.

And, due to the temporary nature of digital media (either due to formatting issues or deletion or loss) we have more features of an oral culture than a literate culture. And that isn't bad. Unless one feels, like it seems this author does, that literary storytelling has primacy over other forms of storytelling.

Eh, I don't think so.

Image from . SantiMB .