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 .

DIYbio and Main Stream Scientists – 2004 all over again?

Fortune-Blogs Back in 2004 I was flying all over the place, promoting blogging. It was the year The Blogger entered the public eye, came out in magazines, built empires. One of the great debates was the clash between Main Stream Media (MSM) – the newspapers, publishing houses, and TV stations – versus the citizen journalist, the bedroom blogger, the unwashed masses of online writers.

MSM, of course, said that bloggers were not accurate, were not honest, were temporary, that only MSM was the font of Truth and quality information. Well, so much has happened since then. I feel there is still a place for professional journalism, but blogs have settled into their niches, providing a "long tail" (there I said it) of content of varying quality and scope. And, well, blogs today aren't the same as blogs 5 years ago, in the end, they are still just an online publication.

But watching the style and aspirations of the DIYbio crowd reminds me of those days. It seems that the friction between DIYbio types and Main Stream Scientists – the labs and institutes – hovers around the same issues as in the day of blogger vs. MSM.

And I think the change will be just as profound and the outcome just as mundane.

Image taken from Six Apart's post

DIYbio at iGEM 2009

P1000523 iGEM for me was the first time I got to meet folks in the DIYbio "movement." The DIYbio folks from NYC and Boston had a meeting the first night to discuss where things were going. They all knew each other and had collaborated in some areas.

It was nice to see the easy flow of ideas and decisions. As with iGEM, this group is in a very early stage. But already some things are becoming clear as to what it's going to take to keep growing.

One more thing (and I might be inviting a flame war): there is clearly some friction between the iGEM folks and the DIYbio folks. Part of this resides in prejudices towards amateur biologists (unfounded), part in worries about safety (well founded), part in the small difference in culture.

DIY home base
One of the things that happened is that iGEM required teams to be affiliated with an institution. That was a way to ensure safety concerns (indeed, the FBI was a sponsor of the Jamboree, go figure). Independently, the DIYbio groups in Boston and NYC (and I) realized that, while it would be nice to actually do kitchen biology, groups need some sort of entity with which they can buy supplies, teach safety and techniques, and, of course, enter into iGEM.

I'm all for it. In the past months, reading and following and talking to DIYbio folks, my thoughts on hack-spaces has evolved to include more than just a bench, but also seminars, safety certification, mini-grants, and even a store (check out Pearl Biotech).

I was also glad to finally meet Mac, one of the leaders in DIYbio. He's recently purchased a lab trailer, full of equipment. He's now looking for space (too bad my ample backyard is so far from town). His goal is to build this out as a hack-space, also hoping to mix novice and experience biologists, to get some culture and skills transfer.

That's super. I look forward to getting more involved. Mac has a ton of projects in mind and could use some help. And I want to learn from the DIYbio NYC folks who recently formed a non-profit and are acquiring space so that they can get out of their living rooms and get a nice space to play around in.

This is going to be fun.

And here's a video of the folks at the meeting:

links for 2009-11-06