Saturday, October 19, 2013

DIY Biology or Our Biohacker Future

Science journalist Lee Billings is releasing his long-awaited tome entitled Five Billion Years of Solitude: The Search for Life Among the Stars, (a nod to the Gabriel García Márquez masterpiece One Hundred Years of Solitude, while referring to the apparent absence of extraterrestrial life - at least, so far.)  Lee's book confronts the puzzle over whether or not we are alone in the cosmos, not from a systematic point of view as I have done (meticulously ticking off possibilities and plausibilities). Rather, Billings takes the reader on a journalist's personal voyage of perspective, with each chapter revolving around the story of a scientist or philanthropist or some other personality whose curiosity helped to push back the shrouding fog, opening up the skies a bit, allowing light to fall upon our biggest enigma.

It is an engrossing book that you'll enjoy anywhere, from that transcontinental flight to enjoying it at the beach… as our planet's ponderously reliable rotation makes a glowing ball of fusion-heated gas seem to "descend" in the west.

== Our Biohacker Future ==

Biohackers constructed their temple for amatuer bio-creativity in 2009, with the establishment of Brooklyn-based Genspace, the world's first government-compliant DIY biotech lab.

As Casey Research commentator Doug Hornig put it in Biohackers, Our Next Computer Revolution or Global Catastrophe in the Making?"Genspace is the democratization of science in a nutshell, a nonprofit funded by membership dues, tuition fees, and donations from supportive nonmembers. You can attach yourself to one of the scientists already embarked on a project, or you can set up one of your own. The only credential you need to bring is your enthusiasm for the subject, with Ph.D.s onsite to help you through the rough spots."

The idea is spreading across the globe. In the U.S. alone, there are now about a dozen community biolabs, or "hackerspaces," as they're known. Along with Genspace, they include Boston's Open Source Science Lab, BOSSLABBioCurious in the San Francisco Bay Area, and Los Angeles as well as Bio, Tech and Beyond, which just opened near me at Carlsbad California. More information on local groups and standards for laboratory safety can be found at

Hornig again: "Everyone admits that there are risks involved in fooling around with synthetic life forms. But the biggest one is the threat of bioterrorism, and that's probably not going to come from the public DIY Bio community. The horrible killer virus that unleashes World War Z is far more likely to emerge from a secret lab of some dedicated terrorist group. And you can be sure that the international intelligence agencies are on high alert for signs of any such development."

As for regulation, the U.S. government so far hasn't taken any steps to control at-home biology.

Or will we hack in code? Arduino's Raspberry Pi  "computer on a board" has dazzled members of the Do It Yourself movement. Now Intel has leaped in with an improved version. It will give away 50,000 of them to universities soon.

There are already hundreds of active Hackerspaces around the globe.

Then there are the replicators. Little mobile M-blocks created by researchers at MIT can seek each other out and self-assemble into larger robots.  This article cites Terminator but I recall Stargate.  Let's do it smart, eh?

Or will nature hack us first? Ask the hornets. Some giant varieties are spreading due to warmer weather and people are dying, especially now that Asian Hornets have spread to Europe and Korea. Reminiscent of a novel I just read (and blurbed) -- Invasive Species by Joseph Wallace.

Not if we get real smart, real fast! Do it by emulating Einstein's brain!  Here's an interesting article about how it differed.

== Clues for our next hacks ==

Naked mole rats have what any animal would want. They live long lives—about 30 years—and stay healthy until the very end. Now biologists at the University of Rochester have new insights into the animal's longevity — better-constructed proteins.

Bad news for Singularity Zealots! Our brains may be much more complex than simply the sum of a trillion synapses . Although the human brain contains roughly 100 billion neurons, it contains billions more non-electrical brain cells called glia.  I have long held that this network of cells does a lot more than just support and feed neurons.  Indeed, I've suggested -- way back in EARTH (1989) -- that the glia and astrocytes might be true computational centers and the neurons serve as flashy communications hubs between them. All major glial cell types in the brain — oligodendrocytes, microglia and astrocytes — communicate with each other and with neurons by using chemical neurotransmitters and gap junctions, channels that permit the direct transfer between cells of ions and small molecules.  Research is revealing that glia can sense neuronal activity and control it. Now this "second brain" is getting a fresh look.

our-final-inventionRay Kurzweil may not agree that glia and internal neuron structures do computing. But he does offer an interesting discussion of the tradeoffs in developing artificial intelligence (AI) taken from James Barrat's new book Our Final Invention: Artificial Intelligence and the End of the Human Era. Dolorous musings abound.  For example, as George Dyson wrote, “In the game of life and evolution there are three players at the table: human beings, nature, and machines. I am firmly on the side of nature. But nature, I suspect, is on the side of the machines.” Indeed, Ray asks: "How can we get an AI to learn what our idealized values are?"  I see no sign - alas - that Barrat and Kurzweil and Dyson have thought this through ... as American women are dying younger than the previous generation.

I've just written a creepy story about this:  Tissue Engineering: How to Build a Heart. With thousands of people in need of heart transplants, researchers are trying to grow new organs.  The "scaffolding" approach is gaining steam.  Watch next year for my novelette that takes it to… extremes!

== Sci Miscellany ==

Only 80 light-years from Earth, a 12 million-year-old planet has properties similar to those of gas-giant planets orbiting young stars. Because it is floating alone through space, rather than around a host star, astronomers can study it much more easily. The planet, which has only six times the mass of Jupiter, was identified by its faint and unique heat signature.

Researchers found that some fruits — strawberries, oranges, peaches, plums and apricots — had no significant effect on the risk for Type 2 diabetes. But eating grapes, apples and grapefruit all significantly reduced the risk. The big winner: blueberries. Eating one to three servings a month decreased the risk by about 11 percent, and having five servings a week reduced it by 26 percent.

Substituting fruit juice for whole fruits significantly *increased* the risk for disease.

A PhD student at University College London, is trying to give schools cheap access to the expensive imaging capabilities that allowed her team to capture the first in-water image of the DNA helix structure.  And to do that, she and her colleagues are developing a £300 open-source atomic force microscope (AFM) that uses 3D-printed parts, Arduino computers and Lego bricks.

Rice University theorists calculate that atom-thick carbyne chains may be the strongest material ever, if and when anyone can make it in bulk. Carbyne is a chain of carbon atoms held together by either double or alternating single and triple atomic bonds. That makes it a true one-dimensional material, unlike atom-thin sheets of graphene.

A Penn State anthropologist can identify the sex of some of the people who placed their handprints on rocks and cave walls. Interestingly, he found that the first cave painters may have been mostly women.  

Like something out of a Robert Heinlein novel, students at the University of California, San Diego (UCSD) have built a metal rocket engine using 3D printing techniques and conducted a hot fire test for a 3D-printed metal rocket engine in California’s Mojave Desert.

== And finally… ==

the-clock-of-long-nowMarek Kohn offers an excellent rumination on "horizons" and why some modern efforts are returning to the view held by medieval cathedral-makers… that it is worth planning on the scale of a millennium.  "At a Hindu monastery in Hawaii, the Iraivan Temple is being built to last 1,000 years, using special concrete construction techniques. Carmelite monks plan to build a gothic monastery in the Rocky Mountains of Wyoming that will stand equally long. Norway’s National Library is expected to preserve documents for a 1,000-year span.

The Long Now Foundation dwarfs these ambitions by an order of magnitude with its project to build a clock, inside a Nevada mountain, that will work for 10,000 years. And underground waste disposal plans for the Olkiluoto nuclear power plant in Finland have been reviewed for the next 250,000 years; the spent fuel will be held in copper canisters promised to last for millions of years."

Explore similar topics in a nonfiction book by Gregory Benford: DEEP TIME: How Humanity Communicates Across Millennia.  Here is Chapter one.


Tim H. said...

If the raspberry pi can run moto 68k code there's a huge fan-written codebase available for the young ones to play with and possibly learn from, not to be confused with mostly BASIC 6502 code.

Anonymous said...

As a pet theory/fancy/idea, I believe a closer look should be given to the more radical view of Meme/Gene hardwiring / instinct as evolution lead us toward sapience.

Tony Fisk said...

Copper canisters...?

Haven't the Finns heard of Synroc?

(In copper canisters, if they must!)

locumranch said...

Just a few closing comments on federalism:

You all make good points about the benefits of federal union: (1) Disproportionate federal aid, (2) tariff restrictions, (3) Blue State access to global trade, (4) imperial glory, (5) common defense and (6) modernization.

Problem is that (1) Federal Aid is neither gift nor charity because it comes with strings attached, (2) tariff restrictions work both ways, (3) Blue State utopias like Manhattan & LA couldn't survive a week without the continual support of their poorer & oft-mocked Red State neighbors, (3) imperial glory is an abstraction, (4) common defense (from whom?) went out of fashion with the USSR and, in regards to (5), I ask you what Red State modernization ??

FYI: Most Red States are 19th Century economies, making do with agriculture, telephones, electrification, horseless carriages & Wright Brother aeroplanes.

So, wink wink, keep your Blue State federal charity and EITHER pay the Red States a living wage, renegotiated on a fee-for-service & a state-by-state basis OR buy all your water, power & staples from overseas and choke on your own industrial & carbon waste.

Ever see a power plant, industrial farm, sewage pond or waste pit in downtown LA or Manhattan??

It is to laugh.


David Brin said...
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David Brin said...
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David Brin said...

1. Red states declare faith in capitalism and market forces. Those market forces deem the products of Blue America to be worth vastly more.

If you wish to deem that the produce of farms and farmers to be valuable in some intrinsic way that goes beyond market pricing then fine! I have often had that thought, myself. But in that case, make the argument and admit you are not a member of the incantation system the the Red States themselves espouse.

Indeed, society had gone with that to a degree by institutionalizing farm& price supports and other systems that super-market-value farms and farmers... and still Blue States run away with it.

2. California is by far the most productive state in every term including agriculture, minerals....

3. Yes, Hollywood preaches at Red America and I can understand resentment. On the other hand, it is from Red America that strident declamations that explicitly claim "You city folk are evil and going to hell and we know how to raise children better!" Then we see worse rates of everything from dropouts to teen sex, STDs, domestic violence, you name it.

4. The children in red states vote every year with their feet, right out of high school.

5. I will stop saying these things in a shot, if they stop waging war on science and every other smartypants profession.

Alfred Differ said...

Hold over comment from last thread for LarryHart:

I'm not so much a supply-side fan as I am an Austrian economics fan. If handing tax money back to people is going to produce hoarding behavior it is obviously best to pay down the public debt quickly as savings rates are tied to interest rates. Giving it back to the 'wealthy' or any particular group isn't the goal I would have in mind, though. Revenue that beats interest payments is and that's just like any other business decision. You try to think it through and then act.


LA depends on its red state neighbors?! Heh. I'd laugh till I split if I had the energy for it right now.

Cities are organisms, but LA is a biome. It is FAR more complex than a simple dependence graph. LA ties in to most of the country and across the ocean to a large number of other nations.

rewinn said...

1. Hollywood (and its satellites TV and Internet Video) is one of the most free-market places on earth. It sells whatever sells. If it's preachy, well then it must be that preachy sells. Atlas Shrugged had its chance. Twice. Maybe someone will do a kickstarter for The Fountainhead.

2. Sewer/power plant? I don't know what counts as "downtown" but you sure as heck don't ship raw sewage from LA to Arizona. And "waste pits"? Most of the recycling sorting in Seattle takes place only a couple of miles from city center; the fraction of truly unusable that goes off to s dump (rarely in interstate commerce) diminishes each year.

3. DIY Biolabs. I would be moderately surprised if there weren't moles working at every one of those labs. Doing real work, to be sure, and probably enjoying themselves as much as all the other biohackers, but also reporting up the food chain. It's a pretty cost-effective use of resources on many levels.

Alfred Differ said...

I have to chuckle at the idea that AI would be our final invention. I know book covers are supposed to sell the content, but history shows we just re-invent the term 'human' as we please. I've seen too many childless people referring to their cats and dogs as fur-kids to believe we won't keep doing it. 8)

Hmm... it would be nice to have a cat that knew not to kill critters on the endangered species list and wipe out everything else around us. There is a DIY project. 8)

Alex Tolley said...

Brain complexity: It seems to be an article of faith that complexity = function(neurons, connections). Thus when other brain cell types are implicated in possible cognitive functions, it is assumed that the complexity level must be higher. This then is used as an argument against AI.
While that may be, it should also be considered that it is possible that at least some of this apparent complexity is more about redundancy, and could be replaced with much simpler circuity.
Clearly we use our wetware to do some things that are innately simple to emulate on a [much simpler] computer.
Hopefully we may get some more clues as brain research continues to explode, and simulations start to seriously elucidate some of the mechanisms of components.
We also don't need to assume that super fast, synthetic intelligence will be superior, on its own, to human brains interfaced with super fast machine intelligence.

$300 atomic force microscopes? Just wow! Can someone figure out how to make a small, cheap mass spectrometer?

Tim H. said...

"Second brain" reminded me that someone recently declared Bottle-nose dolphins stupid because of an excess of glial cells. Perhaps OGH can have a bit of fun with that?

gregory byshenk said...
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gregory byshenk said...


"Ever see a power plant, industrial farm, sewage pond or waste pit in downtown LA or Manhattan??"

Yes, as a matter of fact. The ConEd plant operating at 15th and FDR in Manhattan until 2002(?).

I agree, "it is to laugh."

David Brin said...

Guys! Drive traffic to:

Salon Magazine has featured my proposal for a unique and potentially effective way for individual voters - one at a time - to rebel effectively against the political crime called gerrymandering. It requires no changes in law, no court decisions or ballot initiatives. We could all start this rebellion tomorrow, without any cooperation from a corrupt political caste. It would benefit BOTH Democrats and Republics as well as third parties. Above all, it would reduce the radicalization of American politics that is tearing the country apart.

The proposal is simple, effective... but it might call for many of you out there holding your nose for five minutes. A small sacrifice to save the republic.

Have a look... and spread the word.

paul hays said...

Interesting that I come across this the same day O'Reilly announces a new DYI Bio magazine:

Can't wait to get to Carlsbad, although that might not be until next summer.

Paul451 said...

Re: "A modest proposal..."

Interesting how many commenters over there miss the point. "NO the solution is to MAKE them STOP gerrymandering and MAKE those states introduce [my preferred system]!!!!!1one!"

Of course, you can't get make "them" do anything. "They" created the gerrymandering to get into power, it isn't in their interests to undo it. That's the point. Hacking the primary is the first necessary step in getting control from "them". (Or the first few steps.) Get the minority in the gerrymandered district energised again, use them to counter the extreme minority in the dominant party, put more people in power who will negotiate with anti-gerrymandering electoral reformers, end gerrymandering.

An additional point you might want to make in any future columns (or add to this one if Salon allows post-article addenda) is that this isn't just about House elections. Many of the states with the worst gerrymandering in House districts are trying to assign their Electoral College votes according to a majority of (gerrymandered) districts, rather than a majority of the actual vote in the state. If they succeed, they will own the whole system, top to bottom, regardless of the actual vote. Knowing how to fight back under such a system is vital.

Alex Tolley said...

@DB - I don't understand why you are claiming registering as the opposition party to vote in closed primaries is "your" proposal. This solution was being touted by Conservative radio hosts at least back in the 1990's to upset Democratic candidates in local and state elections in California.

It even worked for Conservatives because of their relatively high listener population and their ability to evoke so much emotional energy to overcome their "enemy".

matthew said...

My buddy Dave points out a factual error in your Salon article. To quote Dave "Arizona, a red state, has an Independent Redistricting Commission and it's been there for the past two redistricting cycles."

David Brin said...

Arizona is purple.

matthew said...

I disagree with Arizona being "purple." On a state level it is deep red - Governor, both houses,the courts. Both US Senators are deeply red. Only on the Congressmen level is it close to "purple," 5 Dems to 4 Repubs. And the breakdown in the US House is *due* to the independent redistricting. The House went Blue in the 2008 tsunami, then Red in 2010, now Blue again, bucking the national trends in 2012. The commission has a lot to do with this.
Demographics make it "purple," but this whole discussion is about demographics not matching political representation.
I just do not see your argument here.

David Brin said...

MAtthew one might as well say "west coast" since Arizona can be lumped with CA, OR and WA all of which have done this. The Progressive movement of 100 years ago had its heart here in that region. Arizona is decidedly not deep red.

David Brin said...