Overweening Generalist

Tuesday, October 29, 2013

Synthetic Biology: Potentials Perilous and Promising

"Synbio," or synthetic biology, is here. It's alive!:

It's already been three years since Craig Venter's team made a species that was self-replicating...and its parents were not a mom and dad, but a computer.

In 2003 the human genome was sequenced. It costed billions of dollars to sequence and took up the energies of people in over 160 labs. Now you can buy a sequencing machine for a few thousand and sequence your own genome overnight. Or pay 23 and Me $99. By this time next year it'll probably be half that.

Synthetic biology, according to Venter, will change everyone's life at some point. Its upside: we can make microbes that eat carbon dioxide. We can generate flu vaccines almost overnight. Tiny critters that generate clean biofuels that are cheaper and as efficient as fossil fuels seem possible. The brilliant Drew Endy of Stanford is gung-ho about genetic engineering and synthetic biology, claiming it already constitutes 2% of the Unistat economy and is growing at 12% annually.

Venter commissioned a panel to study the potential issues in public health and national security arising from synbio. Two big problems jumped out at us:

1. Synthetic biological work had become so cheap that most of the people who were doing it weren't even trained biologists, so there was no understood consensus about standards, ethics or safety.

2.) What standards existed by governments and international bodies were ten years old and so may as well have been 100 years old.

You're probably wondering what I'm wondering: when will someone get hold of some genome of a relatively benign virus or bacteria, tweak it using known methods, then use it as a bioweapon?

You can email a genetic sequence to someone else. You need to buy a few things to tinker with, but it's doable. I'm trying to spook you for Halloween. Is it working yet?

In the 18th century, Giambattista Vico, countering Rene Descartes, asserted that humans can only know what they have made. Only true understanding can come from something the mind makes, and Descartes's notion about "distinct ideas" in the mind as a basis for philosophy was flawed because we did not make the mind; Descartes was doing metaphysics. Vico called his principle, verum factum. That which is true and that which is made convert into each other; anything else is an abstraction. (I linked Vico's idea to Niels Bohr's Copenhagen Interpretation of quantum mechanics HERE, in case anyone wants to see how bent I can get.)

Back to biology, there's the GOF, which is also growing at an exponential rate, or at least ultra-quickly. It's short for Gain Of Function. Here's how it applies to the Pandora's Box of synbio: biologists attempt to combat some potential horrific pathogen by creating it in the lab, so then they can figure out a way to develop a vaccine for it. We can only know what we have made, as Vico said.

At a conference for scientists a researcher said that he'd tinkered with the H5N1 virus then being talked about as a potential killer of millions, if it mutated. It's a simple coronavirus, but he tinkered with it so a host could infect another via transmission through the air. Then another researcher said he'd done the same thing. They both published their papers, in bigtime journals Science and Nature. They knew what they had done could be interpreted as reckless, and indeed: both journals were persuaded to omit the part of each biologist's work that detailed the techniques by which they took a dangerous virus and made it far more dangerous, because who knows which band of deranged and sick mo fos would read this stuff and get ideas? And carry it off? (Beside The State, of course, by which I mean Google "Tuskegee Syphilis Study.")

But...can you really keep info under wraps? ("Paging Mr. Snowden! Mr. Edward Snowden; Please come to the white courtesy phone...")

In reading about the uncooperative governments (SARS in China, anyone?), the paranoia about Western governmental power (read up on Indonesia and their lethal coronaviral outbreaks), governmental snafus, international differences between countries, and just how hopelessly behind the curve biosecurity experts are in Unistat alone...I'm not sanguine, friends. It's only a matter of time. Let us pray the international bioterrorists make a crucial mistake and the deaths are limited.

However, when it does happen? There's nothing more paranoia-inducing than a massively-social-mediated group of people terrified of the invisible death-bringing entities that may be in the very air they're breathing. All bets are off, and it seems just the thing to get Ted Cruz elected President. (Then: watch out, "liberals": all that NSA data could be gunnin' fer ya!)

With seven billion on the planet now, even if a pandemic arose "naturally" and killed off 3-5% of the population (like the Spanish Flu of 1918 did), how much more paranoid are we now than then? Many people who didn't die will go to their grave convinced the Other was responsible...

I hope you're scared now, or I'm not doing my job, on this, October 29...

The old Biology: you observed life from outside that life, wondered about details and behavior and then dissected to see how it worked, or placed the life in some environment and observed.

The new Biology: You're an engineer: you know the life-form because you created it, from genomic information and computer models. Now you watch to see how it plays out. If it moves, eats, respirates and replicates, you've created a new species!

So...yea. The scary part is anyone with a serious political beef, or simple hatred, can align with others and send away for stuff and do what's called 4-D printing: those microbes that were just info on a screen are now ready to be released into your enemy's territory. You send away for stuff, you use steganography (al-Qaeda left a code in a porn video). Sequencers are cheap. The data is there. One fleeting problem: many biotech companies are keeping track of "nucleotides of concern": any known dangerous sequences are tracked: who is it that wants this info?

So: we have bioterror security experts who aren't sure how to determine threats, or if a threat is all that important; they don't know how to surveil those who'd go the whole nine and release something unspeakable, and they're not sure how to combat the pathogens anyway. Supposedly the International community is getting their act together along these lines. But...let's recall some sobering facts: in 2002 at SUNY Stony Brook, researchers took the genetic code for polio and made that virus. Because...verum factum, and Gain Of Function (GOF). If we truly know these bad boys we stand a chance of combating them when they come at us.

And let's not forget that in 2005 researchers sequenced the 1918 Spanish flu virus that killed 50 million people. They sequenced it...and then of course they made it. And the speed and cost of doing this is becoming ever-quicker and ever-cheaper. Just think: the Spanish Flu killed 50 million, but its lethality was only 2.5%. On the other hand, the H5N1 killed 59% of the people it infected. Can you imagine a huge batch of H5N1 tweaked (like two researchers have already done) to become transmissible via air?

(By the way: now is not the time to read this article about how Unistat labs are insecure. Just don't read this, or it might even bum your Halloween.)

Other Bad Signs: in Unistat the CDC and NIH don't have the infrastructure to develop massive amounts of vaccine for something that might appear. How many would need that magic shot or pill? Not as many as those hundreds of millions who'd take Lipitor or Viagra, paying for it all and making investors happy. Big Pharma is in the Big Money game; they cannot afford to spend an estimated $700 million to $1 billion to develop a vaccine or pill, when maybe after the bioterror attack quarantine and international cooperation stops the spread. There's no money in that! (SARS was stifled largely because of quarantine and cooperation.)

To sum up: synbio offers incredible promise, but just one really "successful" bioterror attack by angry young men who take their own version of a merciless God and some old border dispute very seriously...and life on Earth will have truly changed, and not in a good way. Because we have cops and monitors on one hand, but cheap technology, sheer fluid-like information and motivated ingenuity on the other hand. (Please make sure you wash both hands, thoroughly, when you're done reading this morose report.)

Dr. Frankenstein's imperative makes every day from here on out all the more fraught with drama, eh?

Happy Halloween! Muahahahahaha<cough>ahamuahahaha! Okay that's it: I may have failed to scare you, but in writing this - consulting 13 articles and taking notes - I've grown pallid, anemic and weak in my anxiety attack, and it further sickens me to say, "Well, I just hope that all happens after I'm dead and gone, 'cuz..." What kind of morality is that? It's like saying, "I hope all-out nuclear war happens after I'm dead, while your children are still around to experience it."

Now if you'll excuse me. I need to go rest. Oy! (No, but seriously: don't drink and drive on Halloween.)


Bobby Campbell said...

I still get goosebumps over Mark Pesce's throwaway comment on the news in 2010 about a synthetic bacterial genome taking over a cell, "today biology became a branch of engineering."

I took a biology class last year where the professor expressed grave concern over the emerging possibility of curing all disease and conquering death because it would exacerbate resource scarcity problems. To me that seems ridiculous beyond belief!

If we're going to imagine a world where humans can live forever, why can't we also imagine a world where resources can be efficiently allocated, and so long as we're pretending, I would like a pony and some ice cream, please!

In theoretical scenarios, since we're basically just playing pretend, the conclusions seem arbitrary to me. Bad things will happen! Good things will happen! Unforeseeable things will happen!

Though I must say I really enjoy imagineering favorable outcomes...

"In the province of the mind, what one believes to be true is true or becomes true, within certain limits to be found experientially and experimentally. These limits are further beliefs to be transcended. In the mind, there are no limits... In the province of connected minds, what the network believes to be true, either is true or becomes true within certain limits to be found experientially and experimentally. These limits are further beliefs to be transcended. In the network's mind there are no limits." – John Lilly

Eric Wagner said...

Interesting piece. My wife and I watched a Kathleen Madigan comedy video a few days ago in which she praised the show Doomsday Preppers. This led us to watch a bit of Doomsday Preppers yesterday. I wonder if some doomsday preppers have tried to prepare for the sort of catastrophes you discuss.

Anonymous said...

You can't scare me !!

Mainly because I have already been
scared witless by the real things
people have done along these lines.

Island off Britain so contaminated
it will never be clean enough to
live on.
Huge factories abandoned in Russia
with giant empty vats used to cook
up biowar bugs.
The desert around Las Vegas now
blooming just enough to allow the
Deermouse to move into the area.
(It's the vector for Hanta, one
of the lovelier natural problems).

The worst dangers along this line
are twofold, governments who have
already shown they are stupid
enough to make and use anything as
weapons, and the ordinary fools
who think they can safely hit a
real or imagined enemy without being done in by their own batch.

Chernoble taught the Rus about
nukes, the same way Lop Nor taught
the Chinese the same lesson. The
next lesson will probably be just
what you have spoken about here.
There have already been some things
that might be loose bioweapons in
the news on the back pages.

Arguments about nanotech safety
are still raging while the labwork
continues at a hectic pace.

Or as the Vaugh Bode character in
the sewer eating rats said while
the AI machines fought it out on
the surface. "It's only a matter
of time before God intervenes on
our behalf." Cruz is probably of
a like mind.

I was thrilled by the NSA Spanish
phone call harvest for a single
month. Just how many Spanish
speakers are working at NSA these
days ? Enough to listen to it all
or is it for the puposes of making
sure the few who work there will
never be able to produce any real

I realize any meaningful job can
be described as shovelling shit
against an incoming tide of it.
So what is the plan of all this collection, it seems to be to make
sure no one can ever achieve any
useful results.

By the same token, if the spooks aren't listening in on every foreign head of state they should be fired instantly. However a big
budget cut would do them wonders
in the efficiency realm and salve the budget cutting nutties.

Now there's a scary thought.

michael said...


I'm with you on the preference for optimistic imagineering. One thing I wonder about is: we live in this science fiction world, where people have the Internet and phone in their pocket, etc, etc, etc...and yet all too often it seems like, "Yea, but what do YOU have that's better?" I'm not sure we have much perspective on the imagineered "good" while the asymmetry of that one big "bad" seems to hold far too much weight.

I'm not sure if that makes any sense. Maybe amazing tech is now to be expected, while that one very bad tech-based thing that kills a whole lot of people in a spectacularly horrific way...might bring us down. And if so, we seem to be wired to respond to FEAR all out of proportion compared to the "good" stuff (and what we do when we shop for things, bring 'em home, power 'em up, start using them, incorporating them in our lives, and very quickly take those things for granted).

I say let's cure all disease and conquer death and THEN worry about the ramifications.

Biology seems indeed now a branch of engineering. Such a brave new world! I wonder how it'll play out between now and 2023?

All of the ideas you brought up NEED to be discussed much more, in my opinion. And the public needs to be better informed about what's going on with synbio. Just because producers look at the stories and think, "Too complex. We'll bore our audience and they'll change the channel," doesn't mean they're right. Synbio is endlessly fascinating, and I accentuated the scary aspects for a traditionally scary week, when we're supposed to think about death and our own lives.

But there's a ton of very positive stuff we can get from synbio and other mergings of basic research, engineering, and tech.

michael said...


Supposedly the NSA were listening in on EVERYONE when the Sarnaevs were planning their thing. Guess their fancy algorithms weren't up to snuff.

The budgets for spying and big data collection? How are we supposed to get that back in the box? Esp. when NSA has FEAR on their side. And the assertion of something that scares us but is largely unprovable: "We've already stopped 93 attacks."

"You said six weeks ago it was 42."

"Did I? Well, what I meant was the parameters of coordination inherent in the timetables we were given under the document Q23, certain immanent attacks were conducively allowable as countable 'actualities' by National Security memoranda, in full conjunction with the White House and the intelligence committee...that...do you want another 9/11 to occur on our soil or would you rather let us do our duty: to protect and serve the American people."

"Thank you, General. No further questions."

michael said...


I've studied the Prepper community a bit. I find it ultimately as depressing as the Tea Party person who shouted about getting big government's hands off their Medicare. I have no doubt many are building stockpiles of things they think will keep them alive when it's a Mad Mad Mad Max World.

Most entertaining book on prepping I've read so far: Emergency: This Book Will Save Your Life, by Neil Strauss.