maradydd | [PSA] Biohacking FAQ #2: "But what if you end up making grey goo?"

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[PSA] Biohacking FAQ #2: "But what if you end up making grey goo?"

Over the last 24 hours I've seen a lot of concern and speculation about what happens if one of my experiments somehow "goes out of control" and turns into some kind of "grey goo" event. It seems that there's a mistaken impression that I'm just randomly mutating things (perhaps with UV stimulation) to see what comes up. This actually couldn't be further from the truth, so let me explain what I'm really doing.

How Your Genes Work can be summed up in a single sentence: "DNA makes RNA makes protein." Your genes are instructions for making several different types of RNA, and those RNA molecules assemble the proteins that your body is made of and which make your body run. Some proteins are structural, some are enzymes used to catalyze chemical reactions (such as digestion), some are used to transport other molecules around (e.g. hemoglobin, which carries oxygen around in your red blood cells) -- proteins are everywhere. So, when I think about something I'd like for a cell to do, I start looking around for relevant proteins.

In the case of "let's detect melamine", I went to MetaCyc -- a browsable database of metabolic pathways -- and looked for proteins which interact with melamine. I found one, called melamine deaminase. It's the beginning of a metabolic pathway called the melamine degradation pathway, which -- go figure -- takes melamine apart. To use this reaction in our detector, we'll need to give some species of bacteria the ability to produce melamine deaminase, which means giving it the appropriate gene. To do that, we either extract the gene from a species that already has it, or we get a lab like IDT to make it for us. Then we insert the gene into a plasmid, which is a circular DNA molecule that a bacterium can "take up" in order to gain some new function.

So, no, there is no deliberate randomness going on here -- rather, it's a concerted effort to make just one type of bacteria do just one additional thing (or, really, some sequence of additional things). The whole experimental setup is also designed so that if I screw something up, the bugs die and that's it. And, naturally, I'm doing everything I can to make sure that stray spores, phages, and other contaminants don't end up in my experiments -- heat sterilization, alcohol sterilization, flame sterilization, you name it.

Do you need to worry about these synthetic bacteria degrading you? Only if you are a whiteboard or certain species of plastic fork.

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Over the last 24 hours I've seen a lot of concern and speculation about what happens if one of my experiments somehow "goes out of control" and turns into some kind of "grey goo" event.

Wow, idiots.

More like "ignorance", IMO. But ignorance is easily countered by fact.

Of course, if people don't listen to the fact, then they're idiots.

Completely brilliant!

http://www.cannabistv.com/action/viewvideo/169/tissue_culture_media_prep/?ref=Loki777

Nice clean box! Did you make it yourself?

I see you also put your plates in ziploc bags. I use them because lactic acid bacteria are facultative anaerobes -- put the plates in bags, add some CO2, and close the bag up. What's your use case?

He's got a thread here... Its not mine, but I think its hella cool...

http://forums.cannabisculture.com/forums/ubbthreads.php?ubb=showflat&Number=1399459&fpart=15

What are you using for a power supply for your gels?

I put one together from discrete components; it runs off wall current. I can try and dig up the schematic if you'd like a copy.

Thanks for the link! The pictures are awesome. I want to put together my own clean box now.

I've got one and I was just curious if you preferred constant current or constant voltage, or both?

I loved the pics too. Do you have any pics of your setup?

The reason he puts the dishes in ziplock bags is they are sterile and the gloves break often. Having the dishes sealed keeps them sterile while gloves are replaced and the box is preped and de-contaminated.

I love this thread. "Now, they've sequenced the THC gene..."

"They have? This is so? That's a super big piece of the puzzle for cripes sake. How large a sequence is it?"

[INSERT SEQUENCE OF ENTIRE THC GENE INTO FOLLOWING POST]

I like this Loki person. He has style. If you're a member of this forum and noone's mentioned it yet, can you direct Loki to the Tobacco Mosaic Virus? It's a large tobacco virus that can be induced to infect other species and is a common tool in plant recombination. It might/might not be a better delivery method than a gene gun.

Your idea horrifies me.

What? Why?

Well, before we go on, I may be misunderstanding something... you said "induced" so... how infectious is this virus?

I had the vision of a virus that makes plants produce THC unleashed on the world ;-) I know that would be some people's nirvana fantasy, but...

Modifying the viruses payload wouldn't make it a universal infector. Modifying viruses for gene therapy is even more anti-competitive than modifying bacteria. In modifying a virus, you don't just add traits to the existing genetic payload, you swap out great chunks of the viruses existing machinery. A highly infectious virus carrying a trait you want does no good if it wipes out every cell it infects. So, what you end up with is more of a nano-scale lab tool than a viable disease.

But, let's suppose I am totally wrong and your fears are entirely justified. I'm not taking this tack to bait you or anything, it's just a good thing to consider. A pan-species infecting form of THC-adder virus gets out and starts infecting random plant cells with the genes that could conceivably be used to synthesize THC. What happens then? In most cases (and by most, I mean an arbitrary row of nines with a dot between the second and third) nothing noticeable will occur. No THC synthesis, no real change in the plant. Directing a virus to insert its genes into a specific chunk of a cell's chromosome is still beyond us. You have to get lucky to have the gene end up somewhere it can get expressed in an organism.

So, with a spreading plague of reeferness, we're going to see a bunch of "lucky" events, some of which will occur in the seed-forming bodies of plants, producing offspring that will synthesize THC somewhere in their tissues. Then a force much scarier than the DEA steps in and probably wipes every last one of them out. Every erg of energy a plant gets is normally devoted to growing. metabolizing, or reproducing. If you've stuck in some plans that say to spend it synthesizing a molecule that's otherwise useless to the plant, it's not spending as much energy doing the stuff it needs to do. When it's not performing as well as its neighbors and predators are, it's going to fall behind and probably go extinct. Since no-one would realize that this particular plant was of the rare THC-making strain, noone's probably going to care when it shuffles off.

There are two common exceptions to the old innovation-equals-death problem. One is isolated areas. If the virus manages to catch a plant somewhere with low competition for resources, the gene-expressing plants might well survive and even last long enough to mutate up a use for all that THC. The other area? Human-controlled areas. We love to take crazy, messed-up plants and cultivate them at the expense of everything else. If humans find your non-pot THCmaker, they might choose to cultivate it for whatever reason. Heck, we already cultivate deeply malformed crab apples and bananas - and the founding fathers wouldn't even recognize what we call maize these days. One more cultivated plant in human history wouldn't come as much of a shock to anyone.

I love the phrase "spreading plague of reeferness" more than anything I have seen all year.

I PM him once in a while and will mention it to him.

He just sent me pics of his upgraded clean box. He's got a mini-centrifuge in there now. And a homemade 3 tube micro thermo-cycler that's about the size of 3 packs of cigarettes.

Rock! I love my microcentrifuge, and have been meaning to put together a thermocycler (an OD600 meter is higher on my list of small projects to knock out, but I'll be PCRing soon enough). Did he use Peltier devices?

Yeah, two 138w 4cmx4cm ones with heat sinks for a PC on either side of a lead core. Its pretty cool. The core is a lead block he machined with a dremel tool. :)

Sadly, the place most of his pictures were hosted changed domains or something and everythings gone now. I'm sure he'll repost stuff because he was pretty excited about the degenerative primer PCR work he's done. He told me he's been checking out used DNA sequencers on eBay. He's totally OCD ;) He can't stand not knowing exactly whats going on. We've chatted for hours about testing for gene expression.

What if I am a psychotic schizophrenic and really believe I am a plastic fork?

It seems to me that the statistical potential for someone such as yourself to inadvertently loose a catastrophic biological agent onto the world is minuscule at best, particularly when contrasted with the statistical potential for such an incident to occur as the cumulative result of (a) the notorious and well-documented inversely proportional relationship between the efficiency of a man-made complex system (such as a military-industrial laboratory) and the number of variables in said system (such as employees), and (b) one of any number of highly-classified, but nonetheless widely-rumored, directives to such corporate entities to specifically research just such agents, even if such directives are issued with the sole intent to prepare abatement strategies in the event that such an incident occurs at the hands of others.

In short, why the heck are they worried about YOU?!

Most people don't understand biology, and don't believe that someone not wearing a white coat and working in a fancy lab could have any further understanding of it than they do.

People fear what they don't understand.

One of the things I most want to do is help people understand this stuff.

I would nudge the thought somewhat:
Provided that biohackers are being safe and rational people [and posessed of both sense and intelligence] there is a near zero chance of evil plauges. The flip side is that, like every other field, some number of incompetents get in thinking they are briliant and replace careful detailed work with reckless wankery. One of the latter people is more likely to get on a darwin award list through explosion, poisoning, turning themselves into a pitri dish, but could [low but nonzero chance] let something bad loose on the world.
That said: I have met enough of that later group well on their way to, if not already having, PhDs.

Even if you were just "randomly mutating things", you'd be doing no worse than the natural world. I have a hard time picturing the vacant ecological niche your critics expect the result of "a lab mistake" might come to occupy. Do they imagine that outside of the lab there is some vast expanse of unoccupied, non-biologically-hostile planet that the "escaped experiment" could suddenly take over? Maybe you should clarify that the majority of your sterilization concerns do not involve preventing your monsters from getting out, so much as preventing the monsters already randomly wandering around every surface of the planet from getting in and ruining your work!

To quote Rudy Rucker (http://www.boingboing.net/2007/05/29/rudy-rucker-on-synth.html) on what is likely to happen when lab-developed microorganisms escape into the wild:

I have a mental image of germ-size MIT nerds putting on gangsta clothes and venturing into alleys to try some rough stuff. And then they meet up with the homies who’ve been keeping it real for a billion years or so.

Word.

One of the key points we make in the DIYbio safety manual (a work in progress) is that attentiveness and good safety practices are key to good experimentation, because an accident can ruin weeks' worth of work.

But ... but what if it turns into The Blob and gets loose? Think of the children!!

If the blob will clean the room before it leaves, the children have to take their chances.

*roffle*

Priorities. :)

Now, the question becomes how do we replicate several hundred million MORE of you while fostering the collaboration and cooperation so essential to achieving the continued Uplift and Upgrade of All Civilization as we Know It Could Be?

I understand the fear, but I don't subscribe to it. I believe that those mongering in said uncritical fear are to opposed -- through the power of education -- at every opportunity.

IMO, "we" cannot control whether or how the Gray Goo ultimately destroys us, if it gets us before the ice caps do; we can only educate and advocate responsible investigation and Open Scientific Innovation such as long championed by social entrepreneurs and colleagues such as Joseph P. Jackson.

Personally, I think methane hydrates (http://www.independent.co.uk/environment/climate-change/exclusive-the-methane-time-bomb-938932.html) will get us before the ice caps do, but that's neither here nor there.

I've been eager for clones and braintaping since I was a small girl, but so far, the best I can do is be an evangelist for science by learning from others, sharing knowledge, teaching people, and encouraging others to do the same.

Good explanation; looks like pitchfork sales are down 40% and most of the torches went out.

However, I'm afraid The Outer Limits is still writing a screenplay for a cautionary morality tale about how you shouldn't be "playing god" with the universe, as doing so invariably results in your slow and horrible death via latex prosthetic makeup.

The Law of Unintended Consequences can be a real bitch...

I'm not a proponent of "gray goo" hysteria, and I'm only asking out of curiosity, but is there any chance that adding a gene to a bacteria will cause the other genes to change in unexpected ways?

Second- and third-order effects are always difficult to predict, but this is a good question. It largely depends on what new functionality you add. If the function you're adding has some interaction with some other metabolic pathway already in the bacterium, then that certainly applies some pressure. For instance, if the function you're adding provides some simpler route for producing something the bacterium needs to survive, then the less efficient way might evolve out. (There are a lot of speciation events like this.)

Thus far, nothing I'm working on has any real likelihood of doing this, and the odds are actually quite high that the functions I plan to add will evolve out, as they're not of any particular advantage to the bacteria themselves.

That's pretty cool, and thanks for the explanation :)

Another question! :D
Is there any particular place that you put a gene? Do you stick it at the front or the end? Or somewhere in the middle next to other specific genes?

If memory serves, you dope the plasmids in the bacteria's path and it adds in where the whatever the bugger's DNA and RNA process it to.

if you make grey goo and it eats me and the rest of humanity, i wouldn't mind cos its you who made it. :)

I think that's the sweetest thing anyone has ever said to me. :)

Wow. I gotta get on the ball; last things stood, I was the one who said the sweetest thing anyone had ever said to you -- though I don't remember what it was!

That said, I think you have about as much of a chance as creating grey goo to wipe out humanity as you do having a direct hand in the LHC creating a black hole to wipe out humanity. Yes, you personally -- that should tell you what I think about most doomsday scenarios. This sort of "fear of the mad scientist" goes back a long ways, and is especially prevalent in modern culture. I can think of dozens of movies where the premise is "well-intentioned but misguided mad scientist (or lab scientists working on government funded programs, the more realistic of the two mostly unrealistic scenarios) experiment with Things Nature Never Intended Man To Know, and Bad Things Happen. It obviously betrays an underlying anxiety about scientific advancement among the members of our society, but it is somewhat depressing when people take mostly irrational fears about one are of near-future science and apply them to other areas of newly-developing science. I hope, at least, that the histrionics who are seriously worried about grey goo realize that that is a nanotech scifi doomsday nightmare, and not a basic at-home biohacking one, and that they're just using that term for lack of established Canonical Thing To Be Afraid Of With This Area of Human Knowledge Advancement.

You're doing a good job managing these questions; better than I would have the patience for. Thanks for being the public face of this stuff -- I'm hoping people are coming away with their interactions with you with their concerns addressed and their fears explained and reasonably satisfied. They seem to be.

(Note, I don't fault people for having these fears -- society, through bad popular science articles and popular science fiction, haven't exactly been good at preserving realism when looking for sensationalist or thrilling new threats to create to further a plot, and the overall quality of scientific journalism is such that it's hard to tell a serious article about a serious technology apart from an article about a pseudoscientific synthetic hysteria, and thus no reason for those not familiar enough with the subject to realize what is unrealistic fluff and what is reasonable reporting. I suppose the problem is the need for mass media to appeal to the lowest common denominator of its readership.

I blame Mary Shelley.

OMFG You're as likely to make Grey Goo as you're as likely to construct the Loch Ness Monster. WHAT IS WRONG WITH PEOPLE?

Your answer is factual, of course, but it misses the bigger point that Grey Goo is impossible by the laws of ...Everything.

Not to mention that AFAIK it's not even about GMO organisms in the first place, but about self-replicating nanobots. So they don't even have the right FUD to science mapping in their concerns.

Yeah - Charlie Stross coined the appropriate term in Saturn's Children. Pink Goo is an uncontrolled bioloigcal replicator. Due to bad environmental management practices in the book, Earth was mostly sterilized - so there are the occasional giant unexploited niches for organisms to exploit.

Oh yeah! The NANOBOTS!!

*hahahhahah*

So far the nanobots remain fully organic in form.

Sounds like there is a real opportunity for someone to start a fake doomsday cult dedicated to the production of grey goo.

If you start one, I want a portion of the take. ;)

The extropians are half way there. :p

(http://www.partiallyclips.com/pclipslite.php?id=1586)

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[PSA] Biohacking FAQ #2: "But what if you end up making grey goo?"

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