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

[maradydd]

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.

Comments

[graydon.livejournal.com]

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!

[tangaroa.livejournal.com]

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.

[spider88.livejournal.com]

Word.

[maradydd.livejournal.com]

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.