![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png){kind=small}
maradyddOver 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.
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.
Re: BioHacking
Date: 2008-12-26 06:16 pm (UTC)http://forums.cannabisculture.com/forums/ubbthreads.php?ubb=showflat&Number=1399459&fpart=15
What are you using for a power supply for your gels?
Re: BioHacking
Date: 2008-12-27 05:54 am (UTC)Thanks for the link! The pictures are awesome. I want to put together my own clean box now.
Re: BioHacking
Date: 2008-12-27 07:05 am (UTC)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.
Re: BioHacking
Date: 2008-12-27 09:19 am (UTC)"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.
Re: BioHacking
Date: 2008-12-27 09:41 am (UTC)Re: BioHacking
Date: 2008-12-27 09:58 am (UTC)Re: BioHacking
Date: 2008-12-27 11:14 am (UTC)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...
Re: BioHacking
Date: 2008-12-27 11:47 am (UTC)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.
Re: BioHacking
Date: 2009-01-27 07:16 am (UTC)Re: BioHacking
Date: 2008-12-28 07:54 am (UTC)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.
Re: BioHacking
Date: 2008-12-29 11:22 am (UTC)Re: BioHacking
Date: 2008-12-30 03:32 am (UTC)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.