Biohacker Meredith L. Patterson: DIY DNA
p2pnet news view | Cool:- “Why is there toilet paper sitting on your lab table?”
That’s one of the questions on Meredith L. Patterson’s Radio Free Meredith blog.
Answer? “It’s absorbent and good for wiping up spills, and it wastes less paper than using full paper towels to wipe up the occasional spill of less than 2mL of liquid. (The paper towels weren’t in the frame. Nor was the sharps bin, or the fire extinguisher, or any other safety equipment. It’s all within reach, though.)”
“As a science fiction author, Patterson has published numerous short stories in such magazines as Fortean Bureau, Strange Horizons, in compilations such as The Doom of Camelot and The Children of Cthulhu, and is credited as contributing to the Steve Jackson Games game GURPS Villains,” says the Wikipedia.
So maybe it’s not too surprising to find she’s also a biohacker who’s into DIY DNA. Hence the ‘good for wiping up spills’ toilet paper.
“Using homemade lab equipment and the wealth of scientific knowledge available online, these hobbyists are trying to create new life forms through genetic engineering — a field long dominated by Ph.D.s toiling in university and corporate laboratories,” says the Associated Press, going on:
“In her San Francisco dining room lab, for example, 31-year-old computer programmer Meredith L. Patterson is trying to develop genetically altered yogurt bacteria that will glow green to signal the presence of melamine, the chemical that turned Chinese-made baby formula and pet food deadly.”
People can, “really work on projects for the good of humanity while learning about something they want to learn about in the process,” the story has her saying.
However, “critics of the movement worry that these amateurs could one day unleash an environmental or medical disaster,” although, “Defenders say the future Bill Gates of biotech could be developing a cure for cancer in the garage.”
But, no worries, blogs Meredith.
Unless you happen to be a plastic fork.
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,” she says, going on »»»
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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