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My pals Tito Jankowski and Josh Perfetto have been working for the last, oh, nine months or so on designs for an Open Hardware thermocycler -- basically a Xerox machine for DNA. They've finished their first working prototype, and have set up a Kickstarter project to fund the process of turning this into a full working device that you'll be able to buy for less than $400, or build all by yourself with parts you can easily obtain online. If they can get to $6000, this will happen.

I'm particularly interested in this because its software will be the second real-world demonstration of some of my theoretical work. Some of you might remember Dejector, the "kills SQL injection dead" library I built back in 2005 (and have been really slack about keeping current, though it really needs a serious rearchitecturing). Dejector uses a technique I call "restricted sublanguages" to make sure that SQL queries which don't fit into a very limited (programmer-specified) subset of all possible queries -- that is to say, queries which have had a malicious clause injected into them -- are rejected before they get near the database. The OpenPCR machine is a networked device; you'll be able to plug it into your router and configure a PCR run via a webpage, rather than having to key instructions in on a tiny little keypad. It'll also log data for you (which you can also view in a browser) and, if you want, report results to you over Twitter or SMS.

All this fancy web stuff will be made possible -- and secure! -- through a restricted sublanguage of HTTP which I will be implementing for the AVR series of microcontrollers. (We're actually starting with an Arduino, but we might move to pure AVR by the time we're done.) Your contribution will help go toward making that happen, along with tools for generating custom restricted HTTP sublanguages for other embedded devices. (Networked lab tools are cool; networked lab tools that get hacked to pump out Twitter-spam, not so much.)

If you can spare a few bucks, please kick something in, and please signal boost anywhere you can think of. Thanks!
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The following was delivered yesterday at the UCLA Center for Society and Genetics' symposium, "Outlaw Biology? Public Participation in the Age of Big Bio".

It is inspired by, and deliberately follows the form of, "A Cypherpunk Manifesto" by Eric Hughes.

Scientific literacy is necessary for a functioning society in the modern age. Scientific literacy is not science education. A person educated in science can understand science; a scientifically literate person can *do* science. Scientific literacy empowers everyone who possesses it to be active contributors to their own health care, the quality of their food, water, and air, their very interactions with their own bodies and the complex world around them.

Society has made dramatic progress in the last hundred years toward the promotion of education, but at the same time, the prevalence of citizen science has fallen. Who are the twentieth-century equivalents of Benjamin Franklin, Edward Jenner, Marie Curie or Thomas Edison? Perhaps Steve Wozniak, Bill Hewlett, Dave Packard or Linus Torvalds -- but the scope of their work is far narrower than that of the natural philosophers who preceded them. Citizen science has suffered from a troubling decline in diversity, and it is this diversity that biohackers seek to reclaim. We reject the popular perception that science is only done in million-dollar university, government, or corporate labs; we assert that the right of freedom of inquiry, to do research and pursue understanding under one's own direction, is as fundamental a right as that of free speech or freedom of religion. We have no quarrel with Big Science; we merely recall that Small Science has always been just as critical to the development of the body of human knowledge, and we refuse to see it extinguished.

Research requires tools, and free inquiry requires that access to tools be unfettered. As engineers, we are developing low-cost laboratory equipment and off-the-shelf protocols that are accessible to the average citizen. As political actors, we support open journals, open collaboration, and free access to publicly-funded research, and we oppose laws that would criminalize the possession of research equipment or the private pursuit of inquiry.

Perhaps it seems strange that scientists and engineers would seek to involve themselves in the political world -- but biohackers have, by necessity, committed themselves to doing so. The lawmakers who wish to curtail individual freedom of inquiry do so out of ignorance and its evil twin, fear -- the natural prey and the natural predator of scientific investigation, respectively. If we can prevail against the former, we will dispel the latter. As biohackers it is our responsibility to act as emissaries of science, creating new scientists out of everyone we meet. We must communicate not only the value of our research, but the value of our methodology and motivation, if we are to drive ignorance and fear back into the darkness once and for all.

We the biopunks are dedicated to putting the tools of scientific investigation into the hands of anyone who wants them. We are building an infrastructure of methodology, of communication, of automation, and of publicly available knowledge.

Biopunks experiment. We have questions, and we don't see the point in waiting around for someone else to answer them. Armed with curiosity and the scientific method, we formulate and test hypotheses in order to find answers to the questions that keep us awake at night. We publish our protocols and equipment designs, and share our bench experience, so that our fellow biopunks may learn from and expand on our methods, as well as reproducing one another's experiments to confirm validity. To paraphrase Eric Hughes, "Our work is free for all to use, worldwide. We don't much care if you don't approve of our research topics." We are building on the work of the Cypherpunks who came before us to ensure that a widely dispersed research community cannot be shut down.

Biopunks deplore restrictions on independent research, for the right to arrive independently at an understanding of the world around oneself is a fundamental human right. Curiosity knows no ethnic, gender, age, or socioeconomic boundaries, but the opportunity to satisfy that curiosity all too often turns on economic opportunity, and we aim to break down that barrier. A thirteen-year-old kid in South Central Los Angeles has just as much of a right to investigate the world as does a university professor. If thermocyclers are too expensive to give one to every interested person, then we'll design cheaper ones and teach people how to build them.

Biopunks take responsibility for their research. We keep in mind that our subjects of interest are living organisms worthy of respect and good treatment, and we are acutely aware that our research has the potential to affect those around us. But we reject outright the admonishments of the precautionary principle, which is nothing more than a paternalistic attempt to silence researchers by inspiring fear of the unknown. When we work, it is with the betterment of the community in mind -- and that includes our community, your community, and the communities of people that we may never meet. We welcome your questions, and we desire nothing more than to empower you to discover the answers to them yourselves.

The biopunks are actively engaged in making the world a place that everyone can understand. Come, let us research together.

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 Unported License.
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The summer 2009 issue of h+ Magazine is out, and there's an interview with yours truly. The reporter, Tyson Anderson, and I had an interesting conversation about the history of biohacking, how I got started with it, the diverse nature of DIYbio, the importance of the amateurs in the history of science, and some of the ethical issues surrounding this hobby.

(Yes, yes, [ profile] enochsmiles, I need to put together a press page for my website. I know.)

But until then, check out that nice interface! They've definitely achieved the look and functionality of a paper magazine (minus being able to dog-ear the pages or scribble notes in the margin), and halle-freakin-lujah, each page is uniquely addressable! There are only two things I can dock them points on. First is the fact that their "share a bookmark" feature is so tightly coupled to a host of social networking services, many of which are walled gardens. (LJ happens not to be one of them. When did we jump the shark, guys?) This is, however, the fault of AddThis, provider of the feature in question; I can extract the URL I want by, say, clicking on the Google Bookmarks link and then copying said URL, but that is kind of a pain. Hey, AddThis, can we have a plain ol' "URL" option? That would be swell, thanks.

Second, not being able to copy and paste text == also a pain. Minus that, though, I could totally get used to reading magazine content online with an interface like this.
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If you live in Europe, happy Labour Day!

Also: not swine flu. I note with pleasure that the overwhelming majority of respondents to my poll sensibly chose "No" (though "tickybox" has quite the crowd of supporters!), and with even more pleasure that a few of you were game-theoretically clever enough to vote "Yes" -- since, if it had been a real betting pool with real money involved, y'all would have made out like bandits if I had been so unlucky. :P Yay not Patient Zero.

Finally, if any of you happen to have photos of me in the act of Science!, and would like to see them alongside an interview with me in h+ Magazine, would you be so kind as to send them my way? The deadline is Wednesday. Since I now have my Arduinos again, I will be endeavouring to spend some time this weekend on some prototyping for the Open Thermocycler Project, but it would be nice to have something more recognisably biological.
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Short notice, I know, but this morning at 9am PST/noon EST, Mackenzie Cowell (founder of and I will be on a talk radio program, The Food Chain, discussing the emergent biohacking movement and its possible effects on food. You can listen in on a number of AM radio stations, or over the Internet, and the audio will be available as a podcast later.

Come join in the discussion!

ETA: Well, that went reasonably well -- I was a little startled at first to find out that the station was a FOX News affiliate, but no one called for our heads on platters or anything. I'll post a link to the podcast when it's up, and y'all can listen to Mac sound extremely intelligent and level-headed, Sandra Porter being cautiously enthusiastic, and me waxing far too rhapsodic about molecular computing and epigenetics. ;) Some day I'll remember not to get carried away...
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A recent but rapidly growing blog that deserves recognition is Eric Fernandez's DIY Bio 4 Beginners. Eric's been busily trawling the Internets for articles, videos, animations and other great resources for the amateur-biology community. Sometimes it's one link a day, sometimes it's ten -- but the information is great and his enthusiasm is (ahem) infectious. Check it out!

In other news, today I'm off to FOSDEM, especially for David Fetter's talk on OLAP and Common Table Expressions in PostgreSQL. Ever wanted to write a recursive expression in SQL? Now you can, and there are some damn fine reasons to. Representing trees in a database in any useful fashion used to be difficult. Now it's not. This takes data representation to a whole new level.
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Gel electrophoresis is one of the most versatile, widely used tools in a microbiologist's or geneticist's toolbox. It's used for separating out DNA, RNA or protein molecules (that you presumably isolated in a previous step of your experiment) based on their molecular weight, so that you can analyze the molecules, clone them, amplify them with PCR, sequence them, lots of different things.

Electrophoresis does require some equipment to perform -- an inner tray which holds the gel, an outer tray which holds a "running buffer" solution (which keeps things cool and keeps pH stable), electrodes, and a power supply (50V-150V is pretty common). You can buy a gel box from a commercial supplier, though they're not cheap, and a fancy power supply will set you back even more; Bio-Rad has some nice ones, but they run to the thousands of dollars.

Happily, there are solutions for the biohacker on a budget. The University of Utah's genetics department has full specs for how to build your own gel box for about $25 in parts (not counting the power supply, which will run you about $50). The main components are clear acrylic and acrylic cement, which I purchased and had cut to size at TAP Plastics -- they also do mail order. My partner-in-science Tito Jankowski built one too, and did some test runs with food colouring which enabled him to separate the individual dyes which make up different colours. (The molecules in food colouring are pretty small, which is why the bands in Tito's video are a little smeary. He used agarose -- an edible, seaweed-derived polymer which you can find on the shelf in any Asian grocery store, also sold as "vegan gelatin" -- as his gel, and agarose is better suited to larger molecules like DNA. But it's definitely a proof of concept!)

Still, electrophoresis using large rectangular gels has some drawbacks. It's a bit messy, and in order to recover the particular band of DNA you want, you have to slice it out of the gel with a razor blade or something similar. Cleaning up the equipment is also a bit of a pain. If you're using acrylamide or polyacrylamide (common for protein electrophoresis), you need to find a safe way to get the used gel out of the gel carrier and dispose of it properly. Also, while DNA electrophoresis is run horizontally, protein electrophoresis is done vertically, so that means two different pieces of equipment.

This was a recent topic of discussion on the DIYbio mailing list. Ben Lipkowitz wondered whether it would be possible to use a narrow, rigid tube to contain the gel, rather than a big carrier. This would allow for the use of less buffer and lower voltage, since a physically smaller amount of gel is a smaller resistor.

Well, what's a narrow rigid tube that's easy for anyone to acquire? A clear drinking straw! Paper clips make for appropriately sized electrodes, and since a drinking straw is rigid, it can be used in either the horizontal or the vertical orientation. For extra bonus points, when you're ready to cut a band out of the gel, no need for mucking around with razor blades -- just take a (sterile) pair of scissors, snip snip, and you're done! Plus, disposal is extra simple, even with polyacrylamide -- just dispose of the entire straw, gel and all, properly.

Tito Jankowski tried this out, using a single 9V battery as a power supply, and after some debugging, it worked beautifully. (He also used alligator clips as electrodes, and they worked just fine.) We're calling these "keiki gels" because they're so small and cute -- and so simple, even a little kid can do them.

This is crowdsourced science at its very finest. Behold the power of collaboration!

Tito's keiki gels!

ETA: Tito wrote a protocol, doo dah, doo dah
maradydd: (Default)
The following is a discussion that [ profile] bunnykitteh and I got into on an old comment thread. It's gotten long and thought-provoking, so with his permission, I'm pulling it into a new post of its own to invite discussion.

[ profile] bunnykitteh:

I don't so much consider hybridization as a "GMO" issue, especially if it's the kind of thing that technically could happen in nature with no outside influence simply by two different plants growing close enough together, etc.

[ profile] maradydd:


Do you believe that there's a difference between, say, corn produced by pollinating one strain of corn with another vs. corn produced by taking strain A and manipulating it to replace some of its genes with genes from strain B, such that the result is identical to the corn produced in the first example?

[ profile] bunnykitteh:

Why is this very low curb something that GMO apologists fall all over themselves to trip over?

Old school hybridization is CLEARLY different in important and fundamental ways from the kind of GMO manipulations that are done today.

What you seem to be asking is: are the important and fundamental differences a result of the techniques themselves?

I don't know, and that's irrelevant. There are important and fundamental differences that are a result of what's done, not how it's done. Genetic modification is used to do things that CAN'T be done in nature... in fact, that seems to be rather the point of it all :-)

The concern that seems to go ignored and unaddressed is the fact that once these changes are released into the wild, there is no containment and no "undo". This affects me and everyone else on the planet in ways that, frankly, I don't consent to and you have NO right to inflict on me.

[ profile] maradydd:

Sadly, it's a question that I have to ask. Believe it or not, there are quite a lot of people who believe that of the two scenarios I depicted (and note that here I mean exactly these scenarios), the first is safe but the second is not -- despite the fact that the outcomes are identical. Simply put, some people are irrationally terrified of any genetic modification that doesn't happen in a field, and it's simply impossible for me to have a productive discussion with someone who's hampered by that kind of fear.

It appears that you're not, though, so we can have a productive discussion. :) Really, I'm sorry that I even had to ask; I think, though, that it's better to waste time with one question up-front rather than getting into an emotionally charged debate that would take up time and would ultimately be doomed to failure. I'm glad that's not the case here.

(I am still somewhat curious as to whether you would eat produce created through the second scenario I posited, but if you think it's an irrelevant question, then let's just move on, k?)

To briefly answer your implicit question: I'm actually very concerned about the "no containment / no undo" problem, and one of my biggest concerns, particularly with respect to the DIY movement, is that experiments must not be released into the wild without rigorous testing.

We've already seen, in the US, India, and elsewhere, that GMOs can and do have unanticipated effects on existing organisms. I'm furious, for instance, at Monsanto's attempts to sue US and Canadian farmers whose crops were pollinated by windborne pollen from GMO produce growing elsewhere. This is a sociopolitical chilling effect which must be crushed -- Monsanto has no right to accuse farmers of "gene theft" when those farmers had no intention of incorporating Monsanto's sequences into their crops. Now, that's a political issue, but it has bearing on your concern as well: I believe that farmers have every right to grow the crops which they want to grow, and if a farmer wants to grow crops which don't incorporate modified sequences, he should have that right. Here's a hypothetical for you: suppose that an organic farmer discovers that his corn has been pollinated with pollen from GMO crops, and as a result, his crops can no longer be certified organic. Should the farmer be able to sue Monsanto for lost revenue? I'm inclined to say yes, although in practice that would likely be a difficult case to win. The end result is basically the same as if Monsanto burned the farmer's fields, since the farmer's crop is no longer fit for sale, but I suspect a court case would hinge on whether the farmer could prove malicious intent or, more likely, negligence.

In fact, that's probably the best way of phrasing my outlook on the subject: I think it's negligent for bioengineers and biohackers to create synthetic organisms which have the potential to affect/contaminate (e.g., via hybridization/sexual reproduction, though certainly in other ways as well) parts of the biosphere for which they were not originally intended. This is a difficult problem to solve, but the onus is absolutely on us, the engineers, to figure out how to do that. You have the right to eat only what you want to eat, and to know what you're eating. You have the right to know what's in your environment, and to avoid organisms that you want to avoid.

(As a side note, the DIY movement is certainly not focused only on synthetic biology -- that's just what's grabbing headlines. One project that you might appreciate is Jason Morrison's BioWeatherMap, an open-source effort to catalogue "local microbiospheres" -- in other words, what microorganisms are present in different areas -- and track the movement of different strains of bacteria, fungi, &c throughout the world. One of my hopes for the future is that projects like this will make it easier for us to be aware of the invisible aspects of our environment. Imagine a world where you could view not only the weather forecast, smog report, and pollen report for San Francisco, but also a bacteria and virus report! Now tie it in to GPS and add a sampling system to, say, your cellphone. This presupposes some pretty major advances in miniaturization, sampling and sequencing, &c, but I think the results would be really awesome.)

Anyway: My own work is certainly affected by the principles I outlined above, most obviously scurvy-gurt. (Let's first stipulate that scurvy-gurt will work at all. I don't know if it will.) If someone doesn't want to have scurvy-gurt in their system, preferring instead to get their vitamin C from citrus fruit and whatnot, I should respect that. There are a couple of ways I can do that. The simplest is to make the enzyme-producing bacterium dependent on some particular nutrient not normally found in the human body (but safe for humans to eat) in order to survive. There's already a dentist in Florida who's developed a synthetic-bacteria treatment for tooth decay which uses this principle: he's modified the mouth bacteria which produce enamel-damaging acids so that they no longer produce those acids, then tweaked them further so that they outcompete their acid-producing cousins. However, he's also made them dependent on an additional nutrient, which he puts in a mouthwash which patients who use this technique must then use in order to keep their new bacteria alive. If the patients don't use the mouthwash, the no-acid bacteria die, and their mouths will eventually be colonized by decay-generating bacteria again. It's actually a cute money-making technique for him, in the spirit of "give away the razors but sell the blades" -- he could give away the bacterial treatment for free, then sell the mouthwash in order to make a buck. And, in fact, that's probably what's motivated his decision. :P OTOH, it has the additional side effect of doing exactly what you want -- making sure that the bacteria don't escape the habitat they're placed in.

We could do something similar with scurvy-gurt, though that presents an ethical dilemma for me. I think it would be nothing short of reprehensible to offer a cure to a crippling and often fatal disease but effectively force people to buy a supplement for the rest of their lives. Really, that's back to square one, since in order to distribute this supplement, we'd need the same kind of supply chain we already don't have for distributing vitamin C tablets.

Well. I say that, though the real-world situation is slightly more complicated than I've just depicted it. The WHO report on scurvy that I read (which I can link for you if you want to read it) points out that scurvy is a major problem in refugee camps, despite the fact that aid packages include cereals supplemented with vitamin C. Why? In a word, culture. In the parts of the world that are having problems with scurvy, it's common to boil grains for much of the day -- and vitamin C breaks down after about half an hour of boiling. I'd really like to be able to develop a "fire-and-forget" solution -- and I won't lie, there's a part of me that thinks it's terribly racist for a person to say "I never want any GMOs to come anywhere near me, ever," when a synthetic-biology solution to a brutal, fatal disease could be saving the lives of brown people in remote countries, with the consequence that one day everyone in the world would have this synthetic organism living in their intestines cranking out an extra enzyme.

As a First World analogy, suppose someone were to develop a virophage (virus which attacks other viruses) which selectively attacked the AIDS virus, destroying it throughout the body of anyone infected with HIV. Since we're imagining, let's also make it immutable. (Impossible in practice, but since we're discussing a particular ethical question, let's just stipulate this to start.) Suppose further that this virophage also remained dormant in the host's system, ready to attack any new HIV which entered the system. This would imply that the virophage could also be transferred to other people (likely via fluid contact). Would it be immoral to create this virophage? To use it as an HIV treatment? If you had HIV, would you use it? If your partner had HIV and decided to use it, what would you do?

(FWIW: in practice, I think it might be possible to develop an HIV-destroying virophage. However, I think it would also be terribly hard to get it to remain in the body after the HIV infection was eradicated. So actually, HIV strikes me as a less dilemma-fraught example, because I don't see any practical way to make a spreadable virophage.)

Anyway, these are the kinds of ethical dilemmas I struggle with every single day: where is the balance between respecting people's freedom of choice and, simply put, stamping out pain and suffering in the world? And, thinking outside the box, is that a choice we must necessarily make? Is there a way to achieve both goals? I'd like for one to be found. I don't care whether I find it or whether someone else finds it, I just want an answer. So I hope that by having discussions like these, we can delve more deeply into the thorny social problems that synthetic biology presents than the discourse typically does, and in so doing, inspire someone to find those out-of-the-box solutions.
maradydd: (Default)
3. Gel electrophoresis uses ethidium bromide, which is a dangerous chemical. How are you disposing of it safely?

I'm not using ethidium bromide. There are a number of other gel stains which are much safer and easier to work with, such as SYBR-Green and SYBR-Safe. I use GR Safe, which is similar to SYBR stains but even better, because it can be stored at room temperature.

Per standard biosafety practices, I sterilize everything before I dispose of it.

4. Why is there toilet paper sitting on your lab table?

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.)

5. Why are there Ziploc bags sitting on your lab table?

The bacteria I work with -- Lactobacillus acidophilus, Lactobacillus bulgaricus and Streptococcus thermophilus -- are what's called "facultative anaerobes": they prefer environments where there isn't much oxygen. (They'll grow when there's O2 around, but they won't grow as quickly.) So, when I plate them on a petri dish, I put the finished plate in a Ziploc bag. Then I put some vinegar and baking soda into an empty Coke bottle and capture the generated CO2 gas in a balloon, squirt the gas into the Ziploc bag, and close it up.

I asked a former boss of mine (a bioinformaticist whose PhD is in population genetics) whether he had any ideas for easy ways to provide an oxygen-free environment for my plates, and he said they used the same Ziploc bag trick when he was in grad school. It's ghetto, but hey, it works.
maradydd: (Default)
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.
maradydd: (Default)
Once upon a time, there were a boy and a girl. The boy ran a tech conference, and the girl worked for a company that made DNA. She submitted a talk about DNA design software to the conference, and it got in, and she was very, very excited.

While preparing to give her talk, the girl mentioned to the boy that if she only had a salad spinner, she could kick off her talk with a cute demo. "I will find you a salad spinner," said the boy, and he did (thanks to [ profile] kragen), and the demo was very cute indeed.

After the conference, the boy and the girl got to talking about other amusing things that people could do with DNA, and somewhere in there, someone had the idea that it would be really funny to take Lactobacillus acidophilus, otherwise known as yogurt bacteria, give it the gene to produce green fluorescent protein, and make yogurt with it. Or "glowgurt", if you prefer.

They were, however, rather busy with a number of other projects, both together and separately, and along the line they fell for each other like a ton of bricks and got married.

This is where the story actually starts.

Scurvy: it's not just for pirates anymore )

My not-so-clandestine project: the melaminometer. Say that five times fast! )


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