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My Hobby: Solving public health problems

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 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.

Back in August, ext_97806 and I were in Houston for my sister's wedding. Naturally, we spent a fair bit of time also hanging out at mycroftxxx's place with his housemate pturing and the other residents of the House of Discord. One evening, we were all kickin' it on the porch, shooting the shit about science (like ya do), and glowgurt came up. This led to some speculation about other things one could coerce bacteria to produce, and ext_97806 hit on a brilliant one: essential micronutrients. In particular, Vitamin C.

See, most mammals synthesize ascorbic acid (as C is also known) on their own. A few, however, have deletion mutations which prevent them from being able to: guinea pigs, some bats, all monkeys, all apes, and us. These mammals must get ascorbic acid in their diets, or else they'll end up with vitamin C deficiency, known as scurvy.

Scurvy is serious business. These days we think about it when we think of pirates or sailors, because during the seafaring days, it was really difficult to lay in enough supplies of citrus fruit and other ascorbic-acid-containing foods to last for an entire sea voyage. It's a really unpleasant disease. Sufferers lose their teeth and fingernails, bleed from the gums and mucous membranes, and experience severe joint pain, as vitamin C is necessary for collagen synthesis. Over time, healed scars can reopen and knitted fractures rebreak. Untreated, it is fatal, usually due to brain hemorrhage.

Thanks to modern food distribution, scurvy is uncommon in the industrialized world, except among one population: the homeless, typically elderly homeless men. Infants who are fed unfortified formula get it too. In the Third World, the situation is much more troubling. It's difficult to conduct studies on the prevalence of scurvy in the populations most likely to suffer from it, because those populations are hard to get to: refugees. An estimate of 100,000 cases of scurvy in East Africa alone is likely an underestimate. And most of the victims are children.

The bitter irony is that scurvy is 100% curable: all you have to do is get vitamin C to people. Of course, this is a big challenge when the population that needs it most is remote and resource-poor: if there were reliable distribution channels and money to pay for distribution, we could get supplements to them. Or citrus fruit.

We can't re-engineer living people to make their own ascorbic acid. But we can engineer bacteria to do it, rather easily in fact. How does that help scurvy sufferers, though? One word: probiotics.

Every human body is home to billions and billions of bacteria. We are their universe, and we literally could not live without them. The bacteria we house help us digest food and provide us with some of our essential micronutrients already -- poor maligned E. coli, for instance, manufactures Vitamin B12. So, pick a bacterial symbiote that lives in the gut and that people are willing to eat -- like, oh, say, yogurt bacteria -- and give it the ability to manufacture vitamin B12, or to help us manufacture it ourselves. (We're only missing one enzyme from the metabolic pathway that produces ascorbic acid.) Make yogurt with it, and just give the stuff away. Teach people how to make more yogurt from the yogurt they already have -- microbes are totally the gift that keeps on giving -- and slowly, one bite of yogurt at a time, we can do to scurvy what Salk and Sabin did to polio.

There are some challenges. (There always are.) Giving a bacterium the ability to produce a new protein has the side effect of making it less competitive: it's spending more of its energy on producing that protein, and thus less on dividing like crazy. Over time, its unaltered relatives will outnumber it, and eventually its population will dwindle to the point where it dies out. Selection is a bitch like that. However, if we can figure out some way to tweak the altered bacteria so that their rate of growth is on par with unaltered bacteria, then we can shift the balance of the game. Can we do this at all? Can we do it without affecting the existing essential roles that lactic acid bacteria play in us and in every other organism out there? I'm not sure. But that's what research is for.

Another challenge is making sure that we don't overdo it. It's pretty hard to overdose on Vitamin C; the LD-50 in humans is unknown, but in rats it's about 12 grams per kilogram, so if the numbers are similar for people, I'd have to choke down nearly two pounds of Vitamin C at one sitting to have a 50% chance of dying from it. Doses on the order of six grams per day over the course of many months can cause diarrhea, headache and other uncomfortable side effects, and people with iron overload disorders (wherein the body is too good at utilising dietary iron) can have their problems exacerbated by too much vitamin C. But there are two pieces of good news here. First, it's much easier to limit the rate of bacterial growth than it is to increase it, and second, there's a lot of wiggle room. 40 milligrams per day is probably adequate, 90 milligrams per day is enough for anyone, and the maximum recommended daily dose is 2,000 milligrams. So if we produce a population density that will provide people with about 40mg/day, it's unlikely that we'll fuck anyone up.

It's gonna take a lot of work. I won't pretend otherwise. We're talking about making major changes to the way humans everywhere interact with an organism that is vital to our existence, and that's a sobering thought. But so is the fact that hundreds of thousands of people suffer from a disease that can be eradicated.

To me, that means we're morally obligated to try. We're also obligated to be damn careful. But we have to try. So we are.

Another project I'm working on, along with engineer Jonathan Cline and a research team at National Yang-Ming University in Taiwan, is a biological method for detecting melamine contamination in food, which we've dubbed the "melaminometer". You might remember how last fall, there was a huge panic about contaminated pet food that was causing cats and dogs to die of kidney failure. This was traced to melamine, a triazine molecule which is 66% nitrogen by mass and can be used to make food products look like they contain more protein than they actually do. Unfortunately, not only is melamine not a dietary protein, it also pairs up with cyanuric acid to form insoluble crystals which accrete in the kidneys and cause irreversible, fatal kidney failure.

Oh, and the stuff has started showing up in milk products, including baby food, in China. The FDA has already banned all imports of Chinese dairy products out of fear for people's safety, and with good reason.

So why a biological detector? Well, as you might have guessed, with simple detection methods, melamine can masquerade as protein, and that's no good. The FDA uses chromatography and mass spectrometry, both of which are time-consuming and require a lot of equipment, plus someone who's trained to use it. A number of labs produce ELISA kits that can detect melamine very accurately and rather quickly (each test only takes about half an hour), but the kits aren't cheap and the cost adds up. We're aiming to produce a bacterium that lights up in the presence of melamine, in order to make available a test that is inexpensive, portable, and accurate.

You can read more about the work we're doing here -- that's right, we're keeping our notes on a wiki. Yeah, open science!


( 33 comments — Leave a comment )
Dec. 26th, 2008 02:29 am (UTC)
IIRC, a human consists of 2/3 water, 10^14 human cells, and 10^15 non-human cells. And 10^11 of the human cells are brain neurons.
Dec. 26th, 2008 02:30 am (UTC)
Have I ever told you how fond I am of DNA and the wonderous things one can do with it?

This sort of thing really fascinates me. Thanks for sharing the wiki link.
Dec. 26th, 2008 03:53 am (UTC)
typo: s/developing/detecting/
"... is a biological method for developing melamine contamination in food ..."

Dec. 26th, 2008 03:45 pm (UTC)
Re: typo: s/developing/detecting/
Fixed, thanks. That's what I get for writing this stuff up while jetlagged!
Dec. 26th, 2008 04:47 am (UTC)
I got hit with God knows what from that salad spinner when I was watching that presentation from the front row, too.

Best presentation that year, I think.
Dec. 26th, 2008 12:31 pm (UTC)
and to think that I was dubious about lending out my salad spinner! Glad I did.
Dec. 26th, 2008 02:36 pm (UTC)
Should have given her a sign that said "People in the front two rows may get wet" too.
Dec. 26th, 2008 03:53 pm (UTC)
Probably just water and shampoo. I used a little too much shampoo, I was nervous and my hands were shaking a bit.
Dec. 27th, 2008 01:10 am (UTC)
I seem to recall something about meat tenderizer too.

Although at the time having some woman in combat boots spraying me in the eye with some kind of cockamamie biological experiment was just a bit more than disconcerting. ;)
Dec. 26th, 2008 08:27 am (UTC)
Oh thank god. Citri-lactobacillis was a _hard_ secret to keep. I've been wanting to crow from the rooftops how cool a project this since the night it was thought up.

I also really like the re-purposing of Glogurt into a self-starting melamine detector. You continue to make me sinfully proud to know you, sweetie.
Dec. 26th, 2008 03:54 pm (UTC)
The news release happened a bit earlier than we were planning; seems the self-organizing biohacking community that I have been waiting for for the last five years has already started attracting enough attention that reporters have come sniffing around, so we figured keeping glowgurt under wraps any longer would be silly. So yes, feel free to talk about that.

(And maradydd just spilled about our hypothetical self-sustaining cure for scurvy, so you can now tell people what really goes on on your back porch. :) We've still got a long way to go before even being ready for animal experimentation with that one, but even if we just get other people thinking along those lines, that will be awesome. The goal is to help diminish human suffering; if someone beats us to making working scurvygurt, I won't be crushed.)
Dec. 26th, 2008 11:58 am (UTC)
That's incredible, and I'm frankly in awe that there are people in this world intelligent enough to actually do it.

Much smarter than me: this borders on magic in my world :D
Dec. 26th, 2008 12:50 pm (UTC)
I would give my eye teeth to hang out on your porch when you are thinking this stuff up.
Best of luck.

go go science!
Dec. 26th, 2008 12:52 pm (UTC)
I suspect you mean that you keep your notes here rather than subwossnamed on your LJ. Otherwise, interesting.
Dec. 26th, 2008 03:45 pm (UTC)
Thanks -- yet another jetlag fail on my part.
Dec. 26th, 2008 02:28 pm (UTC)
How many Gs do you get out of that salad spinner? How long do you have to spin?
Dec. 26th, 2008 03:49 pm (UTC)
For the "purifying DNA with common household items" trick, a minute was more than enough, though I'm not sure how many Gs that was. For centrifuging bacteria, I use a microcentrifuge that I got secondhand off ebay for $30; you really want something that can do about 5000 RPM.
Dec. 26th, 2008 04:00 pm (UTC)
I'm glad to see you've gone public with the Cghurt project; it's been really frustrating not being able to tell people about a project this awesome and cool.
Dec. 27th, 2008 09:56 am (UTC)
LOL I am so glad I found you... and enjoyed the pic of you in that article, even if they made you fuzzy :(

I like science quite a bit. I'm not a big fan of GMO food at all though. And I don't understand how the moral obligation isn't simply to distribute wealth and resources and access to resources fairly enough to ensure people don't die of such diseases.

I think we have a moral obligation to keep non-GMO foods safe for the people who want to eat them. I *never* want any GMO food in my body and don't think anyone else has the right to make that impossible for me. Too late, I know.

Anyway, hope I don't get dismissed as a crazed luddite. I don't think I am. :-)
Dec. 27th, 2008 10:10 am (UTC)
And I don't understand how the moral obligation isn't simply to distribute wealth and resources and access to resources fairly enough to ensure people don't die of such diseases.

One major reason is "lack of an efficient transportation infrastructure". Getting yogurt cultures to local villagers who can pass them amongst each other in a self-sustaining, self-sufficient fashion is a far more reasonable approach than expecting that vitamin C supplements will be, and continue to be, available for distribution to remote communities not easily accessible due to bad roads political turmoil, etc. This is not an argument against distributing essential vitamins and health care to those who need it, but more a practical recognition of the fact that we're talking about a part of the world where leadership roles change on a monthly basis, internal politics are complex and often bloody, and making regular shipments of large amounts of pills or food items may be impractical or infeasible. We're hoping to lower the barrier of delivery for these nutrients in the face of external forces that are not easy to change. If you can find a way to get vitamin C to all the people who are currently suffering from or dying from scurvy, that would be awesome -- but we'd still go ahead with this project, under the assumption that whatever supply and distribution techniques that existed tomorrow might not exist the week after that.

As for never wanting GMO food in your body, I'm in general agreement that people should have choices as to what they consume in their food, but on the GMO issue, if you eat things like cows or wheat or corn, you're eating food that would never have existed if it weren't for a rudimentary form of genetic modification. There's a lot of general misunderstanding of what GMO foods are, and what genetic manipulation of food involves, and that's part of what we're trying to help fix.

Bigger problems with food in America at least, in my opinion, have to do with the amount of high-fructose corn syrup (a chemical produced by a not-entirely-simple process that arguably has a detrimental effect on humans who consume it) and the level of hormones found in various meat products. I.e., the stuff Americans do to their food between harvesting it and selling it is on the whole far scarier and more concerning than food that is improved due to genetic modification.
Dec. 27th, 2008 11:11 am (UTC)
I'm so with you on corn syrup (this is not actually food, although we call it that) and hormones.

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.
Jan. 27th, 2009 06:49 am (UTC)
I don't so much consider hybridization as a "GMO" issue


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?
Jan. 27th, 2009 08:45 am (UTC)
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.

Jan. 27th, 2009 09:15 am (UTC)
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.

Whoops, this got too long! Continued next comment.
Jan. 27th, 2009 09:49 am (UTC)
(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.

Continued again...
Jan. 27th, 2009 09:56 am (UTC)
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. Suppose further that this virus 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.

Wow. This got really long. I'm kinda tempted to spin this off into a post of its own; how would you feel if I were to excerpt the comment thread that led us to this point and repost it as a new journal entry, to invite further discussion?
Jan. 27th, 2009 10:30 am (UTC)
Excerpt away.

Thanks for the thoughtful posts.

I'z too tired to respond and has to go to bed now!
Dec. 27th, 2008 04:58 pm (UTC)
Very cool, congrats on getting this off the ground!
Dec. 28th, 2008 10:12 am (UTC)
BTW - you rock.

I was thrilled to see your picture show up in the AP News app on my iPhone. Coolness!
Dec. 31st, 2008 01:58 am (UTC)
People like you are sixteen kinds of awesome.

Keep up the good work!
Jan. 14th, 2009 05:51 am (UTC)
That's an amazing idea. As others have correctly pointed out, you rock.

Any other vitamins besides C and B12 that could be produced in the same way?
Jan. 27th, 2009 07:02 am (UTC)
In theory, any small molecule can be produced through the action of enzymes. The hard part is figuring out which enzymes; some, such as melamine deaminase, are specifically targeted to just one molecule. (As one example, melamine deaminase will not deaminate atrazine, which is chemically quite similar to melamine [they're both aminated triazides], and the enzyme which breaks down atrazine won't touch melamine.) Custom protein design will be the real biology revolution, and there's a lot of work in biology, chemistry, and CS that will need to be done in order to make these kinds of predictions.

But as far as vitamins go -- any vitamin we eat is already produced by some living organism, so it's a matter of finding the appropriate pathway and transfecting it into a symbiotic organism. This is likely to be challenging for vitamins which are the result of a lengthy metabolic pathway, because the more novel proteins you want your synthetic organism to produce, the less fit the organism becomes overall. I'm not sure why E. coli produce B12; that symbiotic relationship is one of those great happy accidents which has us where we are today.

What we're hoping to exploit with C is slightly different: the fact that humans already have every step of the ascorbate synthesis pathway except the last one. We're hoping that if we can create L-gulonolactone-oxidase-producing bacteria that are symbiotic with C-deficient animals, the animals will be able to utilise the L-gulonolactone to produce their own ascorbic acid. I do not know if this will actually work, but it just seems morally wrong not to find out.

As for whether there are other essential micronutrients for which humans are simply missing a step in the pathway -- I don't know, as I haven't researched that far. We were initially looking into putting the entire ascorbate synthesis pathway into bacteria, then I started reading about L-gulonolactone oxidase and went "WAIT YOU'RE FUCKING KIDDING ME." Again, happy accident.
Jul. 30th, 2009 06:41 pm (UTC)
I'm sure you've thought about this, but, how are you dealing with the fact that the L-gulonolactone oxidase is inside bacteria and the rest of the pathway is in the human cells? Sufficient to rely on diffusion of pathway intermediates back and forth? Tag the bacterial L-gulonolactone oxidase for secretion?

How do our guts get the vitamins out of regular vitamin-producing bacteria? Diffusion out, and then our cells have uptake mechanisms?
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