Darning Genes: Biology for the Homebody

· June 15, 2009

The age of the DIYbiologist has begun. With the price of equipment falling and the open source ideology flourishing, it was perhaps inevitable that we would see the rise of this new DIY community. And while it may conjure pictures of citizens with scalpels in one hand and a trowel in the other, DIYbiology is, in fact, an exciting and potentially productive new field.

Photo courtesy of http://flickr.com/enochsmiles

Primarily interested in the currently fashionable trend of synthetic biology — the creation of novel organisms using genetics and other techniques — they meet in groups, in cities, and unite online. One popular such location is DIYbio.org, created by Mackenzie Cowell and Jason Bobe. Meredith Patterson, the doyenne d’DIYbio, recently caught AP’s eye with her pet project — a strain of the bacteria responsible for yogurt that secretes miraculin as a sweetener. While group discourse focuses on genetics and synthetic biology, there are other hot topics, like creating lab equipment using common household items or building a thermocycler for $25. There are intense debates about bioethics, and projects like the global bioweather map — a map that charts the flow, spread, and presence of various bacteria around the world.

As the diversity of topics suggests, this is a large community. Along with specialists in biological fields, you’ll find educated amateurs with an eye toward starting their own home labs. From academic to soldier to artist, from middle schoolers to retirees, the DIYbio field represents a cross-section of humanity and their convergence makes for varied and interesting discussions.

And while one might envision dozens of isolated home biologists homebrewing genes in their basements and garages, there is a social aspect to this movement that goes beyond the online. Some people who lack the space to store large amounts of equipment have formed co-op labs where they work together. Meetings, arranged over the net, generally happen at people’s homes and have a party vibe. A map of labs on the hackerspaces website shows the highest concentration of interest on the Eastern coast of the U.S. But participants can be found all over the globe, including Asia, Africa, and South America.

Why has this field suddenly exploded? The answer goes far beyond falling costs and the rise of the garage tinkerer, although these are factors. One big factor seems to be a desire to solve some of today’s major problems. Discussions seem to frequently drift towards two particular topics: creating fuel-generating microbes and finding remedies for disease. Indeed, the DIYbio community owes much of its increase in size to do-gooders, concerned citizens who see DIYbio as a method of confronting problems in a novel way. And while this is heartening, many members simply want to pursue science for the love of it. They’re DIY simply because they wish to conduct research into relatively unprofitable fields.

In much the same way that homebrew computer science built the world we live in today, garage biology can affect the future we make for ourselves. For example, the bioweather map could greatly augment the way we understand epidemiology and the environment on a micro scale. When we open science up to the public, we pretty much always get useful results.

Of course, there are bound to be some ethical concerns about, and within, a community tinkering with biology. The ethics of genetic research is certainly not lost on the practitioners. Encroaching legislation threatens to stifle their growth via tight regulation or outright restriction. The DIYbiologists are trying to come up with fair and workable solutions.

To get a better perspective on the DIYbio phenomenon and its issues, h+ talked to Meredith Patterson, a Computer Science doctorate, who is trying to solve issues with food contamination with bacterial warning systems.

Photo courtesy of http://flickr.com/enochsmilesh+: How did you get involved with synthetic biology and DIYbio?

MEREDITH PATTERSON: Well, this goes back to about 2003. I was just starting my PhD in computer science at the University of Iowa, and I didn’t know yet whether I was going to have a research assistantship or a teaching assistantship, so I was looking for a part time job, and ended up taking an internship in the Bioinformatics department at Integrated DNA Technologies. My boss there was a guy named Andy Peek, who just recently became director of bioinformatics and biostatistics at Roche. He’s a really hands-on kind of guy and remembers the days when everything in a wet lab was done with cobbled-together equipment. So we’d talk about stuff like how to do PCR without a thermocycler, or how to isolate DNA using only common household items, like mac’s “DNA shot” instructable.

Fast forward to 2005. I was working on SciTools, which is IDT’s web-based primer design toolkit, and I got accepted to give a talk on it at CodeCon (a software display conference). As an intro to the talk, I isolated chickpea DNA using non-iodized salt, shampoo, meat tenderizer, and a salad-spinner for a centrifuge, and that really blew people away. So that was the point when I started spending my free time reading old papers and thinking more about how to do more advanced genetics research at home.

Fast forward again to last summer, when Len (Sassaman, Patterson’s husband) and I were in Houston for my sister’s wedding and were hanging out at the home of some geek friends of mine. I’d had the idea for GFP yogurt several years before, and we were talking about that, and the conversation progressed to what other kinds of things you could make yogurt bacteria produce. Len hit on vitamin C, and we all went “Whoa, we could cure scurvy with yogurt.”

When we got back to San Francisco, that was when I went fullbore ahead on building out my lab. I found the DIYbio list a couple of weeks later, and the rest is history.

h+: You also talked about probiotics, yes?

MP: Yup. After all, lactobacilli are an important symbiote in the human gut. That’s why doctors recommend you load up on yogurt after a course of antibiotics, to restore the normal balance of your gut flora. This is just taking the notion of probiotics to a whole new level. :)

h+: There has been a lot of discussion about the dangers of people doing this sort of research at home. Do you think this is exaggerated?

MP: I really do. The chances of someone accidentally creating a dangerous organism and the chances of it surviving in the environment outside a laboratory are vanishingly low.

The bioweather map could augment the way we understand epidemiology on a micro scale. When we open science up to the public, we… always get useful results.

Rudy Rucker has a great quote on that, “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.” The bare facts of it are that there’s nothing random about synthetic biology research. When we design a transgenic organism, we’re deliberately adding one specific piece of new functionality, maybe a small pathway that leads to a new piece of functionality — and the organism has to expend energy on producing the new proteins that those new genes code for. Because of this, the synthetic organism is necessarily less competitive than its wild-type relatives who are much better suited for the niche they already occupy in the environment.

So any accidental release is fated to die out within a few generations, because it’s just not competitive enough.

h+: Don’t you think people may be taking some ethical liberties when they try doing this at home because of the lack of transparency?

MP: Do you mean because there aren’t reporting requirements to the NIH or the FDA?

h+: Not just the lack of government oversight, but the fact that someone may be engaging in, forgive the dramatization, Mengele-type experiments and no one would know.

MP: One thing I’ve noticed about the DIYbio list in particular is that the open-source approach leads to more transparency. I come from an academic background in CS and linguistics, and something that’s always frustrated me about academia is the fixation on keeping research secret from other research groups because people are afraid of getting scooped. Here, no one cares about getting scooped — the focus is on learning, and if someone else solves a problem first, then that’s great, because that means the problem has been solved. Egos don’t get in the way. We also have people documenting their research in public list e-mails and on blogs, like what JJ is doing with his “Homebrew Bioscience Research” blog, where he chronicles his experiments with moss.

It’s interesting you mention that. I recently read an article about a town in Brazil that has an unusually high population of twins — and there’s evidence that it was this town that Mengele fled to after WW2. So I think the question of whether people will engage in unethical experimentation sort of answers itself, without getting into DIYbio at all. As a community I think it’s our responsibility to encourage ethical experimentation and to reinforce that on a social level — i.e., taking a stand against work that we think is unethical, and taking a good hard look at our own work to make sure that we’re doing the right thing. I’ve gotten into some interesting discussions on my own blog about the ethical issues involved with transgenic symbiotes that complete the vitamin C synthesis pathway in humans… whether it would be ethical to release them on a global scale or not. On the one hand, hundreds of thousands of people worldwide suffer from scurvy, and I want to help solve that problem and reduce human suffering. On the other hand, there are a lot of people who are strongly opposed to GMOs for a variety of reasons and are angry at the notion of an endemic GMO, even one that prevents a very serious disease. And I do think that their rights have to be respected. So it’s a very difficult tightrope to walk, and the questions about what is ethical and what isn’t are really tough.

They don’t have simple answers. So I think my responsibility as an ethical researcher is to engage with these questions as they come up, and try to find solutions that reduce human suffering but still respect people’s rights.

Photo courtesy of http://flickr.com/enochsmilesh+: In a recent interview with Monitor 360 you compared DIYbiology with birdwatching. Don’t you feel that there is a league of difference between the two?

MP: Well, I’m a generalist at heart, even if I’m working in a very specific area. To be honest, most of the cool things I’ve done scientifically have come from cross-pollinating a couple of different research areas. So I make that point about birdwatching and cataloging trees to remind people that biology is really, really big, and it’s worthwhile for experts in small subfields to keep abreast of what’s going on in other areas of the field, because our expertise can help other people and their expertise can help us. Between synthetic biology and birdwatching, absolutely. On the other hand, both DIY synthetic biology and birdwatching are biological endeavors, and a term like “DIYbiology” is broad enough to encompass both. Western culture has a long and exciting tradition of talented amateurs contributing to the progress of science, and I hope people remember that we’re following in the steps of people like John James Audubon (who discovered and cataloged hundreds if not thousands of bird and mammalian species, expanding our understanding of North American biodiversity) as well as Edward Jenner, Jonas Salk, James Watson, Francis Crick, Kary Mullis and so on. Jenner came up with the notion of using cowpox as a vaccine for smallpox by observing that people who worked with cattle and got cowpox didn’t contract smallpox, and developed his vaccine from that — and he was an amateur just like we are. He used his observations of the larger environment to guide his research, and that’s a really important facet of science — recognizing what’s going on in the world and using our observations to further understanding.

7 Responses

  1. Jordan says:

    They think it won’t escape, but there is evidence that they can:
    http://online.sfsu.edu/%7Erone/GEessays/Klebsiellaplanticola.html

    plus, the majority of cells in our bodies (and all other multicelluar organisms) are not with our own DNA, but are bacterium w/o nuclei and gene-trans is possible and does happen. playing around with the balance of the genosphere really can have unknown consequences. such as all the bacteria in our stomach producing a carcinogen…

  2. Anonymous says:

    The bacteria in your body are constantly bombarded with foreign DNA (just think of all the stuff you are eating) and no, they won’t just start using any gene that comes along from the outside. Producing this additional carcinogen would cost a lot of extra energy and and any cell that tries it would be very quickly out-competed.

    Now about the “escaping monster”. If you would have read the article you are linking to (past the ridiculous monster headline that is), you would see that they didn’t show anything about escape or killing the whole biosphere. What those guys did was to grow some isolated plant in a large amount of some engineered bacterium and yes, the plant died. That was perhaps unexpected and the company should have tested for that. But, in the wild, the “monster” bacterium could never have “escaped”. It was loaded with an extra pathway to produce tons of alcohol that wasn’t useful for itself and was on top of that killing its own host plant. That’s a rather bad strategy for competing with the other bacteria around… In other words, the engineered bacterium would never have managed to spread to other fields.

  3. Jorge Ibáñez says:

    DIY Molecular Biology? Is the world getting crazy? Is it possible that any of those enthusiasts believes that the results of their manipulations are predictable? Just the same anthropocentric and reductionist perspective of nature that Novartis or Monsanto shows when trying to convince everybody that their products have completely controlled effects over organisms and ecosystems.

    I’m biologist, working some time ago in the molecular level, and know involved in a more systemic research. I really fell panic to know that a crew of so-called bio-enthusiats (however, organized in a open source community, very idealistic and collaborative, as well as ethically and socially compromised) are playing with “the algorithms of life” as is they were developing a new linux module or gnome app.

    How is it possible that manipulating the structure of biosfere can be considered a hobby? Who can affirm that he or she know all the consecuences that a given action would have in the highly interconected networks that conform nature, from the microscopic level to the biosferic one? How? It’s impossible as a principle. Even knowing certain restrictions that may push the processes to evolve in a certain way (i’m talking about certain arguments presented above regarding energy costs and selection coeficients against mutants) What can make those people sure about the future evolution of the system? Is it necessary to expose here the thousands of examples in which the egocentric humans have thought to control and predict the evolution of nature, who finally has surprised him in unexpected ways? What type of unconciousness has attacked this community?

    Of course, i’m not saying that any hobby related to nature should be forbidden, even at the microscopic level. Let’s say, people can collect plants, photograph birds or, why not, make world distribution maps of bacterias populations. This could be even usefull and certainly harmless when done in proper way. But the huge risks behind this behaviours should make us reflexionate up to which point bio-hobbies should be allowed. As such, without any explicit legal regulation of this homemade research, without a strict control on what are really people doing in their garages, i think that ethics, and common sense, should make us regret against that social communities. And by no means i’m saying that they are bad people with corrupted ideals or without anything possitive to give to the world. No, i’m sure this is not the case for the mayority. I’m saying that their solely existence as an uncontrolled social reality generates certain catastrophic possibilities that makes the whole enterprise not worth of it.

  4. WesHarris` says:

    I’d honestly have to say that the building blocks of life, are exactly that building blocks. One can, with enough ingenuity, skill, and processing power, determine the inner workings of a particular biological agent. Determine how to effectively change and enhance it, as well as to determine how it can enhance the biological capabilities of a host subject.
    To do otherwise would simply be goofy. Stay ahead by staying sharp. You stay sharp by being open to ideas. Sometimes you have to do things outside of the normalcy.
    _+_+
    Wes

  5. Anonymous says:

    How can the consequences of any Human action be totally predictable? Chaos theory and quantum theory says it’s not possible to predict the future, so just live with it. What procedure does the government or big corporations have to predict the consequences of their actions? Does anyone believe they have the welfare of the biosphere in mind?

    This is just the new chapter of an age old argument, technology will give individuals more and more power, do we try to restrict individual freedom so that they won’t misuse the power, or do we encourage them to use the power to do good? I for one do not want to live in a society where big brother is constantly watching and products cost a fortune because only big corporations can develop any technology.

  6. Thompson says:

    It is only going to be a matter of time before someone realizes that this type of do it yourself excursion will eventually lead to something really bad happening. online casino

  7. Jorge Ibáñez says:

    Risks are something that not only concerns the “Big Brother”. All of us should be worried about it, as all of us are affected by them in a global world. You may find interesting reading something about it:
    http://en.wikipedia.org/wiki/Risk_society
    I understand and share your opinion aginst the monopol of farmaceutics around health resarch, but as any other risky human activity, needs to be carefully regulated. The risks associated with DIY biology are REALLY high.

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