IRA FLATOW, host:
Your wrist watch, your cell phone, maybe even your coffee maker contains more computing power than the earlier room-filling computers of the late �50s and �60s. Shrinking computers down in science is one of the great challenges and triumphs of the cyber world. But the inventors of the future are thinking even smaller. They're envisioning a different kind of machine, microscopic machines that are alive and self-replicating too. Imagine, the billboards of Times Square lit up by glowing microbes that could regenerate if one burned out, or bacteria that could tell you if you're not getting the potassium in your diet, or ones that can suck up all the arsenic from a poisoned well.
Well, these cellular machines don't run software, they run DNA, and just like you can put together circuits from electronic points. They can build circuits into cells by stretching together different fragments of DNA. College undergraduates and even some high school students are doing this, and over a thousand of them gathered at MIT this past week to share their inventions at the international genetically engineered machine competition, or the iGEM. And joining us now is one of the winners of the iGEM competition and one of the judges.
Catherine Goodman was a judge at this year's competition. She is also an associated editor at Nature Chemical Biology in Cambridge, Massachusetts. She joins us from the studios of WBUR in Boston. Welcome to SCIENCE FRIDAY, Dr. Goodman.
Dr. CATHERINE GOODMAN (Nature Chemical Biology): Thank you very much. It's a pleasure to be here.
FLATOW: You're welcome. Vivian Mullin is a member of the Cambridge University iGEM team and an undergraduate in biochemistry at Cambridge University, England. She joins us on the phone. Welcome to SCIENCE FRIDAY, Ms. Mullin.
Ms. VIVIAN MULLIN (University Student): Hi. Thank you so much. How are you?
FLATOW: How are you? Tell us about your project. Can you sum it up for us?
Ms. MULLIN: Yeah. So I'm part of the Cambridge 2009 iGEM team and our product was called Ecromite(ph). And what we were trying to do is to improve bacterial bio-sensors. So I'll just tell you all about - a little bit about what bacterial bio-sensors actually are. They are bacteria that can tell you the concentration of, like, a pollutant in water. And they can do this because inside them they have a detector which switches on at a certain concentration of the pollutant. And then the bacteria is designed to have a way of telling you whether or not the detector is on.
So we were trying to improve this technology - this bacterial technology. So we developed two different parts that help you see whether your detector is on or off and also control when your detector is on or off. So our bacterial machine had a thing called a sensitivity tuner, and this actually tells a detector when to turn on and when to turn off. So you have control over what level of concentration of the pollutant you're detecting.
FLATOW: And how do you know - and how does the bacteria show that it's on or off?
Ms. MULLIN: Yeah, so in the past, bacterial biosensors have used, like, florescence�
Ms. MULLIN: �and other things which need technology to read the output. So, we did is that, we used something called a color generator, which basically means that bacteria changed color when the detector got switched on.
FLATOW: Wow. So they light up in a different color?
Ms. MULLIN: They don't exactly light up. They actually change color, like�
Ms. MULLIN: �it's visible to the naked eye.
FLATOW: So, what is - so, let's say if you put a swab of the bacteria in a polluted river, if it - if the pollution was at a certain level to trigger it, the bacteria will just change color.
Ms. MULLIN: Yup, exactly. But you'd probably want to put sample of your water on a bacterial plate maybe, not the other way around.
(Soundbite of laughter)
FLATOW: Vivian Mullin, how would you envision something like this being used in other ways in the future?
Ms. MULLIN: Well, the idea of bacterial color is really fascinating. I mean, we're trying to think of ways that color might be used in the future. But we think that making bacterial biosensor is a really good application for pigments, because bacterial biosensors, the whole point is that they're user friendly and accessible to the people who would benefit from knowing whether or not their water is polluted. And having a visible output like - that's visible to the naked eye�
Ms. MULLIN: �is going to be the real improvement in the design of these biosensors.
FLATOW: Mm-hmm. But you could use them to sniff the air then. Could you not? Or could you ingest them and they would tell you what's - what different chemicals might be in your body by changing color when they came out?
Ms. MULLIN: Yeah, all we need is a - the detector. There's a lots of different detectors already in the registry, which is the all the parts that we have to use for our project.
Ms. MULLIN: So, if you have a detector for something, then you could use our parts, the tuners and the color generators to make it a good biosensor.
FLATOW: Wow. So it's almost limitless�
Ms. MULLIN: Uh, yeah.
FLATOW: �kinds of things you can do with this. And is it cheap to make?
Ms. MULLIN: It's probably going to be - would be cheaper then using the expensive and fragile equipment that we have to use right now to detect chemical bulletins. And this is like something that's going to be pretty far out in the future. So we don't really know yet.
FLATOW: Catherine Goodman, what a great contest winner.
Dr. GOODMAN: Yeah, she - Vivian was actually the lead presenter of the team from Cambridge. And she did a phenomenal job, and all her colleagues were excellent, as well. So it was a really entertaining presentation.
FLATOW: But it's great that she is able - I know we talk about scientists a lot - able to describe in real English what her scientific work is doing. You know, it�
Dr. GOODMAN: Definitely. It's an important skill for scientists, for sure.
FLATOW: Tell us about some of the other projects that stood out at the competition.
Dr. GOODMAN: Well, there were a bunch. So, this was the largest - I mean, each competition has been getting larger and larger, almost exponentially, I think. And so this year, there were about 120 teams, I think. So, it's hard to narrow down, but some of the very coolest ones that made it into the finalists - aside from the Cambridge team - was a team that was on the track that I was judging, which was the manufacturing track, where you're trying to produce an actual product.
Dr. GOODMAN: And that was the team from Imperial. And they were creating a -kind of a all-in-one drug production and delivery system to your intestine. So, they would have these bacteria that would produce a protein, and then at a separate time, the bacteria would coat themselves with a special carbohydrate coats that would make it safe for them to pass through your stomach. And then in the third step - so this team actually won the Human Practices award with another team. And so that was for considering how these bacteria are really going to be accepted by the public and�
Dr. GOODMAN: �if you ever wanted to have this as an actual drug.
Dr. GOODMAN: People aren't going to want to take a bacteria. And so, the third step was that the bacteria would degrade its own DNA so that it would become inert once it was inside you.
FLATOW: Yeah, that's - that actually answers a question that - a tweet came in from a M.T. Edder(ph), who wanted to know how are we building dead man switches to prevent accidents and release - of the escape of these organisms.
Dr. GOODMAN: Definitely. So this, in their case, there was a specific temperature responsive-element that when you heated the bacteria up a little bit, it would trigger the degradation of the DNA. There was another project from Toronto, I believe, where they were trying to detect Toluene in the environment and degrade it. And their trigger switch was once the Toluene was -had been fully degraded, then the bacteria would sense that the Toluene was gone and kill themselves.
FLATOW: Mm-hmm. 1-800-989-8255. Vivian, where do you go from here? Can you go actually make products that you can sell, or you go in and license your technology to a company?
Ms. MULLIN: Well, we really hope that some more experienced scientists will be pick up on our work, and maybe in the future will actually be a devise that people can use. Yeah, definitely.
FLATOW: Mm-hmm. Is there any one - in one area besides - or is it water pollution that you're most concentrated in?
Ms. MULLIN: Well, the beauty of our parts is that they're made to be interchangeable and usable for anything. So, if you can find a detector that, like, can detect carbon dioxide, maybe, in the atmosphere or maybe in some medium other than water, then, in theory, our parts should be able to be compatible for that.
FLATOW: Could you actually, let's say, detect toxic elements that might be in your body if you�
Ms. MULLIN: Yeah.
FLATOW: Yeah. Is that right?
Ms. MULLIN: Yeah, if you had a detector for it and you were able to - like we were talking about with the Imperial team - make the bacteria able to be ingested and safe for that.
FLATOW: Hmm. And so you could just watch your feces on the way out and see what color there were.
Ms. MULLIN: Yes, you could.
(Soundbite of laughter)
FLATOW: Well, your doctor asks you that anyhow when you get checked up.
(Soundbite of laughter)
FLATOW: Your team collaborated with some art students, right? Was that to help visualize what you were doing?
Ms. MULLIN: Yeah, that's right. We worked with Daisy Ginsberg, James King and Tuur Van Balen from the Royal College of Art. And actually, Daisy and James ran a few color workshops with us to help us, like, get out of the lab and really think about the implications of the future of color. And they actually did a parallel project called E. chromi, and they came to the jamboree and showed it off. And it was really, really fun and a good design perspective on synthetic biology.
FLATOW: And part of this art project was something called the Scatalog.
Ms. MULLIN: Yes, it was. You mentioned eating bacteria and then kind of seeing them come out and seeing them change color. Their idea was that the bacteria would indicate your healthiness, and so they'd be a certain color if you were healthy, but they would change color if, for example, you had low potassium levels or something. So this was a kind of the way of diagnosing yourself.
FLATOW: Mm-hmm. Was this art-science collaboration a common theme this year, Catherine?
Dr. GOODMAN: It definitely was. There are lot of teams that were thinking about bacterial patterns and colors and how you can kind of interface with the real world. One team that really stood out in that way was the team from ArtScience Bangalore, which was, in fact, a bunch of art students that became scientists for the purpose of the competition.
Dr. GOODMAN: And so looking at their Web site, I didn't get to see their presentation, but looking at their Web site and hearing the other judges talk about them, they just brought a really unique idea to what is this competition all about, and what is science? What is art? How can we go forward? And they had started a Web site called hackteria.org, which kind of aims to unite biological artists, which I found quite interesting.
FLATOW: We're talking about science and the arts this hour, in this part of SCIENCE FRIDAY from NPR News. I'm Ira Flatow, talking with Catherine Goodman and Vivian Mullin. Let's see if we can get a phone call in here. Hi, Matt, in Florida. Welcome to SCIENCE FRIDAY.
MATT (caller): Thank you.
FLATOW: Go ahead.
MATT: My question is, he's the - my father used to be a pool contractor, and what he would do is very similar to what you're describing. He would take chemicals and use them to check for certain - like, ph, solidity, stuff like that. My question is these bacteria that you're describing, do they have any negative or detrimental effect to the environment? Like, what effects they have?
FLATOW: Catherine, can you handle that?
Dr. GOODMAN: Yeah, I think that's a really open question right now. Certainly, the teams that produce the participate iGEM do a pretty comprehensive analysis of the safety of their particular projects. And so, like we were talking about earlier, there are some people who design in the kind of these kill switches if they were to be used in real scenarios. But other people are certainly trying to design compound bacteria that will bind arsenic or other toxic metals. And certainly before they would be employed in any real setting, a lot more discussion needs to go on. Synthetic biology is one community that's really advanced in terms of thinking about safety and ethics, and this competition is a great example of that.
FLATOW: Vivian, you must have thought about this when you were designing�
Ms. MULLIN: Yes. Our project, we definitely thought about it. We had fill out a risk assessment form before we even began anything to think about what the implications of what we were doing in the lab. And then just with our lab work, the strains of E. coli that we were using were disabled. So if they managed to escape into the environment, they wouldn't have been able to survive. They would be out-competed by the natural bacteria that are out there. And our lab is like a contained environment, so it was very unlikely that bacteria would actually be able to escape. And we also thought about this for the - for our project. And we understood if this is actually going to become a device that people would use in the future, there would have to be a lot of thought to put into it as to make it safe for the environment.
FLATOW: Catherine, this, I understand, is working on sort of an open access -an open source model for biology. Is that correct?
Dr. GOODMAN: Definitely. So the BioBrick registry this collection of gene sequences and physical DNA that is sent out to the teams is all available freely online, and that's kind of the beauty of this resource, in fact, that all the teams that all the team that are preparing for the competition can just go to the registry, see what parts are available and make use of what they need. So it's a really unique community in science. Most people kind of guard their results, but these�
Dr. GOODMAN: �folks have been really collaborative.
FLATOW: Mm-hmm. And Vivian, how much did you know about synthetic biology before you went into this competition?
Ms. MULLIN: I didn't actually know very much. I learned about it in one of lectures in my second year. The beginning of our summer was actually a two-week introduction to synthetic biology, which we attended, as well as some students from the Royal College of Art and some engineering students. So, right�
MS. MULLIN: �from the beginning, we realized that it was a really interdisciplinary subject, with designers, engineers and biologists all�
FLATOW: You know, I think it's a new term to most of the public: synthetic biology. You know? We've heard about all kinds of genetic engineering and stem cell research, but I think the word - the phrase synthetic biology has not been used a lot lately, but I guess we're going to be hearing more of it.
Ms. MULLIN: Hopefully�
Dr. GOODMAN: Definitely.
FLATOW: Well, do you think, Vivian, next year we'll be getting more of this kind of interesting stuff coming in?
Ms. MULLIN: Oh, definitely. Every year, the iGEM competition produces like - well, hundreds of new projects every year, and every single one of them is really interesting and really unique. And I think that the iGEM competition has been growing massively every year. So, hopefully next year, we'll have even more teams and even more projects.
FLATOW: You hope it gets tougher, Catherine, to judge, I'll bet, because the competition is so good.
Dr. GOODMAN: Yeah. It's almost impossible to judge. Our judges meeting just to decide the special awards and the finalists took four hours on Sunday night. So, it's - there's a lot of amazing talent.
FLATOW: And if you want to get in, how do you compete? How do you find out more about this?
Dr. GOODMAN: You go to igem.org and sign up, basically.
FLATOW: Mm-hmm. And it could be anybody from anywhere in the world?
Dr. GOODMAN: I think at the moment, most of the teams are undergraduates being advised by professors and graduate students. But this year was the first year that they had a team that was only high school students from a high school, and there was also a junior college participating. So I think it's really pretty open to the public.
FLATOW: All right. Well, good luck to you, and thank you both for taking time to be with us today.
Dr. GOODMAN: Thank you.
MS. MULLIN: Thank you.
FLATOW: You're welcome. Vivian Mullin, member if the Cambridge University iGEM team, undergraduate in biochemistry at Cambridge University and Catherine Goodman, who was a judge at this years iGEM competition. She's also an associate editor at Nature Chemical Biology in Cambridge, Massachusetts. It's about all the time we have for today.
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