Genetic Engineering Conference Kicks Off At MIT Eighty-four teams of students from 21 countries are gathering at MIT to compete in the International Genetically Engineered Machine (iGEM) competition. The teams have been working since the summer to construct biological machine systems — and operate them within living cells.
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Genetic Engineering Conference Kicks Off At MIT

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Genetic Engineering Conference Kicks Off At MIT

Genetic Engineering Conference Kicks Off At MIT

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Genetic Engineering Conference Kicks Off At MIT

IRA FLATOW, host:

You're listening to Talk of the Nation: Science Friday. I'm Ira Flatow. Can you heard of the bacterio-clock? Yeah, can't get one for the holidays. How about bactricity maybe a baccum-cleaner? Well, you haven't heard of that? Well, they have one thing in common. They are all synthetic biology projects that whiz kid undergraduates have dreamt up for the 2008 International Genetically Engineered Machine competition, the iGEM. The idea is to use a tool box of biological parts like different snippets of DNA, for example. To build a machine that operates inside living cells, inside bacteria, inside yeast. And using this approach, students are making cellular biofuel factories, they're devising organic sensors, even solving simple calculations with bacterial computers.

In five years, the program has grown from just a few teams to over 80 and the budding scientists this year hail from four continents and they are on their way to the Massachusetts Institute of Technology right now, to show off their creations in the 2008 International Genetically Engineered Machine competition, the iGEM, and that's what we're going to be talking about. If you'd like to join us, our number is 1-800-989-8255, 1-800-989-TALK, also we're now tweeting. Twittering, you know what that is? You can - if you want to send us a tweet, if you don't know how to do that. Here's how you do it. Just write the @ sign followed by scifritter, that's our address, scifritter. Your name @ sign scifritter, and we'll get a tweet from you. Also in Second Life, you can join the folks over there in Science Friday Island.

Let me introduce my guest, my first guest is a mentor to the Harvard team. She's been involved in the iGEM since the beginning. Pam Silver, is a professor of systems biology, director of the Harvard University Graduate program in systems biology at Harvard Med School, and she joins us from Boston. Welcome to the program, Dr. Silver.

Dr. PAM SILVER (Professor, Systems Biology, Director, Harvard Medical School): Hello, Ira. How are you?

FLATOW: Hi. How are you?

Dr. SILVER: Good.

FLATOW: My other guest has tackled his first iGEM project last year when he was still in high school. Joining up with the University of California, San Francisco team and this year he's working with a Chinese team. And he'll tell us a bit about he ended up there. Eric Meltzer, is a competitor on the Beijing Peking University iGEM team. He joins us over the phone from MIT. Welcome to Science Friday, Eric.

Mr. ERIC MELTZER (Member, Peking University iGEM team): How's it going?

FLATOW: It's going well. Well, let's talk about these projects. Dr. Silver, why call these things Genetically Engineered Machines? Aren't they cells or something? What's the difference?

Dr. SILVER: Sure they're cells. But they're machine, so machines do work, Ira. They take in energy, and they do things. So if you think about the kinds of machines you know. Your car takes you to work. Drills make holes, we use computers to do calculations, but these are all non-renewing machines they don't self replicate themselves. Then you think about what nature does. Nature presents this with an overwhelming number of engineering ideas that aren't even being tackled by regular engineers. Cells are incredibly elegant machines. They can capture light and make things, they can sense single-odorant molecules, and sent signals to your brain. So we have all of nature at our - we need to take advantage of all of nature and understand it to build interesting things.

FLATOW: So, basically are we hooking up sort of parts of our bodies to parts of machines or give me an example.

Dr. SILVER: Well, the simplest examples are some of the ones you began with are taking various - taking bacteria which is - probably the one of the best well-oiled machines that nature makes, and programming it to do things, so for example programming it to count, programming it to take pictures. One of the original iGEM projects in the first year was making the E. coli graph. So these were bacteria that were sensitive to light and could either make themselves either black or white. And so you could make a picture from a group of cells growing together. So those are some of the simplest examples. I think you mentioned some this year, I happened to like the Harvard team one, obviously, of making cells that could measure current. There is one I was looking through - there's making cells that will stick to things because they're going to make them muscle that the protein from muscles that causes them to stick to surfaces.

FLATOW: Mm hmm.

Dr. SILVER: So those are examples - those are very simple examples, and we work with bacteria usually in the iGEM teams because they grow fast. We have a number of parts that can be use in bacteria - as I said they're already the well-oiled machine that nature gives us.

FLATOW: Yes.

Dr. SILVER: To work with. That said, going forward, my laboratory and many others hope to extend this beyond simple organisms.

FLATOW: Mm hmm. Eric, let's talk about your project. You're competing this year with the Peking University team. How did you end up there?

Mr. MELTZER: Actually, we met Peking at the Jamboree last year, and there was kind of talk of a bit exchange and I immediately thought that it will be really, really cool so I kind of jump on the opportunity, and it ended up that two Peking students came to UCFF this year, and I went there.

FLATOW: Mm hmm. And what is your project?

Mr. MELTZER: So our project is an evolution machine. So essentially like in the same way that species will evolve to suit its niche like Darwin finches, for example, proteins will also evolve to better suit their purpose.

FLATOW: Mm hmm.

Mr. MELTZER: So like maybe you'd have a protein that a bacteria might use to copy DNA, and it will get better and better in copying DNA or maybe you know other protein will get better and better at breaking down the certain nutrient. But in nature, it takes millions and millions of years to actually do that. And so, in the lab you can actually - you can shorten that period down. You can shorten that down to maybe a few months or maybe half a year to produce a new protein by directed evolution. But it's a really, really difficult process to do, and it's also - it's not very creative work, so it's kind of the work the most scientists hate to do. And at Peking we thought this work was actually much better suited for bacteria than it was for people. So we created this genetic circuit to run the whole process. And actually very recently we got back some data that says it works. So we're really excited.

FLATOW: What do you mean it works? What does working mean?

Mr. MELTZER: Well, so essentially we took a protein we called the GAL4(ph), and it's a protein that found in yeast. And actually we're using yeast rather than bacteria because yeast is - of other single cells it is very, very similar to a lot of mammalian cells and a lot of the cells that make up our own body. Yeast is that you carry it which means that it has real nucleus, and it can process proteins in a very complex whether maybe bacteria can't. So we decided to actually put our whole project into yeast. Suddenly when we took this protein called GAL4, and we essentially broke it. We made it so it doesn't work anymore and cancels all its function. And then we put it to our evolution machine and then setup the machine such that it would evolve the protein back to full function. And you know, this is a kind of a first proof of concept thing. We weren't entirely sure it would work and no one was, you know, that optimistic, and then it ended up working terrifically. So it's back to full function.

FLATOW: Mm hmm. Dr. Silver, tell us what the Harvard team is working on this year?

Dr. SILVER: The Harvard team is trying to take advantage of cells that produce electrical current and to use that current as a measuring device, so they are going to interface this current producing cells with other cells that say, secrete something, and then the current producing cells will registered that as a current, and send it off to a vault meters. So you can measure how much - directly how much is going on in the system. So they're basically using the cells to generate current and as a measuring device.

FLATOW: Mm hmm.

Dr. SILVER: And there's actually - it looks like theirs actually may work too.

FLATOW: We have a tweeter - we're twittering. Do you know what twittering is, Dr. Silver?

(Soundbite of laughter)

Dr. SILVER: Yes. Of course I know that. Of course. Do you know...

FLATOW: Well, I'm just finding out. We're - actually Science Friday is twittering. We have as we...

Dr. SILVER: So we need to make a bacteria that can twitter, right?

FLATOW: Can you make us one?

(Soundbite of laughter)

Dr. SILVER: Sure.

FLATOW: I know seriously - can you make a bacteria that could twitter? I mean, if somehow work with that...

Dr. SILVER: That's in essence making a simple counter which is - there are many iGEM teams trying to make bacterial computers or...

FLATOW: Right.

Dr. SILVER: Computer in yeast for examples, that those are some of the iGEM projects.

FLATOW: Well, we are twittering at Science Friday starting this - today and here's how you can twitter with us.

Dr. SILVER: That's really exciting.

FLATOW: You can write - do you write the @ sign followed by scifritter, that's our name - scifritter and you can twitter along with us, and we'll be very happy to hear from you. In fact we have our very first Twitter message or tweet as they call it. Coming in from Elainetrain(ph). The question is can a grad students come from any school? How do you get involve in this?

Dr. SILVER: So hi, Elaine and congratulations on being the first Twitter. That's really exciting. And so the beauty of iGEM is - it's very much grassroots, so any school can start a team. The first step is you go to the website, iGEM, and it gives you very precise instructions on how to start a team, you don't need a lot of money to start a team. What you really need are students that are willing to be engaged and willing to empower themselves to spend the summer doing this and asking themselves what do you want to build. So Elaine, what do you want to build?

(Soundbite of laughter)

FLATOW: She'll answer back and I guess she'll twitter back her answer.

Dr. SILVER: OK.

FLATOW: Eric, tell us your thoughts on that. How - is it scary? Do you feel like you're up against some big competition?

Mr. MELTZER: Well, I mean, so I guess last year when I was on the UCFF team, we were all from various high schools, and our team was the only high school team among a bunch of undergrads, and I mean UCFF was very supportive in that process and I think I'd like to echo what Pamela said that really anyone can get involved in iGEM. All it takes is interest and at Peking University we had a 160 or 170 people in the iGEM club, you know, fighting to be on the team. So, the really - the interest is definitely there, and it's just very open thing which is great.

FLATOW: Let's go to the phone.

Dr. SILVER: And I think...

FLATOW: OK.

Dr. SILVER: Well, can I echo in?

FLATOW: Oh, go ahead.

Dr. SILVER: Another thing that Eric - I'm really impressed with the high school students that were involved in this and we're hoping to engage more high school students. They've really exemplified what iGEM is all about, and kudos to you Eric for doing that.

FLATOW: We're talking this hour about a synthetic biology science fair if you just joined us, coming up at MIT this weekend. It's called iGEM the International Genetically Engineered Machine Competition. Let's go to Shamari(ph) in Oakland. Hi, there.

SHAMARI (Caller): Hello. Thanks for taking my call.

FLATOW: Sure.

SHAMARI: Yeah, I just had a question about Dr. Silver had mentioned that a bacterial-like machine? And my question was how do you make a bacteria machine? Do you modify the DNA of the bacteria or? How do you do that?

FLATOW: Yeah, take a - good question. Dr. Silver or Eric take us through the steps. How do you put the parts together?

Dr. SILVER: So, there are pieces of DNA and they are introduced into the bacteria on what we call vectors. These are pieces of DNA that are capable of self-replicating as the cell divides. And that's how you introduce the parts into the cell. You add a bunch of salts and things like that to get the DNA in, and then you use a drug resistance marker or some other way to make sure that the plasmid has gotten into the cells. That may have been a little technical.

FLATOW: Keep going.

Dr. SILVER: It's a piece of DNA.

FLATOW: And then what when...

Dr. SILVER: And it goes into the cell and because DNA is the genetic material it is capable of replicating itself.

FLATOW: OK, keep going. So it replicates in the cell, and then how does it turn it into a machine.

Dr. SILVER: That's where the design component comes in. So, if you want to, for example, make a cell that can count then you need to design the parts that you need, and then you produce the DNA that you need for the cell to make those parts.

FLATOW: So, the DNA...

Dr. SILVER: And those parts can be DNA, they can be RNA, they can be proteins, they can be lipids, they can be any part of the cell.

FLATOW: Any part - and this - can we make the cell light up when it comes up with the answer?

Dr. SILVER: Yes. Absolutely. In fact the Nobel Prize was just given for a protein - a very special protein from the jellyfish which naturally fluoresces, and so it's a very powerful tool in that you can put in bacteria, and they will turn green when they have this protein so they can tell you an answer. So, for example there was an iGEM project from the University of Edinburgh team where they made cells that could sense the level of arsenide in water. And so they would light up in response to how much arsenide was there, and this actually turns out to be a very useful machine because arsenide in well water is a serious problem in the third world. So, that's a really nice example of a team doing something that has a direct application in the world.

FLATOW: Talking about iGEM this hour on Talk of the Nation: Science Friday from NPR News. Talking with Dr. Pam Silver and with Eric Meltzer. So, you theoretically could then take all these little parts and put them into people? Into our own cells to monitor you know if we're getting sick or ill or poisoned?

Dr. SILVER: Sure why not.

FLATOW: Or any of that kind of that stuff?

Mr. MELTZER: Yeah.

Dr. SILVER: Sure that's the dream.

FLATOW: Eric, Eric.

Mr. MELTZER: Well, yeah. A group that came to mind at Berkley that's making a bacteria that essentially can go through your veins and can search for cancer, and so it detects tumors because tumors tend to have lower oxygen than the rest of the body, they are not as well served by blood vessels. And so this E. coli which has been specially modified to not set off your immune system can then just hunt through your body for tumors and when it finds one they can do a lot of things, they could you know, as we previously mentioned they can light up using that green fluorescent protein and then another thing that it could do that the people who are working on this at Berkley have engineered it to do is release a factor called tumor necrosis factor that actually shrinks the tumor.

FLATOW: Wow.

Mr. MELTZER: You could really have these bacteria you know, patrolling your body for cancer and that's just one of the kind of human interest...

Dr. SILVER: And I think it extension on that same idea is you could have cells that will deliver drugs under certain conditions. So you could have imagine having a drug delivery device that will only deliver drugs at night or something like that.

FLATOW: Eric, tell us what's going to happen this week, and there's a competition does everybody like those dioramas you see at science fairs?

Mr. MELTZER: Not quite. Everyone has posters, and I guess actually some people do bring physical product to iGEM. Last year, the Berkley team had this bacto-blood, and so it's basically bacteria that had been engaged to express hemoglobin and they actually showed up with a few vials of this, you know, red liquid which is pretty cool.

Dr. SILVER: And remember the smelly bacteria?

Mr. MELTZER: Oh, right. Also, MIT had a project where they had bacteria. So normally E. coli smells really, really bad, and they knocked out the genes that made it smell bad and they put in some genes it made it smell like a mint and smell like bananas and all sorts of nice things. So they had that and they have people sniffing it which is pretty cool.

FLATOW: Wow, so you can make that sounds like a product?

Mr. MELTZER: Oh, yeah.

Dr. SILVER: Those are called Eau d'Coli.

FLATOW: And so there'll be people be competing - is there a prize? You make - do you win big prize money here?

Mr. MELTZER: It's not money. There are a few awards there's like finalists and there are various medals given out for compliance with standard which I guess the big part of iGEM is that they are really trying to get people to make this standardized parts so that other teams can use them later and they are giving awards for, you know, the degree of compliance with that and then there's also you know, real awards for like how well the project did and all that kind of thing. But there's a competition.

FLATOW: Do you patent it? I mean will somebody could steal your idea? I would think.

Mr. MELTZER: Well, thats - I guess the real beauty of iGEM for me is that it's really this open source thing, and it's like I guess at some conference is that if you go to a conference people are kind of jealously guarding their ideas and at iGEM it's the total opposite everyone is really you know there and sharing their ideas and there really is this phenomenally open thing which is great.

Dr. SILVER: I think there's also an atmosphere at least what we started - when we started iGEM of sort of everyone is a winner just showing up makes you a winner.

FLATOW: Well, where should we show - is it open to the public? Can people go this weekend?

Dr. SILVER: Absolutely.

FLATOW: Where is it?

Dr. SILVER: It's at MIT in the Stada Center, it's a fabulous thing. It's a you know - there is a registration but it's going to be really crowded this year, this is the biggest year yet, there's 800 students and participants there, but people can come.

FLATOW: All right. That's this weekend at MIT at Harvard, if you want to go see those great projects. Good luck to you.

Dr. SILVER: Thank you.

Mr. MELTZER: Thanks a lot, Ira.

FLATOW: Thanks Pam, thanks Eric. Pam Silver is professor of systems biology and director of the Harvard University graduates program in system biology at Harvard Med School. Eric Meltzer is a competitor on the Beijing Peking University's iGEM team. Stay with us, we're going to come back and talk about what you think Barack Obama should pay attention to in science. We'll be right back after this break. I'm Ira Flatow. This is Talk of the Nation Science Friday from NPR News.

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