Base Pairs Episode 16.5: Fuels of the fuels

Transcript

BS: Hey everyone, I’m Brian.

AA: I’m Andrea.

SRM: And I’m Sara.

BS: This is Base Pairs, this is one of our chat episodes where we talk about stuff from the previous episode and riff off it from there. So last episode, what was that about Andrea?

AA: Well last episode we talked about biofuel and a very exciting new potential source of biofuel that a plant scientist here named Rob Martienssen is working on. The crop that he wants to use for this biofuel is duckweed, which you’ve probably seen and thought of as just pond scum, it’s all over the place, it’s that tiny, tiny green plant that forms a mat over ponds and he has found a way to, as he puts it, “persuade” duckweed to make oil.

BS: Right, and Rob, if you listen to the episode, you’ll find out Rob has a very charming classical English accent, so he sounds very persuasive, at least to us Americans, every time he says something.

AA: Yeah, Rob can be pretty persuasive but he needs more than his charming accent to get duckweed to make oil. He had to do some genetic tricks to do that and the way that he and his team of researchers made that happen is they actually transferred a gene, a gene called WRINKLED1, from corn into duckweed.

BS: Okay, corn though, really? When I think of corn, I think of corn ethanol, kind of like what we talked about last episode with the different generations of biofuels but in that case, ethanol is not oil, it’s ethanol, it’s alcohol. How the heck is he turning it into oil then?

SRM: Well actually, I just typed it in on my phone and apparently corn oil is a thing. So it’s used as speed stock for biodiesel but it’s also in soaps, salves, paints, rust proofing stuff for metal surfaces, inks, textiles, nitroglycerine and even insecticides.

AA: There you go, yeah corn knows how to make oil and basically Rob and his team just borrowed corn’s method, or at least part of it, for making oil and stuck it into duckweed and it worked. It got duckweed to start making oil.

SRM: But wait, wouldn’t that then make it a GMO?

AA: It would. So since this is a gene coming from corn, pretty much under any definition of a GMO, this would qualify but I was talking to Rob and there is a potential for getting duckweed to make oil without going through this more GMO route, where you’re taking a gene from another organism and sticking it into a new organism. There could be a way of using this newer tool called CRISPR that does something called gene editing, where you’re not taking genetic material from some other species and moving it, but you’re just making a little cut in the DNA, or just making some other chain that essentially looks indistinguishable from what you would see arising naturally, and so-

BS: That’s CRISPR, that’s C-R-I-S-P-R, we’re not talking about potato chips here or anything?

AA: Right, no. So here’s Rob talking about that.

Rob Martienssen: It certainly would yes, there’s no question that it’s a GMO. There are some strategies that we could use perhaps with CRISPR that would make it less … I don’t know, it’s still a debate and I know that it’s been decided pretty much in some parts of the world that it’s … So in the United States, CRISPR is not regarded as GMO, whereas in Europe it almost certainly will be and in Australasia it is. So exactly what’ll happen to that in the future is very hard to say. I think it’s actually made people really think about what they mean by GMO and genetic modification of course is something that’s been practiced by breeders for thousands of years and actually results in changes in the DNA sequence which are indistinguishable from those that are generated by CRISPR.

What we mean by genetic modification is something that needs to be discussed a lot more, I think in a sort of public debate. In truth, I think really high impact climate changing biofuels are probably going to be produced in GMO plants and there’s not much we can do about that.

BS: So here what we’re talking about with the corn genes, this is a transgenic GMO and usually one of the big concerns with that was, “Oh no, what’s it going to do to me if I eat it?” This Frankenstein food.

AA: Right, what if you have an allergy not to what you think that you’re eating but to the gene that was spliced in.

BS: Right, but in this case we’re not eating it, it’s fuel. At least I don’t want you to eat it.

SRM: Well isn’t the other worry about GMO’s that they might get out and sort of infect the native population?

AA: Right, yeah, there’s this concern that if scientists are creating these GMOs to be stronger, better plants in whatever respect, if they get out are they going to out-compete everything around them and destroy ecosystems? That is certainly a concern that you might have about biofuel crops but in the case of duckweed, Rob is less concerned about that, though certainly looking into it for a number of reasons which he told me about.

Rob Martienssen: A big advantage of this sort of indoor growth thing is that it’s all contained and for example, the duckweed producing oil, even if it did escape, would have absolutely no way of competing with anything else because it’s very, very unique niche and one that can only be maintained by humans. Yeah, clearly this is going to be an issue for most biofuels. That is a question that is important to address and so for example, we have a grant from the department of energy now to do this work and part of that is very much … is what they call bio-containment and we have to think about this pretty hard. As I said, most of our engineered strains … the great thing about duckweed in the wild is that it out-competes everything so it’ll certainly out-compete anything that we manage to make in the laboratory.

AA: So Rob and his team were successful in getting duckweed to make oil but there was this unintended consequence of it slowing down the plant’s growth overall.

BS: Right, and we described that a little bit more in the full episode but based off what Rob just said, my impression is that it kind of winds up being a silver lining, at least right now, where these plants are dependent on the people who are making them, but the more we know about the genome, the more scientists could even intentionally do that, right? Where it’s making it so if the plant gets out it’s not going to cause harm because we know exactly what we’re adding to the environment?

AA: Yeah right, the more we know about how these genomes work, the better chance we have of getting these plants to do what we want them to do and not anything that we didn’t expect them to do. That’s a lot easier said than done of course, but it is getting actually significantly easier to the point that a post-doc in Rob’s lab was able to do a lot of the DNA sequencing of these duckweed genomes with a device that looks a lot like a USB stick. Sometimes he would pack it up at the end of the day and take it home to his apartment in Brooklyn.

You mentioned that Evan’s analyzer looked like a USB device somehow?

Rob Martienssen: Yes, exactly things have changed so much. Human genome projects, and I forget exactly how much it cost, but it was in the order of half a billion dollars and took the efforts of thousands of people and it was only 20 years ago. Now, a single person, in my case Evan Ernst who’s a duckweed meister in the lab, also a computer guy and genomics guy was able to do the sequence of two complete different duckweed genomes on his own, using a new technology called Oxford Nanopore which is literally a USB stick-like device where you pipette the DNA onto it and you get these wonderful long reads, it’s just amazing. He did some other things, he did some Illumina and other things as well, but yeah it produced a really beautiful genome.

SRM: So you’re telling me that somebody can map a genome while binge-watching Netflix in their own apartment?

AA: Yes, using the very same device, it’s pretty incredible.

BS: I remember when I first started working here and there was a meeting going on and I got to see one of these things for the first time in person, this little … what I thought at the time was pretty just like an outdated, oversized USB device. I’m like, “What do they use that thing for?”

AA: What’s this piece of junk?

BS: Right and it’s still mind-blowing that somebody is pipe heading just a little bit of plant matter or what have you onto this device and bam, genome.

AA: Yeah, definitely sounds pretty sci-fiesque to me but this is the reality we live in now. Actually speaking of sci-fi, I know that Ssts, our pop culture aficionado has some examples of fuels of the future from the movie world for us.

SRM: Yep, that’s right. Since basically the dawn of sci-fi, people have been really interested in the future of travel and that means the fuels that power it too. Usually it’s really interesting, you can tell how a cultural mindset, or the cultural miasma feels about the future by what fuels are being used. Either they’re hopeful and bright or they’re dark and dismal. So one of the first ones I wanted to bring up is, you guys remember way back in episode 14.5 when we talked about Back To The Future?

AA: Yes. Sara

BS: Mm-hmm (affirmative).

SRM: Doc Brown had to steal that plutonium in order to power the DeLorean.

AA: Right, right, that very old looking car.

SRM: Yes, that very old winged-looking car. Well luckily in Back To The Future 2, he didn’t have to steal any more plutonium from terrorists, instead, he goes all the way to the futuristic year of 2015.

AA: Oh boy.

SRM: And gets himself something called the Mr. Fusion, which we don’t hear much about but we do see it turn a banana peel and some beer into nuclear energy to power the time traveling car.

BS: Wow, so my impression here is it’s basically … it’s not really a biofuel but it’s taking the matter of these organic waste-

SRM: I mean, we don’t 100% know but just imagine waking up in the morning, going over to your car, popping a little hatch and throwing in last night’s leftovers and then being able to drive into work just on that.

AA: Wow, yeah, that sounds pretty ideal though I wonder what kind of efficiency he’s getting, especially out of that old car.

SRM: Yeah.

BS: Right, how many miles per banana peel?

SRM: Right, how many miles per beer can? It’s a very bright future, that’s the same movie that has the infamous hover board that everybody and their mother wants to be a reality and since this movie took place in 2015, it seems we’re lagging a little bit behind. But not all biofuels are portrayed positively. The cyber-punk classic, The Matrix, basically shows us a future where the robots have taken over earth and well, they use human bodies to power their entire mainframe.

Morpheus: Human body generates more bio-electricity than a 120 volt battery and over 25,000 BTUs of body heat. Combined with a form of fusion, the machines had found all the energy they would ever need.

AA: Do the human bodies get to live?

SRM: Well actually, that’s the interesting part. So the humans, without mental stimulation, die. So the robots build this thing called The Matrix, which is basically a sort of virtual reality illusion where people believe that they’re living their lives in the 20th century, when they are in fact plugged into a mass of machines with billions of other people.

BS: As for anyone who hasn’t seen The Matrix, apologies for the extensively broad spoiler that we just threw down there, but it’s not really ruining all that much.

AA: No that’s a pretty grim figure of the future, I think we’d be much better off with some duckweed.

SRM: The last movie I want to talk about is actually a movie series and it looks at a world where we don’t adopt biofuels and rely solely on power sources like gasoline that are not renewable and that’s a pretty famous one that I’m sure you guys have heard of called Mad Max.

BS: Right, Fury Road was one of the best movies I’ve seen in a long time.

AA: Sell it to me because I’ve not seen it.

SRM: Right.

AA: Shocker.

SRM: All right, here we go. So the film, the films excuse me, take place in Australia in a world where all the resources are starting to fall away, gas, water, electricity starts to dwindle down, so people start taking to the roads in these really elaborately made junk cars to fight it out for the last of these super valuable resources, especially gasoline.

BS: Right, to get more gasoline, you got to burn gasoline.

SRM: Exactly, and the more the movies continue with the story, the more you see the earth deteriorating around them until you get to probably one of the most popular entries in the franchise, the very recent Mad Max Fury Road. In this movie, actually probably one of the most heartbreaking portrayals is this character, Furiosa, is trying to get these women to the Green Place, this home where she used to live that was green and lush and beautiful, not the horrible desert where a war lord essentially controls when people have access to important life sources like water and gasoline. In the end, when she finally meets up with people from her old tribe, they tell her that the Green Place is now nothing but an inhospitable, desolate marsh.

Speaker 8: The creepy place with all the crows, the soil.

Speaker 9: We had to get out.

Speaker 8: We had no water and-

Speaker 9: The water was filth.

Speaker 8: It was poisoned, it was sour.

Speaker 10: And then the crows came.

Speaker 8: We couldn’t grow anything.

AA: Hopefully not covered in duckweed.

SRM: No, not covered … unfortunately, maybe it would be better off if it was covered in duckweed?

AA: Yeah it’s true, maybe they would be.

SRM: Yeah but unfortunately it’s just a sad, desolate wasteland of darkness and creepy people on stilts walking around.

AA: Well I think we have an uplifting sequel idea.

SRM: Exactly. Mad Max, accept the biofuels.

BS: Yeah, so I guess that’s it, thanks for listening, apologies for the movie spoilers, but at this point you should have seen these movies, guys.

SRM: You should have seen them.

BS: So thanks again, stay tuned for next month’s episode, what’s that going to be about?

AA: We are going to dive into some of the implications of having access to personal genetic information, what’s in everyday people’s genomes.

BS: And if we know about it what does that mean?

AA: Yeah.

BS: All right, so thanks. Stay tuned.

AA: We’re coming to you from Cold Spring Harbor laboratory, a private, not for profit institution at the forefront of molecular biology and genetics. If you’d like to support the research that goes on here, you can find out how to do that at cshl.edu and while you’re there, you can check out our newsstand which showcases our videos, photos, interactive stories and more.

BS: And if that’s still not enough, you can always pay us a visit. Between our undergraduate research program, high school partnerships, graduate school meetings and courses, and public events, there really is something for everyone.

AA: I’m Andrea.

BS: And I’m Brian.

SRM: And I’m Sara.

AA: And this is Base Pairs, more science stories soon.

SRM: I mean that’s what I would do.

AA: That was perfect.

SRM: I’d get a pipette and watch Buffy the Vampire Slayer. Like boop-boop-Buffy. I’m sorry.

AA: Yay.

BS: All right, let me add that, I’m probably going to include the Buffy the Vampire part by the way.

SRM: Oh no.