Interviewer: Lydia Morrison, Marketing Communications Writer & Podcast Host, New England Biolabs, Inc.
Interviewee: Aaron Pomerantz, Ph.D. candidate, Integrative Biology Department, University of California, Berkeley
Hello, and welcome to the Lessons From Lab and Life Podcast. I'm your host, Lydia Morrison, and I hope that our podcast offers you some new perspective. Our podcast today focuses on the value of firsthand experience. I'm joined by Aaron Pomerantz, who's current a PhD candidate in the Integrative Biology Department at UC Berkeley. His lab work focuses on understanding the nanostructures that create the structural color of a butterfly wing, but his passion lies in the jungles of South America where he conducts field research.
Hi, Aaron. Thanks so much for being here today.
Thanks for having me.
So, I've been doing some light, what I would call, online stalking of you in preparation for our meeting.
Yeah. I have a couple questions. Firstly, would you classify yourself as an entomologist or a molecular biologist?
Yeah. I get asked that question. I kind of feel like it's hard to answer, because, yes, I feel like I'm a little bit of both maybe, but I definitely started my foray into science as an entomologist. I was that little kid who was running around in the mud and playing with bugs. I think part of that was because my mom would garden a lot, and so we had a lot of native plants and animals growing up, where I'm from in Los Angeles. Then I went to school for entomology, so I got my undergraduate degree in entomology. I went over and got a Master’s degree in entomology, but then I started to get a little more involved in molecular science. In particular, I was interested in next generation sequencing and things like RNA interference at the time. Now, I mean, this is sort of a long winded answer of saying I feel like little bit of both. I'm currently a PhD student in the Integrative Biology Department at Berkeley, so I just like to say I'm an integrative biologist now.
Okay. I totally get it. It's hard to pigeonhole your kind of curiosity. Follow up question. Your social media profiles state that the coolest discoveries are the ones that you make yourself, so what does that statement mean to you?
Well, when I was working as a field biologist in the Peruvian Amazon, it was a really amazing opportunity to just sort of wander around and kind of play Darwin. In fact, I was working with an ecotourism company who had hired me to be a field biologist. I said, "What's my job description?" They were like, "Whatever you want it to be." So, I thought it was a really amazing opportunity to just sort of wander aimlessly and just give me the opportunity to just make discoveries of my own. Some of them were finding organisms that were doing things in new ways, describing new life histories, and some of them were likely new species. At the end of the day, I felt like these might not be groundbreaking things, they're not going to end up in nature papers, but to me they were very important, and to me I felt very excited as a scientist to find these things. It kind of felt like this discovery of one. That's sort of why I made my little motto is like I think the coolest discoveries are the ones that you make. These are the things that really excite you.
So, let's talk about some of your personal discoveries. Can you explain to our listeners about your interest in the source of the colors that we perceive in butterfly wings?
Definitely. This all started, again, when I was wandering around the rainforest, and there were a couple of interesting, new types of butterflies that I found. One of these was a collaboration with another scientist, and we found that there was this butterfly that hung out with ants. This was sort of bizarre, because normally there is no described association between butterflies and ants like this, but it even turned out that these butterflies had a wing pattern that looked like the ants.
Oh. That's so interesting.
So, that got me really interested in wing patterns, mimicry, but what was actually the root of these colors and patterns in butterfly wings is that we see and how there are these amazing mimics that have evolved in nature. These are sort of textbook examples when you take a biology class, right? You'll see these orange butterflies that mimic one another, because they're toxic, but where do these colors actually come from. At the time I was looking into PhD opportunities. I thought it would be advantageous to go back and develop a greater skill set, especially with sequencing, because I was trying to get more involved in portable DNA sequencing.
So, I found an opportunity at UC Berkeley. There is a lab. Nipam Patel is the advisor. They were really interested in looking into the development of structural coloration, which we can talk a little bit more about in detail, but this was I thought a really cool opportunity to dig into this mechanism, this really fundamental question of where does color come from in animals?
That's really interesting. I know pigment color, the colors that we all think of, is light hitting the color, being absorbed, and then the other light being reflected, right? And that sort of absence of light, specific wavelengths of light, results in the color that you see, but how does structural color work?
Yeah. You're exactly right. So, when white light comes in, if there's a pigment molecule that it hits, that might absorb certain wavelengths, and then whatever reflects back is the color that you see. So, exactly right. Those are pigments, but on the other hand, sometimes in nature there's no pigment involved, but rather light is just interacting with the surface, and then the light is refracting back at some sort of wavelength. This might not seem very intuitive. I think most people I talk to, they're sort of familiar with pigments, but not so much structural color, but if you've ever looked at say a rainbow or light hitting a prism, like on a Pink Floyd poster, you can see white light bending into these rainbows, because they're breaking down into their different compartment wavelengths.
Animals can take advantage of this, just like a prism would. They can do this by producing what are called nanostructures. They're these really highly modified bits of ... If it's on a bird feather or a butterfly scale, they can modulate their chitin or some sort of surface, and so when light interacts with that surface, it will come back as the color that you see. It's a really powerful tool that animals can use to make a certain type of color.
How can scientists studying this sort of structural color in organisms, how does that benefit the scientific community at large?
Yeah. For myself I thought it was just sort of interesting from an evolutionary standpoint, but there are lots of really fascinating applications as well. For a long, long time, dating back, people have looked at butterfly wings and structural color to serve as sort of bio inspiration for physics principles and mechanical properties. You know, these nanostructures are some things that we don't even know how to replicate, and so there's a lot that we can learn by looking at these animals and trying to figure out how they're producing these nanostructures. This can have all sorts of really interesting applications when it comes to producing something that say you want to be hydrophobic, or self-cleaning, or maybe produce a certain type of color that doesn't fade. These are really cool properties that mechanical engineers have tried to gain their bio inspiration from.
So, I want to switch gears just a little bit and have you tell me a little bit about Field Projects International and specifically about the Genomics in the Jungle event that's going to be taking place at the end of July.
So, Field Products International is an organization that I've worked with in the past. They're a nonprofit organization, and they were founded by a couple of PhD students. They were doing a lot of field work I think in Peru and in India and basically spun that into organizing these short form field courses that anyone is really open to register for. So, some courses have been more geared towards ecology and botany. I've taught one that was actually field entomology course. They're a lot of fun. It's also a lot of work, because you have to not only be a teacher, but also kind of make sure everyone is safe and well taken care of for two weeks in the jungle.
Yeah. Make sure nobody wanders off and gets lost or steps on a venomous snake or anything like that, but overall, these are really fun. So, the motivation for this upcoming course, which we call Genomics in the Jungle, is having a two week field course, doing what we normally would, like collect samples, and process data, but also perform all of the necessary downstream molecular analyses. For instance, we want to extract DNA or RNA, do microbiome analyses on primate samples, and also plant and animal species identification with DNA bar coding.
How do you know whether or not you've discovered a new species of something, like how quickly do you get that information? Then if you think you have, what are your next steps?
Yeah. That's a really good question. Once you have a DNA sequence in hand, what can that tell you in the moment? It can tell you a lot, but there are some necessary requirements. Identifying species is not always as easy as it may seem. Sometimes we just sort of intuitively know, like you can tell that we are humans, just based on looking at us, or you can tell what a certain bird or common snake species is. But if you're really getting into the details and you want to know if something is a new species, you really need to have a good job of all of the other closely related representatives already in hand to compare it to.
Like a rich database.
Exactly. What we might consider a reference database of all these at least sequences or maybe also morphological characteristics. This is why a lot of time and effort goes into species identification and building phylogenetic trees that represent the tree of life. So, it's no small feat. Sometimes it's challenging, even if you have a sequence pack, to know if it's a new species or not. There are some cases where, for instance, when we were in Ecuador, I was with some highly trained herpetologists, and it was clear to them, based on looking at the morphology of this gecko species, that it was likely new. With the additional data set of having a DNA sequence and having an existing reference database, it looked pretty clear that this at least had never been in the database before.
So, it's hard to say for certain that something is just a new species, but you can gather a lot of necessary evidence, and this can be very informative while you're in the field, because classically you have to collect samples, transport them back to a lab. Maybe you even have to wait to get permits to ship it internationally to find a sequencer. This can all take weeks or months. Maybe the sample gets lost or degraded. So, the ability to actually take your equipment out and sequence it within say a 24 hour time span can really have immense applications and is very beneficial.
Can you tell us about your lab in a backpack?
Oh. Totally. Well, I was first sort of inspired by portable technology. When I first started working in the Amazon, we used to have a microscope at the research center that I worked at, but like many things in the rainforest, it gets degraded over time. This particular one actually got wet, and fungal mycelium grew into it.
It's probably a moisture issue.
Yeah. Totally. So, that's a problem if you're trying to do research in remote places like this. I went online at the time, and I was searching for portable microscope alternatives, just what was out there. I had stumbled upon a research group at Stanford University. They had invented what they called the Foldscope. This was a $1 origami microscope. I just thought that was so cool that people were developing a paper based microscope. I tried it out. It works really well. It's really cool. It can magnify like 140X. You can connect your cell phone to it. This was also around the time that I had found Oxford Nanopore Technologies, and so this company had been developing the first ever basically handheld DNA sequencer. These were all sort of newly developed tools. This was just a few years ago. This really lit the spark for me that, wow, we're getting to these technological advancements that are allowing us to take tools out with us into the field. What else is gonna change.
Since then, I've been testing these tools. In part, what's helped is having grant funding from the National Geographic Society. I also used the miniPCR, and that's a really great, little, portable thermal cycler. It was more recently that I started to try and get into developing my own tools, and in collaboration with the Jacobs Institute for Design Innovation at UC Berkeley, I've been getting into 3D printing and prototyping, so I made my first ever handheld centrifuge, and so this is 3D printed. It can fit these little column tubes that you can find in DNA extraction kits. By just pulling and spinning with your hands you can extract DNA. You don't need an external power source.
A lot of things are still under development and ongoing, but I think it's a really cool time to synthesize all of these little tools, and develop your own, and put these into a backpack, and just go.
So, what's your favorite tool in your backpack?
I think the fact that we have a portable sequencer now is really a game changer, and so the development of the MinION and other portable aspects from the sequencer company has been really invaluable for doing some of these analyses. A few years ago we could do say like portable PCR, but to actually decode DNA or RNA in real time is just incredible to me. That to me is a really cool game changing tool, and I can't wait to see what else gets developed in the coming years. It's all moving very quickly.
Absolutely. I noticed that you have some really stunning photography on your social media feeds. Is that something that you consider sort of part and parcel to your research?
Yeah. I mean, actually, before any of this, I was doing photography, especially macro photography, so, you know, using these large lens that can let you get very close in high detail with small organisms. This to me was really awesome, because you can just make observations, take pictures, take video, analyze it in detail. For me that was sort of critical in being able to make natural history observations that then led into all of these downstream questions. You don't need any fancy tools to go out and make discoveries. You just need the ability to go out and make observations. Darwin didn't have any portable sequencing tools, but he did have this power of observation that he later synthesized.
I think that's a great take home lesson for our listeners, that you don't have to have a fancy microscope. You don't have to have a handheld genetic sequencer in order to really make contributions. Speaking of those contributions that you make in the field, can you talk a little bit about how they support conservation efforts?
Yeah. Absolutely. It was not until I started going down to places like Peru and into the jungles that I started to really notice some of the adverse effects that are going on in the rainforests. For instance, logging and natural resource extractions are really prominent. Effects of gold mining are really apparent out there, wildlife trafficking and catching primates and birds that they're selling. These are all big problems in the rainforest definitely, and this can impact us on a broader scale, because life on our planet really depends on these ecosystems. You know, how do we conserve these areas is something that has been a really big question for me and for lots of other. How do we protect these areas? When it comes to portable DNA sequencing, something I said in the writeup for when we were writing up a publication on it, is this isn't designed to be a silver bullet.
It's not going to prevent anything per se, but I think a critical aspect of conservation is knowing what's out there. It's very hard to protect an area or establish it as a national park if you can't convince other people to care about it or tell them what's actually out there that's worth protecting. To me the ability to go out and rapidly do biodiversity surveys, incorporate this with DNA sequencing to identify species, this to me can be another powerful tool that can help you in conservation efforts.
It's great to see the impact of technology innovations and field research and how those are being applied to conservation efforts. Do you have any last thoughts for our listeners before we let you go?
Oh. Definitely. Well, I think no matter what level of scientific background you have or what age you are, I think there's never been a better time to be involved with the sciences, especially biological sciences. There are just so many amazing technological advancements these days, especially with gene sequencing and portable tools, but also with social media and how we can communicate with broader audiences, but we still face really big challenges today, right? So, deforestation, and disease transmission, food shortages, overpopulation, these are all really big problems that we can try and address together. I think there's never been a better time to be a scientist, and it's a really good time for all of us to work together and try and tackle these big problems that we face today.
Absolutely. It's been such a pleasure having you here today. Thanks so much for joining us.
Yeah. Thank you very much.
Hopefully you enjoyed listening to this episode of our podcast as much as I enjoyed making it. Be sure to check out the transcript, which contains lots of helpful links to learn more about Aaron's research. Also, join us for our next episode, when we'll chat with NEB scientist, Greg Patton, for the second part of our two episode piece on the polymerase chain reaction, better known as PCR.
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