SOLS Podcasts

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Peggy Coulombe: Hi, this is Margaret Coulombe with the Arizona State University School of Life Sciences. Welcome to Science Studio.

Today is our first podcast. It's fitting that my first interview is with the man who proposed Science Studio in the first place, Jim Elser. Jim is professor in the Ecology, Evolution, and Environmental Science faculty group, and a limnologist.

Welcome to Science Studio, Jim.

Jim Elser: Thanks a lot, Peggy. Can I call you Peggy?

Peggy: [laughs] Yes, you can.

Jim: Thanks.

Peggy: So tell me. What exactly is a limnologist?

Jim: A limnologist is a scientist who studies inland waters. Inland waters being defined as normally thinking as ponds or lakes or streams or rivers. And sometimes you might go as far as an estuary, to call it an inland waters. So a limnologist is sort of a freshwater oceanographer.

Peggy: And is this an area that you always expected to pursue? What took you to this study?

Jim: Well, that's an interesting question. I was thinking about this the other day. When I was in fifth grade, I remember writing down that I either wanted to be a priest or a marine biologist. And I don't think I ever got very close to being a priest.

But I did get pretty close to being a marine biologist, I think. So it's something I've thought about since I was pretty little, I think.

Peggy: I noticed in your list of grants and papers that your work takes you all over the world, in regions that aren't normally considered water rich regions, like Inner Mongolia.

Jim: Well, that's true. The Inner Mongolia project is a spin off or an outgrowth of concepts and theory we've worked on in freshwaters. We're taking some of our ideas up onto land and seeing if they work. And understanding grasslands. So that's a project in collaboration with Jengu Woo, who's a colleague in the School of Life Sciences, a colleague at Columbia University by the name of Shahid Naeem.

And we're collaborating with a large group of Chinese ecologists from the Institute of Botany at the Chinese Academy of Sciences, to conduct this extremely large scale manipulation of plant diversity in the grasslands there. To examine its effects on ecosystem services or ecosystem functions.

So it really doesn't have anything to do with water in that project. But it relates conceptually to the work we've been doing elsewhere.

Peggy: And so is it essentially a spin off from your work that is ecological stoichiometry? I have your book here in front of me.

Jim: Sure. Well that book, $27 from Princeton Press. You can get it at Amazon.com. That's less than a nickel a page, I'll point out. It's quite a deal. Anyway, so yeah.

This book is something I did with my colleague Robert Sterner. I started it during my first sabbatical leave in Japan in 1996, 1997. It took us a few years to finish it.

But essentially--he's also a limnologist. It's where we lay out our ideas about analyzing ecological systems from a chemical perspective. This idea of stoichiometry is a chemical concept referring to the proportions of chemical elements in compounds and how those constrain the rates of chemical reactions.

And so our thesis is that all living things are made of chemical elements in certain proportions. And what we're trying to do is understand what those rules are that govern the chemical or elemental composition of living things.

And given that we might understand those rules that determine those proportions, then we want to understand how those limits or those rules affect ecological dynamics, in terms of population growth rates, or nutrient cycling in ecosystems. And how food webs work, and how pollutants affect lake ecosystems and other sorts of environments.

So, yeah. The grassland work was motivated out of that theory. And in fact, a stoichiometric framework provides the conceptual hooks that we hung that project on. We were able to get our funding from the National Science Foundation, using that.

Peggy: Have you done research in China before?

Jim: No, I've never actually had a research project in China itself. A couple of years ago, I was involved in leading a US-China exchange project that was funded by the National Science Foundation and the Chinese Academy of Sciences.

In that project, I went with ten or so American ecologists to interact with Chinese colleagues on a theme that was called Ecological Complexity and Ecosystem Services. And we spent about two and a half weeks in China, meeting with Chinese ecologists in Beijing. We visited Three Gorges Dam and the Yangtze River and Shanghai, etc. And made a lot of excellent contacts.

Then the following year, a group of Chinese ecologists came here to go around the United States and meet with colleagues. They went to the east coast and to Vermont, and then they came here to Arizona for a workshop, and then they went off to the San Diego Zoological Society.

So that hopefully made a lot of connections between our side and their side, because there are so many huge issues that need to be struggled with in ecology, as China sort of explodes on the scene environmentally and economically.

And this Chinese project in Inner Mongolia is an outgrowth of some of those connections that were made during that exchange.

Peggy: In your book, you have a chapter entitled, 'How to Build an Animal.' Do you think nutritional limitations or abundance have an effect at a genomic level of plants and animals?

Jim: Well, yes. That chapter is sort of about the rules that are involved in determining the elemental composition of animal bodies or biomass. They deal with issues related to how animals allocate major molecules that have a lot of nitrogen in them, or have a lot of phosphorous in them.

A lot of that focuses on phosphorous, especially, and how animals allocate, possibly, to ribosomal RNA, which is a very phosphorous rich molecule. And also how they allocate to bone, in the case of vertebrate animals, which is of course a very phosphorous rich tissue in vertebrate animals.

So when we were thinking about--that book is seven or eight years old now. Since then, we've moved onto other sorts of questions, which suggests that the stoichiometric aspects of animal and plant composition are manifest at the genomic level. That is a level of what we can infer from the genome.

Of course, what the genome codes for are proteins, mostly. And more recently, we've been working on, and have some new funding from NSF to investigate, how, using genomic data, we can make estimates of the elemental composition of the proteins used by animals and plants.

We published a recent paper in Molecular Biology and Evolution where we show that plant proteins, much to our surprise. Plant proteins are lower in nitrogen than animal proteins across the entire proteone, and this surprised us because our simplistic assumption was that a protein is a protein is a protein--they're just mixtures of amino acids in some random assemblage; but it turns out that they're not, proteins are not just random mixtures of amino acids that many differ in how many nitrogen atoms each one has. Instead, plants seem to use a disproportionate number of amino acids that are low in nitrogen, and animals use a disproportionately higher number or proportion of amino acids that have more nitrogen atoms in them. And using the genomic databases, we were able to make the first analysis of this kind of pattern.

It's pretty exciting, and now we have a new grant from the National Science Foundation. Sidia Kumar in the Biodesign Institute is one of the co-PIs. Bill Fagen, University of Maryland, is a co-PI. We're going to be developing database infrastructure to be able to access the rapidly expanding databases that are out there for genomic data, to allow people to make these types of analyses of the elemental usages in proteins, in all kinds of organisms, whatever is in the genome databases could be analyzed in this way.

Peggy: This year you took the helm as the co-director of the Office of Research and Training Initiatives at the School of Life Sciences. How do you see technological innovations changing the way we teach or do science?

Jim: Well there's a lot of technology always involved in how we do science, and a lot of times there are great examples in the history of science where new questions are raised and answered just based on the invention of a new way of analyzing things, whether you're talking about the electron microscope, or whether you're talking about the confocal microscope, which is very popular now, or whether you are talking about the concept of using radio isotopes during the post-bomb era in the middle of the 20th century. All of these things make whole, entirely new questions available to biologists that could now be answered.

I think now we're seeing things like the $1,000 genome becoming available, where everyone's going to be able to sequence their organism within some reasonable amount of time and expense. That's going to radically change the types of things that people do, I think. The real challenge there, I think, is going to be keeping track of all the information. I have this analogy that I use sometimes when I give a talk. The analogy, of course, is making a discovery is sort of like finding a needle in a haystack, and the problem is, right now, that the haystack is expanding exponentially because of these high-throughput machines that are being created to generate massive amounts of genetic data, massive amounts of metabolic data, massive amounts of gene expression data, routinely, robotically even. So the haystack is growing hugely, exponentially, and somewhere in that haystack the needle is hidden.

So the technology doesn't necessarily make it easier to make that discovery. In some ways it makes it harder, because the haystack is bigger. But presumably once you have the whole genome right, you know you have the entire haystack at least, so at least you know that the needle is not hiding in a piece of the haystack you don't have yet. So I think all the technology is exciting, but it needs all to be sort of taken from the perspective that we don't have any way of generating ideas or hypotheses robotically or with high-throughput machinery; we still need people thinking creatively about their data and about their questions, and then using the technology appropriately to answer those questions.

So we live in a pretty unique time, technologically-speaking, I think, about what capabilities in biology are going to be available to us.

As far as teaching, well there's a lot of technology out there in teaching. I, even though I teach a large introductory course, and presumably technology would seem to be very advantageous in that environment--and it is, we use it quite a bit in terms of Internet dissemination and discussion, etcetera. But actually, I don't have a lot of trust in technology when it comes to teaching and education. Actually I think, really, teaching and learning is really a personal activity. And there is a reason, even in a lecture hall of 300 people, there's a reason that the students should be there, present with the instructor and with other students, because I think there is a lot that is conveyed emotionally and physically by the actual presence of someone that you don't get from a podcast or from a teleconference and such. So I still think that, as important as technology is as a supplement to learning and teaching, I think that in the end it still comes down to a student and his or her teacher, and their interaction, and the way that that teacher models learning for the student.

Peggy: So jumping to another subject, what book do you have on your nightstand?

Jim: Well right now I'm working my way through "Collapse" by Jerry Diamond, which, I'm probably two years late in reading that compared to all my colleagues, but I'm enjoying it. He is a great writer. It's pretty fun to read that. I just finished the chapters on the Vikings in Greenland, Iceland, Norway, etc. Having spent a fair amount of Norway, I found those sections to be pretty interesting. It's fun to learn about the Vikings.

Peggy: Yeah, you mentioned Norway. You're going to be doing some work there. What project are you working on?

Jim: We're now in the second year of a project funded by the National Science Foundation which is attempting to determine how atmospheric nitrogen deposition to lakes may have affected food webs in those lakes. So atmospheric nitrogen deposition has been increasing quite a bit worldwide, depending on different regions.

Peggy: And where does the nitrogen come from?

Jim: The nitrogen comes in rainfall and snowfall, but its source, the perturbation comes from nitrogen that is introduced to the atmosphere from fossil fuel combustions, so those are NOX--oxidized nitrogen forms that are produced by cars. There is also atmospheric nitrogen that is introduced by fotilization, or gaseous forms of nitrogen coming off farms or feed lots in agricultural areas. So our project is looking at lakes that are in areas of high nitrogen deposition, and comparing them to lakes in areas of low nitrogen deposition, in Colorado, and also in Southern Norway.

So in Colorado, the Eastern Front Range of the Rocky Mountains receives high nitrogen inputs that have increased quite a bit in the last 30 years from the urbanization process of the Front Range, and also agriculture. And we're comparing those lakes, many of which are in Rocky Mountain National Park and the environment around there, to lakes in the Central Colorado Rockies around Crested Butte and Western Colorado, and around Silverton. We did that work this past summer, and next summer we'll be in Norway, where there is also a very strong nitrogen deposition gradient. The southern tip of Norway gets a lot of nitro deposition blow off from industrial areas in Northern Europe and England, and as you move inland and north from the southern part of Norway, the deposition goes down quite a bit, so we'll be working there.

Peggy: And how does high nitrogen affect the plant life or animal life in lakes?

Jim: Well, our thesis of the project is that, well, all ecosystems, terrestrial and freshwater, are very frequently limited by important nutrient elements, so especially nitrogen and phosphorus. These are things that people are careful to include in fertilizer when they want to grow crops or houseplants and such. So the same thing happens in lakes. If you add nutrients to lakes then the plants tend to grow more, and in lakes what we're talking about are microscopic plants--algae, phytoplankton as they're called--which are frequently limited by nitrogen or phosphorus.

So our thesis is that as you add nitrogen to the lake from the atmosphere without adding anything else, you'll tend to relieve the phytoplankton of their nitrogen limitation, and then they tend to become limited by something else, something else runs out, and our proposition is that what they run out of quite easily is phosphorus. And so our prediction is that lakes that are receiving high nitrogen deposition should have strongly phosphorus-limited algal production.

Now we're interested in the effects of that on the food web, and the consumers of phytoplankton production are the animal plankton or the zooplankton; and normally you would think, well, adding more nitrogen, making more algae, should be good for the zooplankton, but our theory, our stychometric theory, predicts that this might not necessarily be the case, because it is well-known that phosphorus-limited algae are very poor food for zooplankton consumers. That's because algae, or plants in general that are phosphorus-limited, have very little phosphorus in their tissues, in their biomass, and so when an animal consumes phosphorus-limited algae, it doesn't get enough phosphorus in its diet and the animal itself becomes phosphorus-limited. It's sort of like eating junk food.

So it's sort of like feeding your kid Twinkies all the time--the kid's not going to grow up very well or be able to build its bones and other tissues that need phosphorus, for example. And so we think that atmospheric nitrogen deposition may have the effect of turning algal production into sort of unhealthy junk food for zooplankton, and therefore impair the operation of the food web and transfer of plant energy upwards to higher trophic levels like fish that people like to catch, etc. So that's what we're trying to find out.

Peggy: How can your theory be applied to things like cancer or life on Ancient Earth, like all these things listed in your CV.

Jim: Well yes, if you look at what we've been doing, in our publications recently, we've been doing some work, for example, on application of stychometric theory to understand things like the Cambrian explosion. That work was funded by NASA Astrobiology Institute, and allowed us to work in a really exciting place in Mexico called Cuatro Cienegas, which is a set of mineralized springs in the Chihuahuan Desert. In these springs, they have an amazing diversity of life and chemical conditions. Especially interesting to us is that this is one of the few places on the modern Earth where you have living examples of stromatalites.

Peggy: And what are stromatalites?

Jim: Stromatalites are the primary form of life that we find in the fossil record for a couple of billion years, up to about half-a-billion or 600 million years ago, when the first large-bodied metazoan animals appear.

The question has always been, well what constrained--this appearance of large-bodied metazoans is called the Cambrian Explosion, and a lot of paleontologists have wondered for a long time about what caused it, or what kept animals from proliferating for so long. We took advantage of the fact that there are living stromatalites in Mexico at Cuatro Cienegas to test the stychometric theory or hypothesis for the Cambrian Explosion, which proposes that the quality of algal production or stromatalite production was so poor throughout much of the history of Earth that the Metazoan lifestyle could not succeed or evolve. And especially we're arguing that the pre-Cambrian era was severely phosphorus-limited, and that this was a constraint that limited animal proliferation.

So to test that idea, well, it's hard to test, right, because you can't go back to 600 million years ago; but if you have an analog of that system on the modern Earth you can do experiments, and that's where Cuatra Cienegas comes in, so we were able to work down there. We did indeed show that phosphorus is severely limiting to production in these ecosystems, and indeed, by adding phosphorus to the system, to the water, and increasing its content in the stromatalite algae and microbes, we were able to stimulate the growth and reproduction and survivorship of the snails that are consuming them. So we consider that to be indirect but consistent with this idea that food quality constraint may have been at least one fact contributing to the long-term delay in Metazoan evolution in the early Earth.

So that's one application that we were able to do.

The other one you ask about is how this idea relates to cancer. This comes from work that we're doing in collaboration with several mathematicians and some other biologists at the University of Kansas. This is a joint anacephonite project. We are proposing that cancer cells, because they are growing and proliferating more rapidly than normal tissues, have allocated differently to molecules which are rich in phosphorus; and again it comes back to molecules such as ribosomal RNA, which is a phosphorus-rich molecule that cells need to produce a lot of in order to produce proteins, in order to grow rapidly.

So in this project, we are attempting to test whether or not it's true that cancer or tumor cells are higher in phosphorus than normal tissues because of their increased allocation to RNA, and if that is true, then you might imagine that the proliferation of tumor cells might themselves become phosphorus-limited in the same way that we've shown that phosphorus-rich animals or phosphorus-rich bacteria, which have high growth rates and high RNA demands, are also very frequently p-limited. It might also apply to cancer. So we're sort of halfway through this project, where we attempt to test that idea, and it looks like it might be true--at least the part about tumors being more p-rich than normal tissues. We don't know what that means in the long run, and it's important to remember that I'm a plankton ecologist, and so no one should take any medical advice from these findings at this point.

Peggy: So switching gears a little bit, I know you're into music and art, and you're one of the co-chairs of a meeting coming up at Santa Fe that's pretty neat, and the title of it is "Water Rocks: 2007 Aquatic Sciences Meeting of the American Society of Algae and Oceanography." In reading through part of the syllabus, I'm struck by how this meeting departs from the typical perspective. It's focused on plankton as art, and the work of Ernst Hegel. Can you tell me something about this?

Jim Elser: Sure. Well, the meeting of course focuses on the aquatic sciences, and it's the annual meeting of this society. It has about a thousand abstracts admitted across the board of what aquatic sciences, Oceanography and Limnology, cover. Plankton, and currents, and organic matter processing and all this normal sort of science stuff that is a little dry.

But when I got involved in organizing it with my colleague Deb Bronc, from Virginia Institute of Marine Sciences, we decided that; and we've been through a lot of these meetings over the years, they're always great fun and the science is always excellent; but my reaction to meetings is that the science always sort of takes care of itself, and as organizers maybe we shouldn't necessarily focus on some esoteric science theme.

Instead, why don't we just make it really fun? Because most of us became scientists because it's fun to be a scientist. There's all this excitement of interacting with other scientists and discovering new things and such.

So, our goal in designing the meeting was just to make it unusual, memorable, and fun. So we have a lot of interesting things that we've folded into the meeting.

One of which is, one of the members has various; a guy by the name of Peter Williams from England, who has had a long term interest in the influence of plankton form on the decorative arts and architecture; a lot of this comes out of the really elaborate and beautiful drawings of marine life made by the Naturalist Ernst Hagel.

Which, it turns out, provided inspiration for various examples of art deco, architecture, and interior design in the early part of the 20th century. And so there's going to be a series of events related to plankton and art.

Including a plenary lecture from an expert in this area. There's going to be exhibits of glasswork from Dale Chihuly, which is inspired by marine organisms. There's going to be some commercial artists who've developed jewelry, and other sorts of things inspired by plankton.

There's a quilt that's been commissioned by Royal Dutch Shell, it's being made for the event. There's going to be a showing of a new film called "Proteus," which is based on the life of Ernst Hagel and his science, and his connection with other areas of culture.

So our goal in the meeting; it's a meeting that's in Santa Fe, which is sort of a world art center, really; is meant to spin off of all the artistic buzz that you get when you're in Santa Fe, and to sort of lay it on top of the science and make it a real memorable experience for the membership.

Peggy: And how do you see art and science in relationship to one another?

Jim: Well, they have a lot to do with each other. I mean, there's a lot of creativity in science, there's a lot of imagination that's needed. Artists sort of are trained to try to find radically different ways of seeing the world, and communicating that vision to others in their medium.

Science is another way of radically changing how you see the world. The way that we understand the world now, if we compare it to what we thought 50 years ago or 100 years ago, it would be shocking. It would be threatening and thrilling to someone at that time.

But of course science achieves that new way of seeing the world in a completely different way, via testing and investigation, and repeatability, and so it's not a personal expression, it's a collective vision that's arrived at after interrogation with the world.

But, essentially, what science is trying to do is to achieve a radical change in how we understand the world that is a radical improvement in how we see the world. And by improvement, I mean a change in our view that is more consistent with data that we can gather.

So in that way artists and scientists are sort of striving to create new ways of seeing things, so I think that there's a lot to be gained by their interaction.

Peggy: Would you say you're living your dream? The one you had when you were a kid, and deciding you were going to become a Limnologist?

Jim: Well, that depends on how many committee meetings I've been to in a given day, whether I'm living that dream or not. [laughs]

This all sort of ties together, because in the program of this meeting we're organizing in Santa Fe, I wrote this little front piece for it that says, "What we're trying to recreate in this meeting is the sheer joy and excitement that we all feel when we're out on shipboard, on the ocean, or in a boat on a lake, doing our sampling."

So when I'm hiking into a mountain lake in Colorado, or, I'm sure when I step foot into the Inner Mongolian Grassland, that's definitely living my dream. And when I do get really cool data, and something really falls together science-wise, that's really what it's all about.

Of course the problem is that there's a lot of heavy lifting that goes between those moments. But you have to keep them in mind, right? That that's what you're working toward, is having more of those. And yeah, certainly as careers go by you tend to sort of lose sight of that.

But yeah, I mean I was in Norway two weeks ago scouting out lakes for the coming summer, and it was great. We were hiking all over the place and we were seeing some really cool lakes and it was raining. We were just imagining what it was going to be like in July when it was 20 hours of sunlight a day, and sampling with our colleagues. It was wonderful thing.

I don't think I ever really imagined, even when I was younger, that I would be interacting with people all over the world, in these enterprises in China, or Japan, or Norway or wherever. That's beyond my dream, I think, I think I always just wanted to be out swamping somewhere, which is what I liked to do when I was a kid.

But I think now, yeah, the whole scope of thing is beyond what I might have imagined, despite how many meetings and grand proposals it takes to get there.

Peggy: I have one last quick question. What is pinnekjott [pronouncing it incorrectly]?

Jim: [correcting her pronunciation] Pinnekjott, pinnekjot.

Peggy: [laughs] Oh, sorry, pinnekjott.

Jim: Pinnekjott is a Norwegian national dish which I ate a couple weeks ago when I was in Norway. It's mutton and cabbage, steamed up and served traditionally in Norway.

I remember that when I was in sabbatical leave there, in 2003, we would often smell it being cooked by our neighbors. But even during that visit we never had any. But this past time I visited the house of my colleague and they made it for us.

It was actually pretty good, it was much better than lutefisk, which of course is fish preserved in sodium hydroxide.

Peggy: That sounds much better.

Jim: Yes. [laughs]

Peggy: Thanks for sitting with us today Jim, and for proposing this science studio project.

Jim: It's my pleasure, Peggy.

Ecosystems key to understanding the Genome?

Transcript - [Printable PDF format]

SOLS Podcasts 2007