Code of the Wild: Genetics and Applied Ecology

From wildlife conservation, to saving endangered species, to removing toxins from the environment, learn how genetic technologies have helped us to understand ecology and manage environments. Note: this program was originally produced in 2001, and updated in 2006 with funds from the Public Radio Exchange.

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Transcript Text: 

The DNA Files:
Unraveling the Mysteries of Genetics

As heard on National Public Radio

DNA: The Code of the Wild
Genetics & Applied Ecology

Hosted by John Hockenberry


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Funding for this series was made possible by generous grants from The National Science Foundation and the Alfred P. Sloan Foundation.

Last reviewed for accuracy: February 2002.
JOHN HOCKENBERRY: Welcome to The DNA Files. I'm John Hockenberry. From the very first life forms, Nature has been keeping copious notes—keeping track of every function and every relationship an organism has had.
JOHN AVISE: The history of life is basically written in the language of DNA.
MIKE GILPIN: It’s as if animals had just incredibly long Universal Product Codes, that they had all over their skin, dropping off their body.
JO HANDELSMAN: Once you can read the code for an E.coli cell, you can pretty much read the code for any organism, a human, or a giraffe, or anything you want.
JOHN HOCKENBERRY: What we’re learning from the DNA, in organisms as diverse as bears, barnacles, and bacteria, is telling us not only intimate details about these life-forms, but about all of life. DNA is the Code of the Wild. We'll meet the people trying to crack it. All this and more, coming up, when The DNA Files returns…

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JOHN HOCKENBERRY: You’ve heard of transgenic corn and genetically modified monkeys, now here’s something new. In the quest for a perfect lawn, genetic scientists are turning to biotech to create grass that doesn’t grow. Erik Anderson has the story.
BRAD MARTIN: When I first got this house, the front lawn was barely alive and the back was brown and I'm not kidding it was.
ERIK ANDERSON: Brad Martin’s dormant lawn in San Diego has exploded with life since he began his regimen of watering, fertilizing, weeding and mowing…
BRAD MARTIN: I'd say I probably spend six or seven hours a week on my lawn and with a fulltime job taking care of a lawn, it can be overwhelming.
ERIK ANDERSON: And costly, with Americans spending six billion dollars each year on lawn care. There’s also the ecological cost of air pollution from mowing, and pesticide and fertilizer runoff. So what if lawns could be made to use less water and grow slower? Genetic researchers are turning to Arabidopsis, a spindly mustard weed, as their model. Molecular biologists recently identified almost 26-thousand genes in the plant, opening the door to understanding how it grows.
Inside a weatherworn greenhouse at the Salk Institute in La Jolla, California, a large fan cools several trays of the fast-growing weed. The plants in one look different from the rest, as geneticist Joanne Chory points out.
JOANNE CHORY: You can see these plants are a lot smaller. They only stand a few inches high as opposed to 12, 13, 14 inches high. And the rosette leaves are much smaller and the plant is dwarfed in general.
ERIK ANDERSON: Comparing the shorter plants' genes to those in the normal Arabidopsis genome, Chory found a genetic switch that regulates the production of a growth hormone. In normal plants, the switch is programmed to be in the “on” position. When stimulated by sunlight, the hormone encourages stem growth. But Chory found that in the shorter plants the switch is turned “off,” blocking hormone production. By isolating that genetic switch and reproducing it in the lab, she can insert it into one of the normal plants … and its offspring will inherit it too.
JOANNE CHORY: These plants will grow more slowly, stay green, utilize less water because they are growing more slowly and also need a lot less care.
ERIK ANDERSON: … all qualities that appeal to homeowners and golf-course-keepers which represent a potential 10-billion dollar seed market. The world’s largest lawn care company -- Scotts -- is just one of a number of large corporations hoping to turn a profit with genetic gardening.
Inside Greenhouse number three, on Scott’s campus in Marysville, Ohio, scientist Bob Harriman has developed a slow-growing bluegrass. Using Arabidopsis and other plants as his guides, he found a genetic switch in bluegrass that controls growth. Now he’s considering adding other traits, like drought and pesticide resistance. But he needs more pieces of the puzzle before he can get the grass to do what he wants and still remain healthy.
BOB HARRIMAN: Knowing how a single gene is turned on or turned off is less important and has less of an impact on how are all these genes working together at different points in its growth cycle.
ERIK ANDERSON: Developers of these new grasses tout the environmental benefits of less mowing, watering and fertilizing, but not everyone is convinced that genetically altered grasses are a good idea. At a recent biotechnology conference in San Diego, Indiana University Biologist Martha Crouch joined other opponents for a teach-in. She believes the research is moving too quickly.
MARTHA CROUCH: The people who do genetic engineering feel they know a lot because they know the sequence of the gene. But they have no idea what that will do in the environment.
ERIK ANDERSON: Crouch is concerned about ecological domino effects in the environment. By sharing pollen, manufactured grasses might transfer genetically altered traits like slow-growth and pesticide resistance to other nearby grasses.
MARTHA CROUCH: They say we're gonna change this little part of the machine, and we're gonna make it so the grass does this. But when you do that the grass is actually a living organism with a mind of its own and you get unpredictable consequences.
ERIK ANDERSON: So what about regulation? Crops are regulated by three agencies, but only one -- the Department of Agriculture -- monitors genetically modified grass research. Because of concerns about pollen flow, regulators do limit the growth and transportation of test grasses. But there’s no clear plan for agencies to oversee low mow grass seeds once they go on sale. Scotts officials are hoping to bring their product to market several years from now. That’s when homeowners like Brad Martin will decide whether the ecological risk is worth bringing the genetic revolution into their backyards.
BRAD MARTIN: There’s nothing more satisfying, then ah, after you get your lawn cut you take a good shower, and you just go out there and survey your kingdom. (laughs)
For The DNA Files, I’m Erik Anderson.

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JOHN HOCKENBERRY: Welcome to The DNA Files. I'm John Hockenberry. Read any good books lately? Here’s something you probably haven’t read. A little difficult to understand, though, only in the past few decades, have we even started to learn what it means.
JOHN AVISE: The history of life is basically written in the language of DNA, and what modern molecular biology has given us are the tools to read that language for the first time. It's just opened up a whole world of possibilities that could hardly have been imagined even twenty or 30 years ago.
MIKE GILPIN: And it's all done with DNA. It’s as if animals had just incredibly long Universal Product Codes, that they had all over their skin, dropping off their body, leaving behind in their feces. And it's made it so much easier to collect information, and make all sorts of inferences about, let's see if this is the population, the daddy must be this animal and things like that. For difficult to observe animals, such as forest elephants, grizzly bears we have a much greater insight into what the population is, what the age structure is, what the genetic relatedness-es are between the animals.
[beeping sounds of Morse code]
JOHN HOCKENBERRY: That's Morse Code. It's kind of an antique, but it's fascinating really. It has only four symbols and you can hear them. There's the dot, dash, short space, long space. Yet, with just these four symbols, you could spell out an entire encyclopedia.
JOHN HOCKENBERRY: Scientists use just four symbols to spell out quite another code, the code for life. A, T, C, G, these are the initials for the four bases of DNA: adenine, thymine, cytosine and guanine. A strand of DNA has millions or billions of these bases, strung together in varying order. And from that order, of A’s, T’s C’s and G’s, we can decipher information, about individual species...
OLIVER RYDER: The closest living ancestor of whales is the hippopotamus.
MIKE GILPIN: And there was a high fraction of grizzlies’ litters of cubs that had two different fathers.
JOHN HOCKENBERRY: And in fact we can decipher things about all species…
JO HANDELSMAN: Now the DNA technologies are so powerful, and have such a wonderful application to ecological and environmental questions, as well as evolutionary questions, and many, many ecologists are using molecular biology, or DNA technology, in their research.
OLIVER RYDER: One thing from studying the genetics of endangered species is the commonality we share. We studied gorillas and some rhinos and some tigers, and they have some of the same kinds of genetic errors that humans do.
ED DELONG: Not only are we all related, in the sense that we had a common ancestor, and we all kind of share the same genetic materials, we're also swapping DNA, that is, collectively amongst organisms, more than we thought we were.
JOHN HOCKENBERRY: Welcome to “DNA, the Code of the Wild,” a look at how genetics and DNA have helped us understand ecology and manage environments.
Game wardens now have a new tool for catching poachers who illegally kill wildlife.
CHARLES SCHWARTZ: DNA is used in a forensic sense to help identify individual bears or species of bears. Law enforcement, for example, can use DNA if they have somebody that’s been identified as poaching grizzly bear, they can then check to see if they can find traces of grizzly bear, either blood or hair, and verify that using DNA.
JOHN HOCKENBERRY: Charles Schwartz is a wildlife biologist at the Northern Rocky Mountain Science Center. He’s seen DNA used to find people that harm animals, and animals that harm people.
CHARLES SCHWARTZ: On a very rare occasion we’ll have a bear that will come into conflict with a human, and injure them. And so those bears are usually removed from the population, they’re trapped and sent to zoos. If there’s no place where they can be put, they’re euthanized. Prior to DNA identification of individuals, basically, if a person had a description of the bear, and if a bear fit that description it was removed. And you may or you may not have the offending individual.
Now, what we have, and there was an example of this in Yellowstone National Park a couple of years ago, there was a bear that was coming into campgrounds and smashing tents. They had a difficult time capturing him, but when they finally did, what they also had was a hair sample from a previous incident. They were able to take both the hair sample that they had and the hair sample from the bear they captured, compare the two and, in fact, confirm that, yes, they had the individual that was causing the problems, and he was then removed from the park and put in a zoo. And so the problem was cleared up and there was no non-offending individual that just happened to be in the wrong place at the right time and get blamed for something that it wasn’t doing.
JOHN HOCKENBERRY: DNA can be used to identify “whodunit,” or who it was done to.
STEVE PALUMBI: We've done a number of different things in marine conservation biology to try to use DNA to come up with answers to questions that otherwise couldn't have been answered.
JOHN HOCKENBERRY: Harvard University Evolutionary Biologist Steve Palumbi.
STEVE PALUMBI: One of the first ones we looked at was what species were really present in the retail market that sell whale meat around the world.
JOHN HOCKENBERRY: The International Whaling Commission banned commercial whaling in 1985. But, for scientific research only, nations can still capture the more-abundant species of Minke whales and those animals can later be sold commercially. So, any whale meat for sale should be only Minke whale. Right?
STEVE PALUMBI: Well the problem is, if you ever go to the retail market in Japan or Korea, once you buy a piece of whale meat, it's a tiny little piece of a very big animal, and all the things that you might need to tell what species of whale it was are gone. But that little piece of meat still has the DNA in it. So we developed a way to go into that market, sample those specimens, and then sequence the DNA to try to find out, one, what the species were and sometimes, where those animals actually came from. But we found humpback whales, and we found fin whales and gray whales and sperm whales, and blue whales, and pilot whales, dolphins, porpoises, a huge number of different species are in this market. And that was quite a surprise to people because it was supposed to be a Minke whale meat market, and it turn out to be much more than that. So the DNA testing has at least the promise to be able to keep the market honest. And by keeping the market honest, that means you can at least try to afford protection to species that really need it, where at the same time allowing the exploitation of species that have been recovering and might be able to be fished at some low level.
JOHN HOCKENBERRY: In the modern biology lab, you can extract DNA from a cell, make copies of it and use, what’s called, restriction enzymes, to grab a specific region of the DNA. Then you can analyze that region, and get computer readouts of the sequence of A’s, T’s, Cs, and G’s. The entire, maybe, billion letter-long sequence of an organism’s DNA is known as its genome. A region of the DNA that codes for a trait is called a gene. Some traits are affected by a combination of genes. But 97% of the DNA is non-coding, it doesn’t code for any trait. We’re not sure what it does. There’s bits of virus DNA stuck in there. There's long sections of repeating sequences which make up about 20 percent of all DNA. We used to call these non-coding sequences “junk DNA.” But in sifting through that junk, we’ve found treasure.
From even the smallest tissue sample, we can extract these repeating sections of DNA and identify not only the species, but also a specific individual, and, sometimes, its whole family.
JOHN AVISE: The beautiful thing, really, about molecular approaches in the studying the tree of life is that one can study branches at any depth in the evolutionary tree, ranging from just the last few thousand years, or even hundreds of years, perhaps, all the way back to some of the deepest branches in the tree of life, which probably separated some 4 billion years ago.
JOHN HOCKENBERRY: John Avise is Professor of Genetics at the University of Georgia. He uses DNA to study evolution.
JOHN AVISE: Every creature is uniquely marked by its DNA. So what we do in my lab is use molecular tools to decipher these genetic marks, and use that information to learn all sorts of things about the behaviors and ecologies and natural histories, and the evolutionary histories of any kind of creature on earth that we'd like to study.
JOHN HOCKENBERRY: Most DNA is in the nucleus of a cell. The exception is in mitochondria, the energy producing part of a cell outside the nucleus. Mitochondria has its own DNA. And mitochondrial DNA is inherited only from the female parent. Mitochondrial DNA is susceptible to changes, mutations, over time. And the children inherit the mother’s mutation. We’re starting to learn the pattern of those mutations, and from that pattern, we can trace an individual’s mother, grandmother, great-grandmother, great-great …
JOHN AVISE: It's sort of like having a phone book or something that mother nature has provided with all the names displayed. And it's just our task then to decipher these names and to use it to reconstruct the female family trees for any kind of creature that we want. And for those of us that are interested in wild life genetics, that was just a tremendous improvement because now we can simply take a little drop of blood or a shed hair or a feather and use that as the basis for our genetic test without having to otherwise disturb the animal or harm it in any way. And quite often the kind of information we gain from these sorts of analyses has immediate relevance to management plans or conservation plans, for example for endangered species.
OLIVER RYDER: The California Condor is the largest bird in North America. It went extinct in the wild; the last birds were removed from the wild in order to prevent the complete extinction of the species. They've been bred in captivity, where their numbers are increasing, and now they've been re-introduced into California and Arizona.
JOHN HOCKENBERRY: Oliver Ryder is the Geneticist for the Center for Reproduction of Endangered Species at the San Diego Zoo. The site of the captive breeding program for condors.
OLIVER RYDER: We've saved DNA from every California Condor. In my refrigerator I have every member of the species, back to the point where they were all brought out of the wild.
JOHN HOCKENBERRY: DNA tests played a big part in the Condor’s re-introduction.
OLIVER RYDER: As a geneticist one of the things I do is try to imagine how genetic sciences can contribute to the conservation effort for endangered species, and the establishment of self-sustaining populations of wildlife, captive and in their native habitat.
Most California Condors alive today can trace their ancestry back to 16 animals. And surely, some of them were related to each other. So, a process of genetic fingerprinting identified that there were basically 3 surviving clans. And that information was used so that the matings of individuals in the same clan were avoided so that inbreeding effects wouldn't reduce the expansion of the population.
Another aspect of the Condors was, if you look at a Condor you can't tell whether it's a male or a female, like many parrots. So a genetic test was used to identify the males and the females. Of course it's very important to make sure that you know the sex of the individuals when you pair them.
JOHN HOCKENBERRY: Okay, so we didn’t save the dodo bird, the passenger pigeon and other extinct species but we might save the Condor. Why should we care? Sure, birds and bears and whales look great on TV nature shows, but is there a reason to protect them, and the thousands of other threatened species? One good reason is biodiversity.
DAVID TILMAN: We are here in the middle of a grassland prairie ecosystem. As I look around I see about 100 species of plants. I know there are about 1000 species of insects, about 5 to 7000 species of bacteria. And large numbers of other kinds of organisms here in this native prairie grassland.
JOHN HOCKENBERRY: David Tilman is Director of the Cedar Creek Natural History Area, and an Ecology professor at the University of Minnesota.
DAVID TILMAN: Ecology is the study of organisms, and the ecosystems in which they evolve and live. An ecosystem refers to all of the organisms that live in a habitat, and to the actual physical habitat itself: the soils, the rainfall pattern, the whole unit of organisms, their physical environment and how they interact.
JOHN HOCKENBERRY: Cedar Creek is a beautiful nine square miles about 30 miles north of Minneapolis. It’s a mosaic of prairie, hardwood and pine forests, cedar swamps, marshland and sedge meadows. On the grounds are dozens of research plots used to study how biodiversity, that is, the variety of species, affects the overall health of an ecosystem.
DAVID TILMAN: Our work focuses on biological diversity. We try to understand why these species co-exist, why there's such phenomenal diversity and what affect that diversity has on how these ecosystems function, their stability, their productivity. We're interested in this, first for fundamental scientific reasons. But also because right now the world is undergoing what appears to be a historically unprecedented, massive extinction event, caused by humans. And we are wondering what effects losing diversity will have on the services that the world's remaining ecosystems can provide to humanity.
JOHN HOCKENBERRY: A study by the International Union for the Conservation of Nature says one quarter of all mammal species and an eighth of all bird species are currently at risk of extinction.
DAVID TILMAN: As we walk through this field, we can look at the incredible diversity of plants, you can see Brown-Eyed Susan, Orange Butterfly Weed There's an ancient plant. This is a Horseweed. These are plant's that were alive back in the time of the dinosaurs basically. There still around with us.
DAVID TILMAN: Organisms, if you will, have a role that allows them to fit in and co-exist with other species, and these differences in roles end up being reflected in differences in their DNA. It's like a more diverse economy. More diverse economies are well known to be more stable. The same is true for more diverse ecosystems. More diverse economies are also often more productive, and that is definitely true in our ecosystems out here. As they have higher diversity, they have greater stability and greater productivity.
JOHN HOCKENBERRY: Remember, biological diversity, or biodiversity, is the variety of different species in an ecosystem. Genetic diversity is the variety of genes within a species. Just as biodiversity contributes to the health of an ecosystem, genetic diversity affects the health of a species. The greater the variety of genes, the more adaptable a species is to changes in the environment, and the less likely a single factor, for instance, genetic or infectious diseases, could wipe out an entire species.
Genetic diversity is a major focus of the U.S. Geological Survey’s Interagency Grizzly Bear Study Team. They provide biological information to policy makers and managers about the population of bears in and around Yellowstone Park.
CHARLES SCHWARTZ: Defining a population is difficult. It's generally a group of animals that are all within a same area.
JOHN HOCKENBERRY: Wildlife biologist Charles Schwartz is the Team Leader.
CHARLES SCHWARTZ: For example we talk about the Greater Yellowstone grizzly bear population. Now, if you go to Glacier National Park, there is a population of bears that live in what's called the Northern Continental Divide Ecosystem. So we have a Northern Continental Divide population of grizzlies; we have a Yellowstone population of grizzlies. The two of them are separated quite a long distance by unoccupied habitat. So you would think of that as two separate populations.
JOHN HOCKENBERRY: That separation means the Yellowstone grizzlies can’t mate with other bear populations. That could cause inbreeding, which could hurt their long-term chances of survival.
CHARLES SCHWARTZ: Historically, grizzly bears in Yellowstone were probably connected to grizzlies that used to be in the Northern Continental Divide; there certainly were grizzly bears east of here out on the Great Plains. So there was a flow of genes through these populations. Once the grizzly was reduced in numbers -- and it was eliminated from approximately 98% of its historic range in the continental U.S. -- the bear populations that are left, particularly the Yellowstone population, is now isolated from all these other bear populations. It's an island bear population. So we no longer have gene flow coming from other areas. And the concerns revolve around loss of genetic diversity, and the consequences of that loss to long-term population health and stability.
LISSETTE WAITS: Yellowstone Park was once part of a contiguous population of grizzly bears that stretched south to Mexico and east to the Mississippi River. And so what we would like to do, as conservation geneticists and conservation biologists, is restore natural connectivity of the Yellowstone population.
JOHN HOCKENBERRY: Lisette Waits, of the University of Idaho’s Laboratory of Ecological and Conservation Genetics, is responsible for monitoring the genetic diversity of bears. Any bear DNA sampled in the lower 48 states is sent to her.
LISSETTE WAITS: There's a wide variety of ways you can get DNA samples. For the Yellowstone study, we've taken blood samples from bears that are handled by managers. We've taken tissue samples. And we've also collected hair samples on barbed wire and extracted DNA from that.
Barbwire is strung around trees, making some sort of a polygon, and then in the middle you would put a scent lure to lure the bears in. And a real commonly used scent lure is cattle blood and fish guts that have been mixed together and fermented at about 100 degrees for about 6 months. The bears really, really like it, and it's pretty scary for humans to be around that. The bears walk in to check out the scent lure. And they leave hair on the barbed wire; and they walk out again, and often leave another hair sample. It's a really nice system, because the bear doesn't get a reward. The scent lure was just poured on a bunch of logs in the middle. But it does give us a sample of DNA, without having to dart them and handle them and capture them. So that is one of the many techniques that's being used in Glacier National Park, to get an estimate of the population size of grizzly bears and black bears in that ecosystem.
JOHN HOCKENBERRY: To help predict the future for Yellowstone grizzlies, Lissette Waits studies bears from the past.
LISSETTE WAITS: The more diversity a population has, the higher probability that population has for long-term survival and long term persistence. All of the samples that have been held in museums or different collections across the country provide an excellent resource for addressing the question of loss of genetic diversity over time. So we have been working with museum specimens in Yellowstone Park that have been collected since the late 1800s. And we can detect that yes they have lost genetic diversity over time. But they haven't lost as much diversity as we hypothesized. We're also using that data to try to estimate what the effective population size of Yellowstone grizzly bears. You can think of an effective population as the number of individuals that are breeding and passing on genes to the next generation, which is really different from the number of individuals that are actually out there.
MIKE GILPIN: So maybe there are 400 grizzlies in the Yellowstone Ecosystem, but effectively it's more like 60 or 80.
JOHN HOCKENBERRY: Mike Gilpin is Professor of Biology at the University of California- San Diego.
MIKE GILPIN: And no dog breeder, no pig breeder, no chicken breeder would sustain a population of only 60 or 80. Bad genes are going to come up, they're going to increase in frequency, and sooner or later you're going to have fixation of bad traits. Now maybe these traits aren't going to directly cause the extinction of the population. But these things are going to be things like hip dysplasia in dogs, where you maybe don't live as long, immunological issues involving disease resistance.
JOHN HOCKENBERRY: It takes time for the DNA samples in Yellowstone and Glacier National Park to being analyzed. When that DNA becomes data, it’ll end up in the computer of someone like Mike Gilpin.
MIKE GILPIN: Well, I'm a mathematician, basically, and I build computer models. And when this model is constructed you can ask questions of it. You know, what if we design this reserve? What if we move bears from Northern Continental Divide Ecosystem down to Yellowstone? What can we expect? What's the response of the system gonna be? Now it can be corrected in two different ways. You can do man-mediated dispersal; but it would be better to let nature herself take care of this. And so that's the issue of corridors.
JOHN HOCKENBERRY: Corridors are wide swaths of protected land, kind of like biological highways that allow wildlife populations to mix from one habitat to another. Steve Palumbi also studies wildlife corridors in parks… Marine Parks.
STEVE PALUMBI: When I'm talking about a Marine Park, I'm not talking about Sea World, or that little pool you can swim in at Disneyworld -- it's a tiny little enclosed coral reef. What I'm talking about are natural environments that are set aside for people to enjoy and use in perpetuity. They're like our terrestrial parks; like the national parks in Yellowstone, and Grand Teton and state parks, except that they include the marine habitat, as well sometimes as the coastal habitat. And it includes the bays and estuaries and continental slopes, and all the sorts of marine organisms that live in them, not just the organisms that live on land.
JOHN HOCKENBERRY: You heard Steve Palumbi talk before about protecting whales. His current research is on much smaller organisms. He’s trying to figure out how to put the concept of marine parks into practice.
STEVE PALUMBI: We don't really know how to do it, exactly. The reason is a lot of marine organisms, although they may stay within a park as adults, they make eggs and larvae that float away in the water. So what we have to do essentially is design networks of parks, so that the production from one park will essentially be captured by another park
We came to Oregon about two week ago to set up a series of experiments to try to use genetic tools to measure the dispersal distance that marine organisms use to get from place to place. Basically the question is: How far do the larvae and eggs of marine organisms float from their parents before they land somewhere and take up their existence as juveniles or adults for the next generation?
A traditional ecological approach might be to track those larvae. And if the were the size of tunas we could put a little radio transmitter and follow them around the world. Or if they were the size of whales we could put a satellite transponder on and track them that way but these are only a fraction of an inch long, we cannot track them individually
But every time a larva moves from one rocky headland to another, it carries its genes with it. And if we use the technology to understand the movement of genes, then this gives us the information we need about the movement of larva. There's no other way to do it, that we can figure out. That's why DNA has added a whole lot to this work.
JOHN HOCKENBERRY: One of the organisms they look at is barnacles.
STEVE PALUMBI: One of the things we can do with barnacles that we can't do with other kinds of critters is we can put out small plates, small plastic squares, on the rocks, that the barnacles like to land on and settle there to turn into adult barnacles. Week by week we can collect those plates, and look on them and what we can see are little clouds of baby barnacles. They're very tiny; they're about a half of a millimeter, or maybe a fiftieth of an inch long. They don't have a whole lot of DNA in them. But again, modern technology allows us to take this tiny little wisp of a barnacle you can barely see, and get enough DNA out of it to do these genetic tests.
JOHN HOCKENBERRY: For biologists studying DNA, it turns out that many nice things come in small packages. Coming up, we're going to get even smaller, in fact, microscopic; and we hunt for Teenage Mutant Nuclear Gators, when we continue with “DNA, the Code of the Wild” On The DNA Files.

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JOHN HOCKENBERRY: Welcome back to The DNA Files. I'm John Hockenberry. And this is “DNA, the Code of the Wild.”
JOHN HOCKENBERRY: Antony van Leeuwenhoek was an amateur scientist who enjoyed peering through his homemade microscopes, and reporting his observations in letters to the Royal Society of London. On September 17, in the year 1683, he recorded one of the what he saw in the plaque on his own teeth; or, as he said: “a little white matter, which is as thick as if ‘twere batter.” He wrote, “I then saw, with great wonder, that in the said matter there were many very little living animalcules, very prettily a-moving. The biggest sort had a very strong and swift motion, and shot through the water (or spittle) like a pike does through the water.” In the mouth of an old man who had never cleaned his teeth—there’s an image for a scientific revolution—, Leeuwenhoek found “an unbelievably great company of living animalcules, a-swimming more nimbly than any I had ever seen up to this time.” What Leeuwenhoek was describing, of course, for the first time, was living bacteria.
ED DELONG: What we know from some of these studies now is that some of the most ancient organisms on earth are actually the microbes. And in fact, it's the evolution of these microbes, and their physiological properties, biochemical properties that have shaped our planet. In fact the evolution of cyano-bacteria is what gave rise to the evolution of oxygen on earth. And let animals like us evolve.
JO HANDELSMAN: So microbes have been evolving on earth for 4 billion years. And they lived without the higher organisms for most of those 4 billion years. So the microbes would go along just fine if the rest of us disappeared, but if the microbes disappeared, all other forms of life would immediately cease, because the microbes carry out all the major cycles on earth. They control the nitrogen cycle, the carbon cycle, the iron cycle. Just about every major nutrient that enters biological systems enters though the action of microbes.
JOHN HOCKENBERRY: From bears to barnacles to the smaller, microbial world, of bacteria and other microorganisms. Ed DeLong is the Science Department Chair of the Monterey Bay Aquarium Research Institute on the Central California coast.
ED DELONG: Well, right now we're sitting here at Moss Landing. And if you could see down through the ocean, what you'd see is we're right by a canyon that's actually larger than the Grand Canyon.
JOHN HOCKENBERRY: His specialty is looking at what you can’t see. He’s a Marine Microbial Ecologist.
ED DELONG: A real change in our thinking, that's related to this DNA technology, has been our ability to relate all these micro-organisms with macro-organisms, plants and animals, on one evolutionary tree. We never could do that before. Because in biology, the way that we relate things is based on similarity really, homology. We know that dogs and cats, for instance, are mammals because they share certain features. And we can distinguish them by their differences. We can't do that with microbes, and we can't compare microbes to higher organisms, because they really don't share any similar morphological or other conspicuous properties. So how do we compare them?
And it turns out that we can compare them when we look at things like DNA and compare sequences that all organisms share in common. We can start to see how similar they are, how different they are, and how they're related.
JOHN HOCKENBERRY: Jo Handelsman, of the University of Wisconsin Molecular Microbial Ecology Group, regularly goes out and digs up soil samples, then brings them all back to the lab to find out, as she says, “who’s there.”
JO HANDELSMAN: We can find the DNA of organisms even when we can't see the organisms. So in my field we study microorganisms that live in soil and in the oceans and all throughout the biosphere. And DNA has really allowed us to see what we think of now as the unseeable, and the previously unknowable organisms.
JOHN HOCKENBERRY: Unknowable, not because they’re too small, but because up until recently, for the most part, scientists only knew the microorganisms they could grow in the lab, in their petri dishes or petri plates.
JO HANDELSMAN: All of the history of microbiology until the last few years has been based on culturing organisms, growing them on Petri plates. But, over the last 30 years we noticed, that, in fact, most of the organisms in the world don't grow on Petri plates. And in the soil, where I work, 99% or maybe as much 99.9% of the microbes don't grow on Petri plates. But we know they're alive and living and doing interesting things in the soil.
So the challenge has been to try to understand who those microbes are, and find ways to study what they do. And DNA has allowed us to do that, because we can find their DNA signatures in the soil, even if we can't grow those organisms in culture.
JOHN HOCKENBERRY: We’ve described only a tenth of a percent of the microbial world so far, but it's an important world. In fact microbes are family, folks. Humans are genetically related to brewer’s yeast from a billion and a half years ago. Of course, we’ve grown distant then, we don’t call, we don’t write. But even after a billion years of evolutionary distance, there are still DNA sequences in yeast and humans that are identical. Some genes you could take out of yeast, put them inside a human cell, and they would function. So what if, in one of these ancient microbes, we found a gene that resists aging? James Tiedje is Director of the Center for Microbial Ecology at Michigan State University. He’s just begun studying some of the oldest and coldest organisms on the planet.
JAMES TIEDJE: One of the interesting projects that were working on is to understand the microbial adaptation that has occurred in ancient Siberian permafrost environments. So our Russian colleagues have studied microbes that have been frozen in the soil for up to 3 million years. And we can recover living organisms from those environments.
[hissing sound]
JOHN HOCKENBERRY: That’s the sound of Cosmic Background Radiation, Cosmic Rays, coming from outer space. They’ll make a Geiger Counter click as much as once a second.
We’re constantly bombarded by a low-level background radiation, not only from space, but also from soils and rocks. Naturally occurring radioactive elements, like Uranium, decay and emit radiation. Over time this background radiation can cause mutations, errors in the DNA sequences.
JAMES TIEDJE: Because of the background radiation in the soil, these organisms would have had their DNA destroyed over that period of time, had they not had DNA repair mechanisms operative.
JOHN HOCKENBERRY: Cells constantly find and fix mutations in their DNA. James Tiedje wonders if cells packed in permafrost for a few millennia repair their DNA in the same way as their room-temperature relatives.
JAMES TIEDJE: It's argued, from a theoretical point of view, these microbes in this permafrost environment are metabolically active, at a low level, over this period of time. So they're not simply arrested in life, but they are carrying on a slow metabolism to repair their DNA and their membranes, for example, over that 3 million years.
And we're interested how they have adapted to the stresses in this environment. And we consider the stresses to be, of course, how does life go on at minus 12 C, over hundreds of thousands of years? How do these microbes adapt to the starvation that goes on in this environment? And finally, how do they adapt to cell aging -- because the body parts of these microbes are probably pretty old? A microbe may have his same membrane for 10,000 years. What's in their genetic code that has allowed them to survive under these conditions for that long?
[sounds of paddling boat on water and all kinds of night pond critters]
TRAVIS GLENN: We've got a John-boat, a small 14-foot John-boat. And what we're going to do is start looking for alligators on Pond B.
JOHN HOCKENBERRY: At the somewhat forbidding federal Savannah River nuclear Site, in South Carolina, Travis Glenn is studying the effects of radiation from a quite different source.
TRAVIS GLENN: What’s unique about Pond B is there was a release of radioactivity from the R Reactor on Savannah River Site, in the early 1960s, so there's elevated levels of Cesium 137 and Strontium 90.
JOHN HOCKENBERRY: The goal here at Savannah River was to manufacture weapons-grade plutonium and tritium for Cold War H-bombs.
TRAVIS GLENN: Really the emphasis was on building bombs faster than the Russians could. If they happened to have a few spills and accidents, well that's part of the price you pay for war, even though it was a cold war.
JOHN HOCKENBERRY: 21,000 people once worked here making bomb materials. Now 14,000 people are employed cleaning up the mess. Travis Glenn is head of the DNA Lab at the Savannah River Ecology Center, which monitors the wildlands and wildlife on the site. Sometimes that means going out at night, in a boat, and using headlamps and flashlights to search for the reflecting eyes of living creatures in the potentially irradiated water.
TRAVIS GLENN: What were trying to do is look at genetic variation in alligators, the effects of site operations on the alligators, and then also we're characterizing the mutation rate between the parents and offspring.
The Savannah River Site is second only to Hanford in the total volume of water and soil that have been contaminated, but also if you look carefully at what the levels are, the levels are really low. Yes, you can detect a level of contamination that's above background. But is it biologically meaningful, that's the real question. Because certainly you can see that's it's an intact ecosystem. There's lots of trees and wildlife here.
And so if you spent the hundreds of millions of dollars that it would take for you to drain the lake, dredge out all the sediments, and haul it off to a landfill and bury it, have you really gained anything? For sure, you've ruined it ecologically for some time to come relative to what it's like now.
There's a gator right straight in front of us. See the orange glow? Looks like sort of a burning ember of charcoal? So if this is the same gator that was back here last spring, it's about a six-foot alligator. So I think when we hauled him out last June, he was a little over 5 feet, so he should be pretty close to pushing 6 feet if it's the same one. And I don't need to catch them more than once. Now you can see how close we can get. We're almost close enough to put a noose on him.
JOHN HOCKENBERRY: The question Travis Glenn poses is how much environmental damage are we willing we risk to clean up environmental damage?
TRAVIS GLENN: If you look out here this is one of the worst-case scenarios in an ecological setting of lots of wide spread contamination. And there's no indication of a change in mutation rate, which is certainly what you'd expect. So the question is: Is there real any biological effects of the low-level contaminants that we see? And I think they'll be a lot of places like where we’re sitting where this new field of phytoremediation, and monitored natural attenuation, which is sort of leave it in place, let the natural processes take care of the residual effects of the contaminants; because really anything that you could go in there and do with bulldozers would be far more harmful than just leaving it alone.
JOHN HOCKENBERRY: Which wouldn’t be the first time in human history caused more problems than they were trying to solve. But did you catch that word Phytoremediation that Travis Glenn said a minute ago?
LAURA CARREIRA: Phytoremediation is the use of living plants to clean up contaminated sites.
JOHN HOCKENBERRY: Biochemist Laura Carreira is a pioneer in phytoremediation. She co-founded Applied PhytoGentetics, the company hired to clean the Georgia State Botanical Gardens.
LAURA CARREIRA: To our left is what used to be an old solvent dump from the University. This is University property. They used to bring solvents from all the research labs out here and dump them in a lethal solvent dump. You can see all the fences around, and the tress have grown up around it. To my right is an unnamed wetlands where all the solvents are now starting to come out.
JOHN HOCKENBERRY: The way to clean most contaminated sites, and the way the University was planning on cleaning this one, is to dig up all the dirt and haul it away.
LAURA CARREIRA: It would have taken more than a year, it would have shut down the Botanical Gardens, it would have cost about 20 million dollars. That's the standard procedure: cart if off to a hazardous waste landfill; let somebody else take care of it. (laughs)
JOHN HOCKENBERRY: Carreira estimates that using phytoremediation on this site, including long-term monitoring, will cost only about a half-million dollars, and will remove all the toxins. Her strategy is to find native plants, growing on the site, that use toxins as nutrients; they turn the toxic chemicals into harmless byproducts, carbon dioxide and water.
LAURA CARREIRA: When we first started this we were looking for any plants which could tolerate growing in polluted sites. So what we did was that we came out here and analyzed 68 different plants, looking for the enzymes that would degrade the solvents that are in the water. And then last December we planted 5600 plants of 9 different species. And now we're going to monitor all next year to make sure absolutely nothing is getting off the site. The highest concentrations of the solvents are coming right down this hill. That well right there has 50 parts per million total VOC's, which is methylene chloride, chloroform and benzene. I put 150 hickory trees going up that hill. And then we started over here and put Yellow Poplar, Sweet Shrubs, Beauty Berry, Sweet Bay, Cypress trees. We left every Azalea on the place; nobody could dare cut any Azaleas (laughs). It doesn't have to be ugly to clean it up. That's the beauty of organic phytoremediation, is that it turns it into non-toxic compounds which are just part of the tree, part of the shrub. You don't have to do anything (laughs). But we can use the fact that they have the ability to do this, to clean up something that we caused, while also making something pretty. I tell everybody that you need to walk softly, and let the plant's take care of us all. Because they will.
JOHN HOCKENBERRY: Another co-founder of Applied PhytoGenetics is Richard Meagher. He’s working on a tougher problem in pollution control: toxic heavy metals that come from industrial waste, things like arsenic, cadmium and mercury. No plants have been found that can efficiently remove these metals from the soil. So he’s building some that will.
RICHARD MEAGHER: So what's going on here is we're trying to prove that adding one new gene is going to make these plants resistant to arsenic. And what you'll see is that the control plants are only a few millimeters long, and are looking very sick and yellow, and they're all going to die. And the ones with this one new gene, they're growing real well. They're already going on to flower. They're looking really healthy and have nice long roots a couple inches long. This tells us that this gene will help the plant be tolerant or resistant to arsenic. That's sort of our first step in terms of making a plant that would clean up an arsenic contaminated site. Arsenic is one of the worse five metals on the EPA's hit list for things to be cleaned up so this is just of the beginning of our arsenic project. We think it's gonna take us about five genes total to engineer a plant that would very efficiently phytoremediate arsenic, extract it and allow us to efficiently take it from the plant.
JOHN HOCKENBERRY: The plants actually take the metals into their tissues. But once the metals are in the plants, it still must be harvested and disposed of. Yet these transgenic plants may solve the previously unsolvable problem of getting the metals out of the soil. Transgenic plants used in phytoremediation are still in the greenhouse, or in confined research plots. But transgenic bioremediation products may soon be leaving the laboratory. Bioremediation is the use of microbes, instead of plants, to clean contamination. Gary Sayler directs the Center for Environmental Biotechnology at the University of Tennessee. He has received the first EPA approval to field test transgenic microorganisms for cleaning up hazardous waste.
GARY SAYLER: And we do that by genetically engineering microbes to degrade specific pollutants, but also introduce into those organisms the genes that allow them to make bioluminescent light. The organism as it begins to degrade that toxic chemical turns on these genes for light production, and the organisms give off light. To do away with toxic chemicals, the idea would be to keep the light on as long as possible.
Now that work is actually moving into new directions where we're integrating these organisms directly on silicon microchips to make tiny remote sensor technology that would allow individuals to use these organisms as very low cost, but very specific sensors of chemical contaminants in the environment. It could have broad implications for soil and water monitoring, even toxicants associated with food. The home residential user could be using it for testing their own well water.
JOHN HOCKENBERRY: Amazing critters, these microbes. And the most amazing, the Superbug, Deinococcus radiodurans, among the world's toughest and oldest organisms, you haven’t heard of it? Well, if you ever see it, It's pink; smells like rotten cabbage. It can survive an atomic blast, acid baths, high and low temperatures, ultraviolet radiation, and dehydration. How’s that for conditioning? By the way, it can take 1.5 million rads of gamma radiation, that's 3,000 times the lethal dose for humans. It lives in cow pies and elephant dung. It's 2 billion years old, and came to the attention of scientists when it refused to die in post-World War Two sterilization tests on canned meat. Researchers call it Conan the Bacterium. Bio-engineers have plans to engineer its genome for a variety of purposes, from eating nuclear waste to providing medicine for Mars-bound astronauts.
So what happens when transgenic creatures, like the perhaps soon-to-be-modified Superbug, mingle with the rest of the not-so-super species? What happens when animals munch on metal-absorbing genetically modified plants? Well, we don’t know yet. Most of the bio-engineered phtyo- and bio- remediating organisms are still in the lab.
JANE RISSLER: About 17 years ago, when people were first starting to talk about commercializing genetically engineered organisms, microbes for bioremediation was a pretty big topic. To use in oil extraction, to use in mineral extraction. There were a lot of suggestions about microbes, but interestingly, they haven't worked very well. Because they certainly have not moved towards commercialization.
JOHN HOCKENBERRY: Jane Rissler is Senior Staff Scientist at the Union of Concerned Scientists.
JANE RISSLER: Ecologically there are more challenges than there are genetically. And we know so little about, for example, the soil or water microbial world, that we just don't know what we're doing when we release transgenic microorganisms into these environments.
JOHN HOCKENBERRY: One of the fathers of ecology, Aldo Leopold, said: “To keep every cog and wheel is the first precaution of intelligent tinkering.”
JANE RISSLER: What we have learned, or should have learned in the last 20 years, is that we need a lot more ecology to understand how to use genetically engineered products.
STEVE PALUMBI: It definitely is a discovery period. We’re just now taking baby steps; kind of evolving ways to understand, really, our planet in a more holistic kind of systems based approach.
JO HANDELSMAN: We've seen a merger of the techniques of molecular biology with those of ecology.
JOHN AVISE: I fully anticipate that within the next 20 years that entire tree of life will be illuminated almost completely. And I think this will a milestone event in the history of biology that will rank with the human genome sequencing project as a tremendous milestone, a great accomplishment in the history of biology.
STEVE PALUMBI: Because DNA is fundamentally built the same, whether it's in humans or whales or barnacles, we can use the technology developed, say, for doing genetic tests in your doctor's office, to ask questions about the ecological situation these animals are in that we couldn't answer in the past. And, really, if you think about it, that was the promise of the human genome project, that we'd have this technology to use in wide-ranging applications all over the world.
JOHN HOCKENBERRY: Even some of the most serious biologists get a little starry-eyed when they talk about Aldo Leopold's 1948 memoir, A Sand County Almanac. Let me read a bit: “It is a century now he said, since Darwin gave us the first glimpse of the origin of the species. We know now what was unknown to all the preceding caravan of generations: that men are only fellow-voyagers with other creatures in the odyssey of evolution. This new knowledge should have given us, by this time, a sense of kinship with fellow-creatures; a wish to live and let live; a sense of wonder over the magnitude and duration of the biotic enterprise.”
We've certainly come a long way since 1948 and Aldo Leopold would be amazed by the technological advances since then. But I think if he were here now, he would also agree, that we're still waiting for that wisdom.
I’m John Hockenberry. Thank you for listening to The DNA Files.

This series, The DNA Files, was produced by SoundVision Productions with funding by the National Science Foundation and the Alfred P. Sloan Foundation.
This program, DNA, The Code of the Wild: Genetics and Applied Ecology, was produced and engineered by Barrett Golding. The editor was Sora Newman, and our host was John Hockenberry.
Our opening feature, “Low-Mow Lawns,” was produced by Erik Anderson, and edited by Gemma Hooley.
The DNA Files is: Managing Editor, Rachel Ann Goodman. Science Consultant, Sally Lehrman. Research and Production support by Adi Gevins and Noah Miller. Technical and Music Director, Robin Wise.
Original music composed by Jesse Boggs and performed by the Stanford Woodwind Quintet, Anton Schwartz, Tom Hayashi, and Jesse Boggs.
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