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

Transcript

SoundVision Productions
2991 Shattuck Avenue, Suite 304
Berkeley, California 94705-1872
(510) 486-1185
feedback@dnafiles.org
http://www.dnafiles.org

For further information about genetics and these programs, as well as the producers who brought you this series, visit the project web site at www.dnafiles.org.
Send your questions about genetics and this project to feedback@dnafiles.org.

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…

● ● ●

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.

● ● ●

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.

● ● ●

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.

CREDITS:
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.
Project Director, Jude Thilman. Marketing by Murray Street Enterprise. Legal services by Walter Hansel and Spencer Weisbroth.
You can visit our website at www.dnafiles.org. Send your responses and letters to feedback@dnafiles.org. For tapes and transcripts, call 866-DNA-FILES (866-362-3453).
The Executive Producer is Bari Scott.
This has been a SoundVision Production, distributed by NPR, National Public Radio.

The DNA Files:
Unraveling the Mysteries of Genetics

As heard on National Public Radio

Life: How to Make a Cosmic Omelet
Genetics & Astrobiology

Hosted by John Hockenberry

Transcript

SoundVision Productions
2991 Shattuck Avenue, Suite 304
Berkeley, California 94705-1872
(510) 486-1185
feedback@dnafiles.org
http://www.dnafiles.org

For further information about genetics and these programs, as well as the producers who brought you this series, visit the project web site at www.dnafiles.org.
Send your questions about genetics and this project to feedback@dnafiles.org.

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. In this program, Life: How to Make a Cosmic Omelet, we’ll be looking at where life came from, and what genetic research is telling us about where else we might find it. The National Aeronautics and Space Administration—NASA—has dubbed the field Astrobiology, a marriage of sorts between astrophysics and biology. As we’ll see, it’s not the search for little green men, but rather the search for any sign of life at all. Even microscopic life. It may be one of the most difficult and most rewarding challenges facing science today, says physicist Paul Davies.
PAUL DAVIES: There can surely be no greater challenge than to understand how a mixture of non-living chemicals turn themselves spontaneously into the first living thing.
JOHN HOCKENBERRY: All this when we return with The DNA Files.
_____

JOHN HOCKENBERRY: Yellowstone National Park. For most of us, it’s a spectacle of geysers and bison; for genetic scientists it’s a hotbed of microbial research, home to nature’s tiniest creatures. What scientists are learning here may help us unravel the biggest puzzles of all time: How did life get started? And what are the most extreme conditions in which it can survive? Joe Jordan has this story…
JOE JORDAN: Imagine the early earth, more than three and a half billion years ago. Boiling mud pools, toxic chemicals … big chunks of rock and ice crashing in from the sky. How could anything have lived through these conditions? For answers, scientists come to a place where our planet’s internal heat still leaks out, in scalding steam geysers and brilliantly colored hot springs teeming with life …
TIM MCDERMOTT: Welcome to Yellowstone National Park, Joe. G'morning; it's a great day to be here in Yellowstone, and it's a great place to work.
JOE JORDAN: That’s Tim McDermott, a soil microbiologist at Montana State University’s Thermal Biology Institute. He studies microbes that live here in the 200-degree Fahrenheit geothermal pools of Norris Basin, a volcanically active backcountry area of the park. Some of these microbes even live on arsenic – a poison to us, but one of several heavy metals found naturally here in Yellowstone.
TIM MCDERMOTT: Mercury, lead -- copper, zinc if it weren't a national park, at least places would probably be designated a super-fund site.
JOE JORDAN: At the edge of a bubbling hot spring, McDermott samples soil for microbes. Back in his lab, he’ll study variations among their genes for arsenic tolerance. Plotting where microbes live and what they eat helps color in the map of evolutionary relationships, from ancient to modern organisms. But most of what we know about microbes comes from being able to analyze their DNA, says University of Colorado molecular scientist Norm Pace.
NORM PACE: Imagine if our entire understanding of biology were based on a visit to the zoo ... And that's exactly the situation we've been at in the microbial world until really quite recently.
JOE JORDAN: In fact, an organism discovered here in Yellowstone gave scientists the enzyme used in most new gene sequencing techniques. Out in Norris Basin, Pace’s colleague, biologist John Spear studies the hydrogen diets of microbes in the crystaline turquoise blue, green and yellow waters. He takes DNA snapshots of whole microbial communities in their natural habitats.
JOHN SPEAR: What I'm doing is I hang a piece of glass -- just regular glass, like a window-pane glass -- I hang it in the pool and I'll come back and get it in 2 weeks or 3 months -- I'll give it an amount of time for it to get colonized with a bio-film.
JOE JORDAN: Spear uses a razor blade to scrape the microbial film off the glass into a tube that he freezes in liquid nitrogen. Then he takes it back to the lab, extracts the DNA and plots similarities and differences between groups of microbes. What starts to emerge is a map of the tree of life, of evolutionary relatedness. Spear’s wearing a tree-shirt today.
JOHN SPEAR: On this t-shirt we have a picture of a tree. It's a tree that has the 3 major groups, or domains, of life – the Bacteria, the Archaea and the Eukarya.
JOE JORDAN: Eukarya is where we humans are on the tree of life, along with all the animals, plants and fungi. Most of us know something about bacteria, too. But Archaea, A-R-C-H-A-E-A -- the name implies ancient heritage. Once thought to be among the bacteria, they've recently been revealed as a whole new category -- with significant differences between their DNA and that of all other modern life. They may be closely linked to the earliest life forms, near the root of the tree, explains Norm Pace.
NORM PACE: When you look at these high-temperature organisms -- particularly the high-temperature Archaea -- you see these very short line segments departing from the last common ancestor.
JOE JORDAN: Archaea turn up everywhere from oceans to the human gut. Among them are many "extremophiles,” organisms that can live in exotic conditions like heat, acid, salt and ice … places we never thought we’d look for life. Astrobiologist Jonathan Trent of NASA’s Ames Research Center in California studies how some of the heat-loving microbes beat the heat by making a heat-shock protein that appears to stabilize cell membranes. He reflects on how genetic adaptations like these are expanding the realm of the possible, opening whole new worlds, in our view of life.
JONATHAN TRENT: It’s probably comparable to the age of discovery that went on in the 19th century, where people were going around on ships and they were finding things living in the deep ocean, in places we had no way of ever visiting before … and now were going in that same direction with the inventories of DNA information that more and more organisms are being sequenced. And many people are now saying that the 21st century is going to be the age of biology.
JOE JORDAN: Now that we are beginning to map the range of extremes in which life can survive, what we learn in Yellowstone could help us plan where to look on upcoming missions to Mars and Europa, environments that now seem just a bit more likely to harbor at least some form of life…
For The DNA Files, I’m Joe Jordan.

_____

JOHN HOCKENBERRY: Welcome to The DNA Files. I'm John Hockenberry. In this program we’ll meet scientists studying the origins of life on Earth and searching for the signs of life beyond Earth. For my own part, I want to know where I’m from. I mean I know where I was born, and where my parents were born and all that. But where am I really from? Where did any of us come from? We’ve asked this question as long as there have been humans to ask it.
VOICE: In the beginning, there were two realms. Muspell was in the south, and it was full of fire and blinding light. Niflheim, the home of fog, ice and snow, lay in the north. Between the two realms was a vast stretch of empty space called Gin-nun-ga-gap, or Yawning Gap.
JOHN HOCKENBERRY: There are probably thousands of stories that start with "in the beginning" and so on, to recount how life began. Every culture has at least one such tale. This one is from Iceland.
VOICE: The drips and drops started life growing…
JOHN HOCKENBERRY: To many ears, such tales sound far-fetched, if taken literally. But scholars of religion and folk traditions like Professor David Leeming say creation tales undoubtedly satisfy a universal human need for an answer to why we’re here. Dr. Leeming, is an emeritus professor of English and comparative literature at the University of Connecticut and author of the "Encyclopedia of Creation Tales."
DAVID LEEMING: Why did people in the Paleolithic dig their way down into caves and sit there in the darkness and then paint paintings, of animals and shamans or whatever? It’s as if we’re driven to tell the story of creation.
JOHN HOCKENBERRY: And it's not just storytellers and shamans who are driven to explain the origins of life, says Leeming.
DAVID LEEMING: And it’s also told by the scientist who says, "Hey, we are all the result of an explosion that took place in a billionth of a second billions of years ago.” There’s a relationship between what the old mythmakers were doing and what the scientists are doing.
JOHN HOCKENBERRY: Some scientists have theories that make the Icelandic story of Yawning Gap seem positively mainstream.
CARL SAGAN: With 400 billion stars in the Milky Way galaxy alone, could ours be the only one with an inhabited planet?
JOHN HOCKENBERRY: Take the late professor Carl Sagan, who used his public television program Cosmos to spread his conviction that advanced life must be common in the universe.
CARL SAGAN: Perhaps near one of those pinpoints of light in our night sky someone quite different from us is glancing idly at the star we call the sun and entertaining just for a moment an outrageous speculation.
JOHN HOCKENBERRY: Sagan was one of the country’s leading proponents of the search for extraterrestrial intelligence. He inspired a generation of scientists and science buffs dedicated to the quest for alien beacons. And he authored Contact the story of a scientist obsessed with finding extraterrestrial life. The book later became a major motion picture.
But many scientists say fishing for intelligent extra-terrestrials at the top of the galactic food chain is unlikely to be successful, even if there are aliens somewhere out there with transmitters trying to reach us. They say the scientific payoff is closer to home, on planets in our own solar system, looking for the simplest life forms possible—single-celled organisms like bacteria and yeast. Biologist Lynn Rothschild.
LYNN ROTHSCHILD: Where the interest is going to be is at the molecular and really the microscopic level. If we find anything that’s alive, no matter how microscopic, no matter how simple in a metabolic sense, that is the most exciting thing. It’s this whole question of life or non-life.
JOHN HOCKENBERRY: A scientist at NASA’s Ames Research laboratory in California, Rothschild says apart from such single-celled microbes, life is probably rare in the universe. The evidence comes from looking not up but down, at the Earth under our feet. On this blue ball we call home, single-celled life made its dramatic entrance some 3.8 billion years ago, but it wasn’t until about half a billion year ago multi-celled plants and worms and the like joined the cast.
CHARLES LIU: We’re here in the northwest corner of the Rose Center and we can see clearly the hanging and mounted models of the planets as we’ve displayed them...
JOHN HOCKENBERRY: To better understand the plot of this cosmic melodrama, we’ve made a visit to New York, to the Rose Center of the American Museum of Natural History.
CHARLES LIU: Earth in front of us here is about the size of a basket ball, Mars—with its red surface and white ice caps…
JOHN HOCKENBERRY: Physicist and museum curator Charles Liu is my guide. Models of electrons, protons, planets and stars illustrate the size of the universe and everything in it. A broad ramp called the Cosmic Pathway illustrates its age.
CHARLES LIU: And it is a 349-foot long spiral walkway--so it’s about as long as a football field plus one and a half end zones. Along this pathway, which describes the entire history of the universe, 13 billion years of cosmic evolution from the big bang to the present day.
JOHN HOCKENBERRY: Quite frankly, it’s a bit humbling to contemplate such vast scales of time and space as we follow the Rose Center’s cosmic pathway…
CHARLES LIU: As we walk down we see a pictorial history of the universe unfold…some quasars and galaxies and proto-galaxies. Followed by radio galaxies,
JOHN HOCKENBERRY: Liu says it’s not until two thirds of the way down the pathway that the sun, Earth and the other planets are created from a humongous cloud of gas. Six yards farther, microbes appear.
CHARLES LIU: We keep walking. Dinosaurs are just two steps—maybe three steps—away from the present day. Along this cosmic pathway we've walked a full length of a football field, and then we realize that all of human evolution, from when the first hominids began to walk on two feet, takes barely an inch and a quarter on this cosmic pathway.
JOHN HOCKENBERRY: Human civilization takes up barely the width of a human hair. Yikes! Seen in this light, life on Earth does seem insignificant. But looking at the flip side, you could say we’ve been 13 billion years in the making. How did the miracle of life occur? Michael Meyer, who has joined me at the Rose Center, says scientists have puzzled for generations about what mysterious process created life from almost nothing. Meyer is the top astrobiology scientist at NASA headquarters in Washington.
MICHAEL MEYER: Darwin’s idea of how life started on Earth is that it could have started in small ponds. You can imagine for instance, a splash pool on the edge of the ocean where big waves come up, you fill little puddles. You have some chemicals in there—whatever is in the ocean. It dries out, it concentrates everything. Concentration causes some chemical reactions. And you have the possibility of something getting more and more complicated, until at some point in time it's complicated enough so that you have something helping itself grow.
JOHN HOCKENBERRY: Meyer says Darwin’s small ponds are only one place life could have appeared. Some researchers say it may have originated in hot springs deep under the ocean. Wherever Earth’s life first sprung up, scientists say it probably used the same simple chemical building blocks found in all known life today: twenty amino acids and some additional simple chemicals used to build DNA and RNA molecules. Today these important building blocks are made by living things. But before life could have started, these raw materials must have already been on hand. Most astrobiologists believe these chemicals were first cooked up in a primordial soup when the solar system was young.
Now somewhere on my desk here I have tape with a recipe for primordial soup. Hmm.
Excuse me. I haven’t tidied up in while.
No. That’s not it.
What’s this…no. Not chicken soup.
[sound of audio tapes being shuffled]
Ah. Here it is!
[sound of tape being put in machine.]
Okay…
JULIA CHILD: Hello I’m Julia Child. I’m in my own kitchen today and I’m boiling up some primordial soup. We’re doing a recipe for the chemical building blocks of life.
JOHN HOCKENBERRY: [chuckle]. Julia is a fine cook, one of the best in the universe certainly but I just want the recipe. Let’s see.
JULIA CHILD: Then we have 24 grams of sodium chloride. That’s plain old table salt. And 24 grams is about a tablespoon and 3/4. Then we have 4 grams of sodium sulfate.
JOHN HOCKENBERRY: Julia Child of course is no astrobiologist, be she got that recipe from one. In fact, fhe first recipe for primordial soup was created by a chemist, Stanley Miller. You’ve probably heard about his famous 1953 experiment where he put a bunch of simple gases—methane, ammonia and hydrogen in a glass chamber with some water. He heated it and zapped the mixture with sparks to simulate lightening on a primitive Earth. Amazingly this simple apparatus produced a number of these amino acids building blocks. Based on new findings, scientists have refined the recipe for primordial soup many times over the years. Julia’s recipe, proposed by chemist Cyril Ponnamperuma contains about a dozen ingredients.
JULIA CHILD: 3, 4. Now take your wire whip. Stir it all up. There! And that’s all there is to your primordial soup.
JOHN HOCKENBERRY: Okay. So as far as anyone knows, amino acids and other building blocks of life were first created in some primordial soup. The soup’s broth was liquid water, which guaranteed that the ingredients would come into contact with each other. Carbon, an essential part of all known life today, was also an important ingredient in the soup. But the building-block products of primordial soup weren’t life. The next steps on the way to life itself are still very much in question.
JOHN HOCKENBERRY: Jack Szostak, a Professor of genetics at Harvard Medical School is researching one popular theory.
In his lab more than a dozen grad students, post docs, and lab techs here are busy operating equipment and pipetting solutions. All this activity is directed toward a single goal: to explain how complex molecules became life. Or, as some scientists say, how chemistry became biology. Jack Szostak.
JACK SZOSTAK: Cells nowadays—they’re the results of billions of years of evolution—and they are very complicated. So we have a complicated system where DNA encodes RNA, which encodes proteins, and the proteins make…
JOHN HOCKENBERRY: Whoa! I guess we're going a little too fast here. Let’s slow this the whole business down, because cell biology can get a bit technical. I’m taking off my journalist’s cap and put on my chef’s hat and apron because I’m going to do some cooking. And I’ve invited you into my kitchen today because in many ways what a cell does is just like cooking. A kitchen contains ingredients—let’s say eggs, milk and butter—to make something like your basic omelet. A cell like, say a yeast cell, takes simple sugars and makes alcohol and carbon dioxide. Both a kitchen and a cell need three essential things to function. Number one: a recipe.
A recipe of course is a list of instructions. In a cell, DNA is the cookbook. The genes, or segments of DNA, are the individual recipes. So DNA equals cookbook. Gene equals recipe. Got that? The second essential element in a kitchen is the chef…that’s me, Chef Jean...who uses the recipe to cook up a meal. I know you're following me. I’m going to start gathering up my ingredients. I need some of this, and some of that. That looks kind of bad... Eww, how long has that been in here.
A cell’s chef is RNA, a molecule that reads the DNA instructions to cook up materials to repair cells walls, make pigments like chlorophyll, digestive juices and other important chemicals in the life of a cell.
The third essential part of a kitchen are all the nifty gadgets like an eggbeater and pots and pans, and this garlic peeler over here. I mean these things are great. You've got to get one of these. A cell has nifty gadgets too, they're called enzymes. And if you’ll excuse me, I’m going to make my omelet while I keep talking. I’ve got guests coming soon…ok. Eggs…
A splash of milk…
Now beat …
[eggs pouring into a frying pan & sizzling of egg in pan]
Without my eggbeater and frying pan my milk and eggs would just sit there. In a cell, the same problem would occur, unless the cell’s cooking gear- the enzymes--make chemical reactions happen. Now there’s something interesting about how a cell works. As I’ve said DNA contains a cell’s recipes and RNA reads them. It turns out that RNA needs enzyme gadgets to be able read the recipes. It’s as if the first instruction for our omelet was to turn on the kitchen light. If the light’s not already on, the chef can’t read. It's this circular very basic, relationship between DNA, RNA and enzymes that makes it so hard to understand how modern cellular life began.
Okay. And now my omelet is done! So from Chef Jean…Bon Appétit!
JOHN HOCKENBERRY: Now let’s go back to what Harvard geneticist Jack Szostak was saying.
JACK SZOSTAK: And so we have a complicated system where DNA encodes RNA, which encodes proteins.
JOHN HOCKENBERRY: And by the way, when he says the word “encodes” he means “has the instructions for.”
JACK SZOSTAK: And then the proteins are enzymes, which are responsible for the synthesis of DNA and RNA. It’s a cycle and every part depends on every other part. It was very hard to imagine how that kind of cycle could have started.
JOHN HOCKENBERRY: It’s hard to imagine because its one of those chicken and egg paradoxes, like the situation where the chef needs a light to read the instructions to turn on the light. Professor Szostak is a leading advocate of RNA World theory, which postulates that before life evolved today’s complicated division of labor, RNA somehow did all the work itself.
JACK SZOSTAK: One of the breakthroughs came with the discovery that the RNA molecules could be catalytic.
JOHN HOCKENBERRY: Meaning RNA that molecules could make reactions go. In the 1980’s researchers showed that RNA sometimes acts like an enzyme, a discovery that earned Thomas Cech and Sydney Altman a Nobel Prize. So enzymes weren’t the only molecules in the cells that could make reactions happen. It's as if they discovered a chef didn’t need any gadgets in order to make an omelet. Jack Szostak:
JACK SZOSTAK: What that showed in principle was that RNA might be able to actually catalyze its own synthesis.
JOHN HOCKENBERRY: In other words, maybe earlier life could actually have been simpler, needing neither DNA nor the enzymes. RNA would have done everything then, including storing the genetic information. The theory is hard to prove, however. If they ever existed, there are no such primitive cells left for scientists to study. The RNA world theory has many advocates in the scientific community. But some researchers say that before RNA could have appeared, early life must have developed a way to produce energy to fuel its chemical reactions. Carl Woese is a microbiologist at the University of Illinois.
CARL WOESE: There are two great aspects of living systems. And one is of course replication but the other is metabolism. And metabolism among other things provides you the building blocks with which to make RNAs, proteins, etc. I favor and a number of people favor that metabolism came first and replication grew out of it.
JOHN HOCKENBERRY: But others say that initially even before the primordial soup would have been too dilute for chemical reactions to have taken place. That what came first was neither RNA nor metabolism.
LOUIS ALLAMANDOLA: Imagine you are in a pond or a puddle or even a large sea. You might have all the ingredients there. But the probabilities and chances of all them getting together and then staying together long enough so that a third essential component might come along is very low.
JOHN HOCKENBERRY: So NASA Chemist Louis Allamandola says life needed a container to keep its ingredients corralled.
LOUIS ALLAMANDOLA: If these things started to happen in a little proto-cell, the odds of interesting chemistry—more complicated chemistry taking place—increase. And so once you have that kind of a proto-cell you could have chemistry taking place inside which is different from chemistry outside. It's considered an important step in this whole process of evolution from chemistry to biology.
JOHN HOCKENBERRY: One of the wilder theories about life on Earth is that it didn’t start on Earth at all. Remember primordial soup needs only water and a few other ingredients and all of these exist in many places apart from Earth. The only really important requirement for this early process to begin is that the temperature be warm enough so that the water isn’t frozen and cool enough so that it doesn’t turn to steam. Scientists call anywhere these conditions exist "the habitable zone.”
[sound of meteorite entering the atmosphere & people exclaiming about it]
JOHN HOCKENBERRY: That explosion is a sonic boom made when a meteorite entered the atmosphere over New Zealand in 1999. Very few meteorites this large ever encounter Earth. But many small meteorites do fall from the sky and more than one thousand tons of fine comet dust filter down every day. In the middle of the 19th some European physicists and biologists proposed that life on Earth—not just such raw ingredients, but life itself--originated deep in outer space, beyond the solar system. The theory, dubbed "Panspermia," postulated that microbes from distant stars seeded planets far and wide. The idea sounds more like science fiction than science. It has fallen into disfavor because many scientists believe living organisms couldn’t reach Earth from another star. But Australian physicist Paul Davies says the notion that microbes travel from one planet to another within our own solar system is not farfetched at all.
PAUL DAVIES: Cocooned inside a rock, say a meter or two across, a microbe would be shielded from the worst of the radiation and it would actually be perfectly comfortable. It would be a very good way to ride from one planet to another
JOHN HOCKENBERRY: Meteorites from Mars fall to Earth every year. One such rock might have been the source of life on Earth. The space agency NASA is sending a series of missions to Mars to see if there is or ever was life on the planet. In preparation the agency is conducting research at one of the most Mars –like regions of Earth. When we return a visit to the Arctic’s Haughton crater.
______

JOHN HOCKENBERRY: This is The DNA Files. I’m John Hockenberry. In this next segment, producer Robin White tells us about the search for life on Mars and how a group of scientists is going to the far reaches of Earth to find out more about our planetary neighbor.
ROBIN WHITE: Fourth in line for the sun, next to Earth in the habitable zone, Mars has always fascinated us Earthlings. We call it by the name the Romans gave it after their God of War. Maybe that’s why we’ve always been a bit leery.
ORSON WELLES: We know now that in the early years of the 20th Century this world was being watched closely by intelligences greater than mans'…
ROBIN WHITE: The 1938 radio drama broadcast of H.G. Wells’s War of the Worlds about a Martian invasion caused panic among listeners who took it for the truth. Early astronomers imagined canals on Mars and others fantasized great civilizations. But when we first sent a spacecraft in 1969 Mars seemed cold and barren. NASA scientist Chris McKay – sometimes called Mr. Mars – says 4.5 billion years ago, Mars was warmer but doomed.
CHRIS MCKAY: Imagine taking a large turkey and a small potato out of the oven - the small potato is going to cool faster even if they left the oven at the same temperature. In this analogy Mars is the small potato. Earth is the big turkey. Mars lost its heat much more quickly…
ROBIN WHITE: And McKay says when Mars cooled it lost its thick atmosphere. But when Mars was a warmer potato it probably had flowing water, lakes, oceans even.
CHRIS MCKAY: If Mars had water... even if only for a few hundred million years, that could well be long enough for life to appear there if Earth is any measure of the ability of life to appear on a planet.
ROBIN WHITE: Mars had the same primordial soup ingredients as Earth. So a few hundred million years could have been long enough for chemistry to start morphing into biology. But Mars’s warm period was over so long ago that if there was life, there’s only a slim chance anything’s left alive now. So we’re looking for traces – evidence - fossils. In 1996, some geologists at NASA’s Johnson Space Center in Houston thought they’d found just that in a meteorite from Mars called Alan Hills 84001.
KATHIE THOMAS KEPRTA: I walked into Dave’s office and …I knew that something important was going on because David’s desk was all cleared off and it’s never cleared off.
ROBIN WHITE: Kathie Thomas Keprta remembers a meeting with her colleague Dave McKay
KATHIE THOMAS KEPRTA: … and David said I have something amazing to tell you and it can’t go any further than this office…he told me why ... because he thinks he’s seeing evidence of possible life forms... he was showing me pictures and I sat there and I looked at him and I thought “Oh my gosh I think he’s nuts."
ROBIN WHITE: It wasn’t living Martian bacteria flying through space - but possibly signs of dead ones. Keprta’s now convinced the rock does show traces of bacterial life from Mars that date back 3.9 billion years. Searchers on the National Science Foundation’s annual meteorite hunt found the grey-green fist-sized rock in Antarctica. It contains magnetite or iron oxide crystals. Some similar crystals are made on Earth by geological processes, but others are made by bacteria.
KATHIE THOMAS KEPRTA: They form them in a chain within their bodies and they use them as a little magnet to orient themselves using the Earth’s geomagnetic field lines. Now they want to make the best magnet that they can make because that’s going to improve their opportunity to survive.
ROBIN WHITE: And so they make very pure magnetites which look identical to those found in the meteorite. But even though the meteorite's crystals look right, how can we be sure they’re signs of life when they come from outer space? Laurie Leshin, Associate Professor of Geological Sciences at Arizona State University, is skeptical.
LAURIE LESHIN: It’s just a real question of whether or not there is such a thing as a uniquely biological shape - the shape of a mineral that would lead you to say "Aha! There’s no question that this was made by a bug." and we still don’t know the answer to that question.
ROBIN WHITE: Leshin says we need to go dig our own samples – perhaps in old Martian lakebed - to find out for sure. In 1997 the Pathfinder mission landed on Mars and millions of people watched on the internet as the Sojourner Rover explored the local rocks. Pathfinder didn’t find signs of life but didn’t rule it out. The current mission to Mars, the Odyssey orbiter, is looking for water. On future missions we’ll go get that soil and bring it back and then probably in twenty years we’ll see humans on Mars.
In preparation for that scientists are landing at the ends of the Earth - on Devon Island, in the frigid Canadian Arctic. Devon’s the largest uninhabited island on the planet and a polar desert with winter temperatures as low as -60 degrees centigrade.
VOICE: Looks like your weather is finally trying to clear up a bit.
ROBIN WHITE: The international scientific team comes here each year because the harsh, dry climate is similar to Mars. Also here is Haughton Crater, one of the best preserved impact craters on Earth. 23 million years ago an enormous rock crashed and left a hole the size of London. Charlie Cockell, chief biologist at the Haughton Mars Project says Mars is spattered with craters like this.
CHARLES COCKELL: The surface of Mars has been hit by asteroids and comets for 4.5 billion years now so the surface of the planet is essentially a shocked surface. It’s where the rocks have been pulverized by comets and asteroids over a long period of time…
ROBIN WHITE: In summer the Haughton Crater is piebald with snow patches and brown melted permafrost. Down inside the crater Cockell shows me enormous piles of blue-grey breccia - rock which was transformed by the thousand-degree heat from the meteor impact.
CHARLES COCKELL: Can you see that green?
ROBIN WHITE: Yeah?
CHARLES COCKELL: That's organisms living in shocked rocks.
ROBIN WHITE: The heat made the rock porous and microorganisms now live inside, protected from extreme freezing and thawing and high levels of polar ultra violet radiation. UV radiation is also abundant on Mars because Mars has no protective atmosphere. UV makes the strands of a cell’s DNA fuse together which causes the cell to die. When you’re a one-celled creature, that’s a problem.
CHARLES COCKELL: The best thing you can do is try and hide from UV radiation and you can do that two ways you can either screen yourself by producing ultraviolet screening compounds, essentially natural sun creams, or you can hide inside things like rocks.
ROBIN WHITE: Darlene Lim who studies geology at the University of Toronto, says another way microbes cope is to build a shell.
DARLENE LIM: Here of course we’re sitting at Haughton Crater, we’re cold, were putting on a lot of clothes to deal with our elements - well if you were on a planet that had a lot of incoming UV that could be damaging to whatever genetic code you may have then you may have to figure out strategies in order to deal with that and one possibility is that you may want to build some sort of exoskeleton or a shell that actually helps to shield yourself.
ROBIN WHITE: And if microbes on Mars had shells they might have left fossils for us to find in sediments on the planet’s surface. Gordon Osinski has found fossilized hot springs around the rim of the Haughton Crater. The University of New Brunswick geologist thinks we should look at hydrothermal vents as a possible haven for life on Mars – even to the present day.
GORDON OSINSKI: If there is life on Mars today, then hydrothermal systems there would pretty much be the only place that life could survive at the present time
ROBIN WHITE: But Martian hot springs wouldn't last forever. When one hot spring dies out, how does life move to the next when we know that nothing can live on the surface of Mars? Critics of the Haughton Mars Project say the scientists are just stabbing in the dark about life on Mars. But Mars scientists have a touch of the believer in them. The team members at Haughton Crater are even locking themselves into an isolated habitat to simulate a manned mission to Mars. Principal investigator at Haughton Crater, Pascal Lee, says looking for life on Mars touches something deep in the human soul.
PASCAL LEE: The fact that we’re interested in going to another planet to look for life is perhaps part of a process of life itself - a process whereby life seeks to expand from one planet to the next. It’s something that would allow it to have a foothold on more than one world. At the same time, it’s something that satisfies its appetite for knowledge and in a technological age it procures an evolutionary advantage. The more knowledge you have the more capable you are - the more likely you are to survive.
ROBIN WHITE: Lee hopes to be one of the first to go to Mars. The person who finds life on Mars, if it’s there, will go down in history. They’ll also answer an important scientific question which is whether life, if it exists on other planets, is genetically the same as life on Earth, or whether it had a second genesis. Charlie Cockell, says whatever the answer, it’ll be profound.
CHARLES COCKELL: If we find life on Mars and it’s like life on Earth, what that tells us is that life was transferred between Earth and Mars in the early history of our planet and in fact we have extinct relatives on Mars or possibly relatives still alive today in the subsurface of Mars.
ROBIN WHITE: It could also mean that life came to both planets from elsewhere, or that DNA is the only way to write the book of life given the chemistry in our solar system. If we find Mars life that’s different from us that could mean that life is common in the universe because it’s occurred twice in our neighborhood. And if we don’t find it at all, it means evolution is very special. For The DNA Files I’m Robin White.
JOHN HOCKENBERRY: Thank you Robin. I’m John Hockenberry. If there is life on Mars, will NASA researchers know it when they see it? You’d think it would be obvious whether something was alive or not. But when you are talking about microbes its not always that simple. Researchers are preparing themselves for the difficulty of identifying live organisms from Mars by learning the limits of life on our own planet. The bugs they're looking for are called extremophiles, microbes that live in places that humans, plants and animals would find uncomfortable if not downright fatal. Like boiling hot springs in Yellowstone - or in shocked rocks in Arctic craters. Compared with what we're used to it's a pretty strange menagerie.
[Calliope Music]
CIRCUS ANNOUNCER: Welcome to the Bacterium and Bacillus Circus. Ladies and gentlemen step right up.
JOHN HOCKENBERRY: When people first hear about extremophiles there’s a temptation to think they’re freaks of nature, or perhaps stars of cable television. But scientists say even on Earth what’s "normal" for life may not be what we’ve always thought. For instance, some researchers suspect that pound for pound there may be more microbes living underground in rock than all life on the surface. In any event, I’ve come to this circus show to hear about some of the more far out microbes yet discovered.
CIRCUS BARKER: Stand back. Boys, girls, ladies and gentlemen. And now for the most incredible, most bizarre, the strangest... the most amazing microbe:
Pyrolobus fumarii.
Folks Pyrolobus fumarii lives at the bottom of the sea... in hot springs... at the hell-defying temperature of 221 degrees Fahrenheit. Nine degrees above boiling water.
For our next act, feast your eyes. Folks, this bacterium is happiest in Antarctic brine pools at a frosty 25 degrees Fahrenheit, almost as cold as your freezer:
Palolobus!
Ladies and Germs, the incomparable ferrosplama acidarmanus!
This feller calls home acid pools hundreds of times more burning, more deadly, more metal melting than acid in your car battery.
JOHN HOCKENBERRY: Hey... let’s get out of here before they start passing the hat.
They’re not called extremophiles for nothing! Research on these bugs help scientists learn about what to expect on other planets. Jack Farmer is a geology professor at Arizona State University and director of the school’s astrobiology program.
JACK FARMER: Twenty years ago when we headed off to Mars with the Viking Missions, we had a fairly limited and narrow perspective on what was possible for life. People pretty quickly abandoned the idea that there could be life there. Since that time, with all the advances in biology, with the advent of knowledge of extremophiles and this broader perspective on biology the door is opened up again pretty wide for many options for exploration on the planet Mars. An outcome of that is the origin of this new discipline called astrobiology.
JOHN HOCKENBERRY: If there’s life on Mars today its probably growing in protected springs or in caves, places the Viking mission didn’t visit. We sent producer Daniel Grossman to a cave on Earth where researchers are learning lessons that could help future Mars missions. He sent us this report from southern New Mexico.
DANIEL GROSSMAN A heavy steel grate marks the entrance to Spider Cave in Carlsbad, New Mexico. I’m joining a crew collecting samples from this cavern, a two-mile network of narrow passageways and bedroom-size chambers. But before we can we can enter, our guide Jim Werker must clear the way.
JIM WERKER: Yo, Bubba, where you at?
DANIEL GROSSMAN: A rattlesnake named Bubba, calls the entrance to Spider cave its home.
JIM WERKER: It looks like Bubba is in here.
DANIEL GROSSMAN: Jim Werker spots the rattler, but before he can nab it with a long stick, Bubba has slithered into a crevice. Lowering myself into the cave, I just hope the snake is more afraid of me than I am of it.
DANIEL GROSSMAN: We’re a team of 8, equipped with helmets, head lamps, rock cutting tools and sterile sample holders. One hundred feet below the blistering desert it’s cool and damp. Orange markers blaze a trail that weaves back and forth up and down past countless other passageways. Unlike the smooth, worn floor, the walls and ceilings are rough: like the surface of a well-cooked pan of brownies, colored in browns and grays.
JIM WERKER: I'm through…
DANIEL GROSSMAN: We stop in a long narrow chamber just high enough for me to stand without hitting the ceiling. University of New Mexico biologist Penelope Boston leads the today’s expedition. She takes out some bottles and tweezers and hands them to summer intern Katie Harris.
PENELOPE BOSTON: So Katie, you’ve probably not done anything like this before?
KATIE HARRIS: No. Not at all.
PENELOPE BOSTON: Well, the idea is to sterilize the tool we’re going to get the sample with. These are sterile inside. They’re not sterile outside. Neither are we.
DANIEL GROSSMAN: I expected the cave to have hard surfaces. But these walls are crumbly to the touch sort of like dry rotted wood. The comparison is apt because the researchers believe the rock is rotten—eaten by microbes. Boston holds a tweezers up and plucks a marble-size hunk of the brown crumbly rock.
PENELOPE BOSTON: Get right up under where you want and just kind of flick it in there. Did it go in? Yea? Good. Just put it in there. Some people have a real hard time with this.
DANIEL GROSSMAN: Until this team began their research, the crumbly crust found on cave walls like these was believed to be result of the chemical breakdown of the rock, a sort of rust build-up on the metal-rich stone. Penelope Boston and her team have shown that microbes are living in the rock, and she suspects that these bugs are actually eating it. If she can identify what these critters consume, the research could broaden the bounds of what conditions are known to support life. Penelope Boston.
PENELOPE BOSTON: All of the work that we are doing in these many different caves are allowing us to approach some of the kinds of problems that we are going to be facing looking for life on other planets. The first, of course is the fact that it’s not obvious life. This is very cryptic stuff. You look at it and it looks like rock, and it looks like dirt and mud.
DANIEL GROSSMAN: When not crawling through cave passages, professor Boston conducts laboratory research at the University of New Mexico in Albuquerque. One of her colleagues Diana Northrup is showing me electron microscope pictures of cave samples. One picture shows a curious object Northrup discovered not long ago.
DIANA NORTHRUP: I was actually running the scope that day. And I went, "Look what we've got!” And there were just like these chains and chains. It wasn’t an isolated one. If you look at some of this there 's chains all over the place. Penny was up in Boulder. I called her up and said, "Whoa, you won't believe what we found.” I was like, this is definitely an organism.
DANIEL GROSSMAN: It was unlike any mineral like she’d ever seen. And it had a suction cup-like structure resembling parts of certain bacteria. Visually it appears to be a living thing, but proving that isn't easy. Northrup has found DNA molecules in this rock, but they could come from other underground organisms. If she could grow the strange object in the lab that would be the most conclusive proof. But so far she's had no luck. Penelope Boston says the difficulty of making sense of cave samples from earth teaches an important lesson for investigators of life elsewhere.
PENELOPE BOSTON: If we here with all our laboratories and big teams of people have a hard time convincing people that this stuff has living organisms in it, it's going to be that much more difficult to demonstrate a biogenic character to something that we find on another planet.
DANIEL GROSSMAN: For The DNA Files, I’m Daniel Grossman
JOHN HOCKENBERRY: Thank you Dan. I'm John Hockenberry. Hard as it will be to figure out if we're actually looking at extraterrestrial life, it might be even harder to make sure our search for it doesn't have the unintended result of contaminating other pristine worlds. We’d, in that case, end up looking at our own footprints, so to speak, rather than something truly extra-terrestrial. Besides Mars, one of the places we’re most interested in exploring is Jupiter’s moon, Europa. Robert Pappalardo, of the University of Colorado at Boulder says Europa might have an ocean under its intriguing icy surface.
ROBERT PAPPALARDO: What Europa looks like from afar is somewhat like a cracked eggshell – or perhaps like a bloodshot eye - it's criss-crossed by lines - dark lines and bands somewhat reddish in color. When you zoom in on Europa, you see that these lines become ridges that crisscross the surface, sort of like looking at a plate of spaghetti that's been scrambled up.
JOHN HOCKENBERRY: The double ridges in the ice are probably cracks formed by warmer ice pushing up from down below. The fact that Europa rotates and also is so close to the giant planet Jupiter causes its ocean and ice sheet to be flexed and heated by a tremendous tidal pull.
With a possible tidal change of up to 30 meters, the ice cracks every half hour and it probably sounds something like this earthly ice sheet.
The possibility of an ocean and hydrothermal vents or even underwater volcanoes makes Europa another good candidate for harboring life. But how do we sample it without contaminating it? Some of the suggestions seem almost wacky
ROBERT PAPPALARDO: It’s been said that the best way to search for life on Europa could be to look for freeze dried fish in orbit.
JOHN HOCKENBERRY: The idea is that something crashing into the ice – a meteor or perhaps a ball dropped from a spacecraft - could spray detritus into orbit. The spacecraft could then check it for it for fish - or microbes - or whatever’s there without ever landing.
At the moment Europa’s being photographed by the Galileo spacecraft and there are plans to send another orbiter to map the whole surface. But what happens when these spacecraft end their missions? Galileo is scheduled to crash into the harsh environment of Jupiter. But the next orbiter is going to end its life on Europa itself.
ROBERT PAPPALARDO: There’s been a recommendation that the Europa orbiter receive a certain critical dosage of radiation so that the orbiter will have to live a certain number of days in orbit before it receives a total dosage enough to effectively sterilize the spacecraft. If any Earth organism is on board that spacecraft we’ll have to know that it’s dead before we allow it to crash into Europa.
JOHN HOCKENBERRY: And we can’t be too careful because any Earth bug could spread all over Europa in its ocean currents. The threat to Europa if contaminated by Earthly microbes is serious, but a concern closer to our hearts is the possibility of contamination going the other way: that some alien species in goop brought from other planets could run rampant on Earth. In the 1971 Robert Wise film, The Andromeda Strain, a satellite falls to Earth contaminated with microbes from outer space. A recovery team is sent to find the satellite in a small New Mexico town.
VOICE 1: the signals from the satellite are getting very strong…
VOICE 2: Sir! See that, lieutenant?
VOICE 1: See what, Frank?
VOICE 2: Over there by the fence — it looks like a body.
JOHN HOCKENBERRY: It is a body and there are others as well. To prevent the kind of plague depicted in the Andromeda Strain, NASA actually has a program to prevent microbes that might be brought back in samples from other planets from contaminating Earth. The agency says any soil samples brought to Earth will be secured in sealed containers. And to prevent anything live from hitchhiking back on the exterior of returning spacecraft, the agency plans to sterilize the vehicles in space, or transfer sealed sample containers from contaminated landers to clean spacecraft that would return to Earth.
NASA insists alien microbes are no cause for concern.
I'm back at New York's Museum of Natural History to chat with astrobiologist Michael Meyer. Dr. Meyer, you see, was once NASA's planetary protection officer.
MICHAEL MEYER: The job of Planetary Protection Officer has the coolest title of any job I ever had. It worked at parties. It worked at bars. Yes I am the Planetary Protection Officer. It was great.
JOHN HOCKENBERRY: You had a badge that said Planetary Protection Officer on it?
MICHAEL MEYER: I couldn’t figure out the paper work to get a badge. I thought it would have been proper to have one just in case I had to arrest someone for violating planetary protection protocol--although nobody knows what that is. Except NASA.
JOHN HOCKENBERRY: Which brings me to the question, what does the planetary protection officer do?
MICHAEL MEYER: Planetary Protection Officer. Reason why it's created is the concept that we’ll be exploring other planets. We should do that responsibly. What does that mean? One of them is, when you start talking about bringing a sample back from another planetary body where there’s even remote chance that there might be something living or have been alive on it, then you should make sure if you are going to bring that back that you don’t contaminate Earth. And when you go out and look at some other place that you don’t contaminate the world that you’re trying to study.
JOHN HOCKENBERRY: When we think about something coming from somewhere else being a contaminant what would be something we would fear most?
MICHAEL MEYER: Certainly the concern is that if you brought something back from another planet that you'd bring back something living. And somehow think wow! This is tasty! What a great Earth! And that it would take over. It's very far-fetched. But it's something where we know how to contain dangerous things. We can do it, and we know how to do it, so it would be stupid not to go through planetary protection.
JOHN HOCKENBERRY: I’ve been focusing on life on Earth and in our solar system, because that is the only life we’re ever likely to come in contact with, at least for the next hundred centuries or so. But many scientists believe that microbes, if not intelligent aliens, are living on planets orbiting distant starts. This speculation has gained considerable momentum since 1995 when the first extra-solar planet was discovered. Since then nearly 100 more have been reported. Paul Butler is one of the world’s leading extra-solar planet hunters. He says so far researchers have detected primarily two varieties.
PAUL BUTLER: They’re either the so called "hot Jupiters" that have these radical four-day orbits, they orbit a hundred times closer to their star than Jupiter does to the sun and as such they’re boiling hot; and then the other class of planets are Jupiter-like planets that are in oblong, or egg-shaped orbits. Both these types of planets are quite stunning, quite startling.
JOHN HOCKENBERRY: With existing rockets it would take tens of thousands of years to send a mission to get a look at even the nearest of these planets. Even so, Butler is certain the hot Jupiters are completely sterile, orbiting so sizzingly close to a star. The planets with eccentric orbits are another story. They are more temperate, though they alternate between quite hot and quite cold. Paul Butler.
PAUL BUTLER: So the fact that planets are in wacky orbits and might have extreme conditions probably doesn’t rule out the possibility of simple, single-celled creatures. We know how hardy they are. It probably does rule out the possibility of highly advanced creatures--multi-cellular organisms.
JOHN HOCKENBERRY: There may be planets out there with just the right orbit for complex life--relatively circular at just the right distance from a star. When I gaze up in the sky, I may be staring at one. But so far telescopes aren’t sensitive enough to detect a planet like ours. NASA is proposing to launch a flotilla of Planet-Finder satellites that could detect Earth-like planets, though it will probably be another generation before the project is launched. These satellites will also be able to gather spectral data from light coming from those distant planets, possibly detecting the first evidence of life beyond our solar system.
VOICE: After they had formed the earth, Odin, Vili, and Ve took the blood that was left from Imir and made the ocean in a ring. The three brothers lifted the skull of Imir and made the dome of the sky. They placed a dwarf at each of the four corners to support the sky high above the Earth…
JOHN HOCKENBERRY: In a little less than an hour, we’ve come a long way from creation tales like the Icelandic legend of Yawning Gap. Or have we? Brother Guy Consolmagno a Jesuit priest and a staff member of the Vatican Astronomical Observatory says searching for microbes on Mars, the origins of DNA, or life on the planets of distant stars is how scientists make sense of the awesome scale of the universe and the incredible wonder of creation.
GUY CONSOLMAGNO: These are all questions that are part of a great puzzle, a great game--and by playing this game I become a in some way little more intimately connected with the fellow at the other side of the board who’s been setting up the puzzles for me. And that’s God, that's the creator.
JOHN HOCKENBERRY: We may not all believe in a creator, but physicist Paul Davies says the need to explain creation may very well be one attribute that makes us human.
PAUL DAVIES: The search for the origin of life in some sense is a search for ourselves—who we are and what our place is in the great cosmic scheme of things. This is one of the big questions of existence.
JOHN HOCKENBERRY: Astrobiology—the search for life beyond Earth and the study of its origins—is inching forward with new findings about the great wonder that began some 13 billion years ago with the big bang. And even though knowing the answers won’t necessarily cure hunger or raise the standard of living, it gives me pleasure each time I learn a little more about where I’m from in this universe we call home. How about you? I’m John Hockenberry. Thank you for listening to The DNA Files.

CREDITS:
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, Life: How to Make a Cosmic Omelet — Genetics and Astrobiology, was produced by Daniel Grossman and engineered by Jane Pippick. The features on Europa and the Houghton Mars Project were produced by Robin White and engineered by Robin Wise. The program editor was Loretta Williams, and our host was John Hockenberry.
Special thanks to Hathfor Ingveson, Daniel McCallum and the Houghton Mars Project.
The opening feature, “Life in Hell,” was produced by Joe Jordan, 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.
Project Director, Jude Thilman. Marketing by Murray Street Enterprise. Legal services by Walter Hansel. and Spencer Weisbroth.
You can visit our website at www.dnafiles.org. Send your responses and letters to feedback@dnafiles.org. For tapes and transcripts, call 866-DNA-FILES (866-362-3453).
The Executive Producer is Bari Scott.
This has been a SoundVision Production, distributed by NPR, National Public Radio.

The DNA Files:
Unraveling the Mysteries of Genetics

As heard on National Public Radio

The Search for the Fountain of Youth
The Genetics of Aging and Longevity

Hosted by John Hockenberry

Transcript

SoundVision Productions
2991 Shattuck Avenue, Suite 304
Berkeley, California 94705-1872
(510) 486-1185
feedback@dnafiles.org
http://www.dnafiles.org

For further information about genetics and these programs, as well as the producers who brought you this series, visit the project web site at www.dnafiles.org.
Send your questions ab