Program 1: The Tree of Life

Who We Are (Part 3 of 10)

Dr. Karen Nelson and Dr. Craig Venter map the genome of Thermatoga, the microbes Dr. Karl Stetter discovered in Episode 1 of this podcast, and find convincing evidence that Thermatoga's origins are very close to the beginning of life on Earth.



{Title: Who We Are}

Narrator, Lillian Lehman: This is The Institute for Genomic Research, called TIGR, for short, one of the world's first genetic assembly lines. Here in Maryland, and around the world, the work that Carl Woese once did by himself, is done by super computers. One project currently underway at TIGR is the sequencing of the entire score, called the "genome," of Thermatoga, the microbe Karl Stetter discovered, living in boiling mud. Dr. Karen Nelson is in charge of the project. Her goal is to determine whether Thermatoga evolved well after life began, or if it is, in fact, one of the closest living relatives of the first life on Earth.

Doctor, Karen Nelson: I'm driven by being able to answer these questions that we could not answer five or ten years ago, with the technology we had five or ten years ago. And now we are sequencing entire genomes in one go, and to me, that's just absolutely amazing.

Narrator, Lillian Lehman: Nelson grew up on the island of Jamaica. Surrounded by nature, and dreaming of becoming a veterinarian.

Doctor, Karen Nelson: What I can remember as a kid, that my mother would allow us to have what ever pet we wanted, so we had pet turtles, pet parrots, pet kittens, dogs, you name it it was roaming around. I just had this absolute love, and at some point, I lost the desire to want to be a vet, and I had more of a desire to understand life, and how life worked, more.

Narrator, Lillian Lehman: Now, Nelson is a part of the greatest explosion ever in our understanding of how life works, brought about by the high-speed sequencing of DNA. A key part of the process is attaching a different colored dye, to each of the four different chemicals that make up DNA. {Reggae music plays.} It's as if the scientists were trying to decode the score of an incredibly long, complicated song. {Man singing: I said woman. Woman singing: I sing my song. Man singing: Oh, woman.} And someone came up with a clever way of attaching a different colored dye to each of the notes. {Woman singing: I sing my song. Man singing: Oh, woman.} When red dye is splashed on the notes, only the "C" notes turn red. {Man singing: Takes two to Tango.} When green is splashed on the notes, only the "A" notes turn green. {Man singing: What will our chances be?} And so on. Then the color coded score is loaded into a special color sensitive machine which sends the data to a computer. Scientists simply check out in what order the colors are displayed on the computer, and they know in what sequence the notes are being played. {Man singing: Said woman. Woman singing: Nine ,and my babe I'm so down. Man singing: Hey, woman. Woman singing: All alone, I carry my strain. Man singing: My little woman.} It sounds easy, but since scientists need a lot of DNA to work with, they have to start out with many copies of the same score. {Both singing: Takes two to tango. Takes two to dance? When the fever's over? What will our chances be?} And since they have to cut all of those copies into thousands of pieces short enough to manage, what the computer spits out in the end is numerous copies of the song, in many short segments, completely out of order. A real cacophony. So the hard work in this technique, called shotgun sequencing, is to go over all the pieces again, and again, and again, until you've isolated just one copy of the notes and put them in the correct order.

Doctor, Karen Nelson: It takes a lot of dedication, but the completed product is really a reward. To see thirty thousand sequences going into one single stretch of A's, G's, C's and T's. It's really a remarkable experience.

{Sounds of Slide changer clicking.}

Narrator, Lillian Lehman: With Thermatoga's genome sequenced, Nelson and her team began analyzing it, and were amazed by what they found. Even though Thermatoga has been classified among the bacteria, it also shares many genes with another branch of life the archaea.

Doctor, Karen Nelson: Although it's a bacteria, it has something that makes it more similar to this other branch of life. And this was a great surprise to us, because we didn't think that archaea would have any relationship like this with Thermatoga.

Narrator, Lillian Lehman: For Nelson, this was convincing evidence that Thermatoga came into being very close to the beginning of life on Earth. Before the bacteria, and archaea branches split apart.

Doctor, Karen Nelson: It's evident that Thermatoga belongs at the base of the tree.

Narrator, Lillian Lehman: The theory that Thermatoga is one of the closest living relatives of the first life on Earth is supported by the fact that every other species studied so far, including human beings, has some of the exact same DNA inside as Thermatoga. For many of us it's very difficult to except that we evolve from microbes, from germs. Perhaps one reason is that we, who live on a average of seventy years have such a limited grasp of time. Time like the four and a half billion years the Earth has been around. To try thinking of those four and a half billion years being sped up, until they all take place, in the amount of time we can comprehend. One twenty four hour day. If the entire history of the Earth were compressed into a single day, microbes would be the only form of life on Earth from before sunrise, {sounds of clocks, ticking and chiming}, until long after sunset. When would the first human beings appear on Earth? Not until a scant few seconds before midnight. Because human beings have been around for so little time, we are mostly made up of of inventions of other species including microbes. Microbes came up with inventions like, shutting down a few hours every day, which we inherited as sleep. As well as the basic mechanism that makes it possible for us to see. But even then, so what? One way or another, we have become marvelously capable, highly successful beings. And why on Earth should you care about how it happened. To find out why you should care, take a trip with one of the people who is helping to decode your DNA. TIGR founder, is Dr. Craig Venter, a consummate sailor, Venter and his crew are on their most ambitious journey ever, a voyage along the path that Columbus sailed from Spain to the Caribbean, and the New World. Venter has been responsible for key breakthroughs in today's genetic revolution. His newest project, is sequencing of the entire human genome. Venter attributes his accomplishments to his different way of looking at the world.

Doctor, Craig Venter: I think each of the breakthroughs that I've been lucky to come up with, with my team have been because I go outside the box. It's much easier to go outside the box, than trying to work up linear through a maze. You go outside and you go around the traffic instead of trying to go through it all. And I think just by doing that, I've been able to get places and see relationships that other people don't see.

Narrator, Lillian Lehman: Some of the genes that make up the human genome, have already been decoded by Venter and others. And perhaps the most remarkable things that research reveals, is how much we can learn about the inner workings of your body, from studying the inner workings of microbes.

Doctor, Craig Venter: It's clear every gene in the human body can be traced to genes in other species. We have sixty to eighty thousand human genes. A bacteria has two thousand genes. But we can trace back origins of all of our genes to things that we find in the archaea, and in the bacteria.

Narrator, Lillian Lehman: This ability to trace our genes to microbes, has given rise to new insights into what happens when things go wrong inside us. Take colon cancer, for instance. It turns out that many people who get colon cancer are missing a gene. How did we discover that?

Doctor, Craig Venter: Those genes were discovered in terms of their function by aligning the sequences in the computer that we have attained from human cells, to those from the bacteria that lives in our guts.

Narrator, Lillian Lehman: Recently, scientists found a gene in these bacteria. That keeps them from suffering genetic damage similar to cancer. Then Craig Venter and a colleague compared the bacterial genome, with a part of the human genome. And they discovered the exact same gene in human beings, and found that it helps keep us from getting cancer. People who are missing this gene can now learn that they are at risk long before cancer develops, knowledge that will save tens of thousands of lives.

Doctor, Karen Nelson: I know I have far greater respect for microorganisms now, because I realize microbes are revealing things about more complex organisms, and their allowing us to make advances in medicine, and are an intricate part of our systems. And there not useless creatures, their telling us about ourselves, what our genetic information means.

Narrator, Lillian Lehman: What microbes are ultimately telling us is that each of us contains within our genetic material, a written history of life on Earth. Take, for example, these human cells. From studying the DNA inside them, we have learned that cells like ours, were born over a billion years ago by a marriage between different species of bacteria.

Craig Doctor, Craig Venter: Our basic cells are a combination of multiple organisms. We're composites of bacteria, lineages from bacteria and other microorganisms. So it's compounding life on top of life. Each genome is the recorded history of life.

{Tropical music plays.}

Narrator, Lillian Lehman: After fifteen days at sea, Venter and his crew arrive at their ultimate destination the island of Antigua. Now its time to celebrate. In the very near future Venter, and his fellow scientists will arrive at another destination, the completion of the human genome. We are in the midst of an unimaginable explosion of knowledge about ourselves, and how we came to live on this planet.

Doctor, Craig Venter: The ultimate point of most science is to try and understand who we are, where we came from, how we fit into the environment, how we fit into the overall picture. Did we extend out from life of these simple bacteria? Did we come from outer space? You know, who are we? What are we? You go out of this context of the laboratory, and you go out and look at a tree, or a fish, or you know, things I encounter on the beach. And I look at them, and I realize that we share, you know, ninety percent, or more of our genes with those other species.

Narrator, Lillian Lehman: Our new understanding of DNA has shown us that, we are beings whose roots lie in the four billion years of life on Earth. But this discovery makes some of us uneasy, because ever since we began telling stories about our origins, almost all of our stories have portrayed us as beings apart.

Doctor, Craig Venter: We all want to feel special. And so much of science, and religion is, trying to define how we as humans are different from animals, from every other species. But now, this is not a time for story telling, this is a time where we can find out the facts. It's the first time in history, of science, of humanity, of religion, to have the tools, to have the ability to understand who we are, and were we came from.

Narrator, Lillian Lehman: In the coming years, we are certain to learn far more about the ways in which we're linked to the rest of life on Earth, and the ways in which we're unique. But no matter what lies ahead, it is unlikely the we human beings will ever again be able to view ourselves as a species apart. From one point of view, that may seem to diminish us. But from another point of view, we are gaining a deeper understanding of our role in what may be the most miraculous story in the universe. Life on Earth. And that new understanding can only serve to increase our sense of wonder.

{Fades to Black.}

Narrator, Lillian Lehman: Next time on Intimate Strangers, microbes are everywhere and our lives depend on it.

Scientist, Steve Giovannoni: Without microorganisms there could be no plant life, there could be no animal life, we would disappear.

Narrator, Lillian Lehman: Keepers of the Biosphere. Next time on Intimate Strangers.

(Transcript provided by Tyler Anderson)



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