The Origins of Life

[Thunderhaw Decorah]

The Origins of Life
A mineralogist believes he's discovered how life's early building blocks connected four billion years ago

    * By Helen Fields
    * Photographs by Amanda Lucidon
    * Smithsonian magazine, October 2010



_{A fossil collector since childhood, Bob Hazen has come up with new scenarios for life's beginnings on earth billions of years ago.}

A hilly green campus in Washington, D.C. houses two departments of the Carnegie Institution for Science: the Geophysical Laboratory and the quaintly named Department of Terrestrial Magnetism. When the institution was founded, in 1902, measuring the earth’s magnetic field was a pressing scientific need for makers of nautical maps. Now, the people who work here—people like Bob Hazen—have more fundamental concerns. Hazen and his colleagues are using the institution’s “pressure bombs”—breadbox-size metal cylinders that squeeze and heat minerals to the insanely high temperatures and pressures found inside the earth—to decipher nothing less than the origins of life.

Hazen, a mineralogist, is investigating how the first organic chemicals—the kind found in living things—formed and then found each other nearly four billion years ago. He began this research in 1996, about two decades after scientists discovered hydrothermal vents—cracks in the deep ocean floor where water is heated to hundreds of degrees Fahrenheit by molten rock. The vents fuel strange underwater ecosystems inhabited by giant worms, blind shrimp and sulfur-eating bacteria. Hazen and his colleagues believed the complex, high-pressure vent environment—with rich mineral deposits and fissures spewing hot water into cold—might be where life began.

Hazen realized he could use the pressure bomb to test this theory. The device (technically known as an “internally heated, gas media pressure vessel”) is like a super-high-powered kitchen pressure cooker, producing temperatures exceeding 1,800 degrees and pressures up to 10,000 times that of the atmosphere at sea level. (If something were to go wrong, the ensuing explosion could take out a good part of the lab building; the operator runs the pressure bomb from behind an armored barrier.)

In his first experiment with the device, Hazen encased a few milligrams of water, an organic chemical called pyruvate and a powder that produces carbon dioxide all in a tiny capsule made of gold (which does not react with the chemicals inside) that he had welded himself. He put three capsules into the pressure bomb at 480 degrees and 2,000 atmospheres. And then he went to lunch. When he took the capsules out two hours later, the contents had turned into tens of thousands of different compounds. In later experiments, he combined nitrogen, ammonia and other molecules plausibly present on the early earth. In these experiments, Hazen and his colleagues created all sorts of organic molecules, including amino acids and sugars—the stuff of life.

Hazen’s experiments marked a turning point. Before them, origins-of-life research had been guided by a scenario scripted in 1871 by Charles Darwin himself: “But if (and oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present, that a proteine compound was chemically formed ready to undergo still more complex changes....”

In 1952, Stanley Miller, a graduate student in chemistry at the University of Chicago, attempted to create Darwin’s dream. Miller set up a container holding water (representing the early ocean) connected by glass tubes to one containing ammonia, methane and hydrogen—a mixture scientists of the day thought approximated the early atmosphere. A flame heated the water, sending vapor upward. In the atmosphere flask, electric sparks simulated lightning. The experiment was such a long shot that Miller’s adviser, Harold Urey, thought it a waste of time. But over the next few days, the water turned deep red. Miller had created a broth of amino acids.

Forty-four years later, Bob Hazen’s pressure bomb experiments would show that not just lightning storms but also hydrothermal vents potentially could have sparked life. His work soon led him to a more surprising conclusion: the basic molecules of life, it turns out, are able to form in all sorts of places: near hydrothermal vents, volcanoes, even on meteorites. Cracking open space rocks, astrobiologists have discovered amino acids, compounds similar to sugars and fatty acids, and nucleobases found in RNA and DNA. So it’s even possible that some of the first building blocks of life on earth came from outer space.

Hazen’s findings came at an auspicious time. “A few years before, we would have been laughed out of the origins-of-life community,” he says. But NASA, then starting up its astrobiology program, was looking for evidence that life could have evolved in odd environments—such as on other planets or their moons. “NASA [wanted] justification for going to Europa, to Titan, to Ganymede, to Callisto, to Mars,” says Hazen. If life does exist there, it’s likely to be under the surface, in warm, high-pressure environments.

Back on earth, Hazen says that by 2000 he had concluded that “making the basic building blocks of life is easy.” A harder question: How did the right building blocks get incorporated? Amino acids come in multiple forms, but only some are used by living things to form proteins. How did they find each other?

http://www.smithsonianmag.com/science-nature/103003019.html

[Thunderhaw Decorah]

In a windowed corner of a lab building at the Carnegie Institution, Hazen is drawing molecules on a notepad and sketching the earliest steps on the road to life. “We’ve got a prebiotic ocean and down in the ocean floor, you’ve got rocks,” he says. “And basically there’s molecules here that are floating around in solution, but it’s a very dilute soup.” For a newly formed amino acid in the early ocean, it must have been a lonely life indeed. The familiar phrase “primordial soup” sounds rich and thick, but it was no beef stew. It was probably just a few molecules here and there in a vast ocean. “So the chances of a molecule over here bumping into this one, and then actually a chemical reaction going on to form some kind of larger structure, is just infinitesimally small,” Hazen continues. He thinks that rocks—whether the ore deposits that pile up around hydrothermal vents or those that line a tide pool on the surface—may have been the matchmakers that helped lonely amino acids find each other.

Rocks have texture, whether shiny and smooth or craggy and rough. Molecules on the surface of minerals have texture, too. Hydrogen atoms wander on and off a mineral’s surface, while electrons react with various molecules in the vicinity. An amino acid that drifts near a mineral could be attracted to its surface. Bits of amino acids might form a bond; form enough bonds and you’ve got a protein.

Back at the Carnegie lab, Hazen’s colleagues are looking into the first step in that courtship: Kateryna Klochko is preparing an experiment that—when combined with other experiments and a lot of math—should show how certain molecules stick to minerals. Do they adhere tightly to the mineral, or does a molecule attach in just one place, leaving the rest of it mobile and thereby increasing the chances it will link up to other molecules?

Klochko gets out a rack, plastic tubes and the liquids she needs. “It’s going to be very boring and tedious,” she warns. She puts a tiny dab of a powdered mineral in a four-inch plastic tube, then adds arginine, an amino acid, and a liquid to adjust the acidity. Then, while a gas bubbles through the solution, she waits...for eight minutes. The work may seem tedious indeed, but it takes concentration. “That’s the thing, each step is critical,” she says. “Each of them, if you make a mistake, the data will look weird, but you won’t know where you made a mistake.” She mixes the ingredients seven times, in seven tubes. As she works, “The Scientist” comes on the radio: “Nooooobody saaaaid it was easyyyy,” sings Coldplay vocalist Chris Martin.

After two hours, the samples go into a rotator, a kind of fast Ferris wheel for test tubes, to mix all night. In the morning, Klochko will measure how much arginine remains in the liquid; the rest of the amino acid will have stuck to the mineral powder’s tiny surfaces.

She and other researchers will repeat the same experiment with different minerals and different molecules, over and over in various combinations. The goal is for Hazen and his colleagues to be able to predict more complex interactions, like those that may have taken place in the earth’s early oceans.

How long will it take to go from studying how molecules interact with minerals to understanding how life began? No one knows. For one thing, scientists have never settled on a definition of life. Everyone has a general idea of what it is and that self-replication and passing information from generation to generation are key. Gerald Joyce, of the Scripps Research Institute in La Jolla, California, jokes that the definition should be “something like ‘that which is squishy.’”

Hazen’s work has implications beyond the origins of life. “Amino-acids-sticking-to-crystals is everywhere in the environment,” he says. Amino acids in your body stick to titanium joints; films of bacteria grow inside pipes; everywhere proteins and minerals meet, amino acids are interacting with crystals. “It’s every rock, it’s every soil, it’s the walls of the building, it’s microbes that interact with your teeth and bones, it’s everywhere,” Hazen says.

At his weekend retreat overlooking the Chesapeake Bay, Hazen, 61, peers through binoculars at some black-and-white ducks bobbing around in circles and stirring the otherwise still water. He thinks they’re herding fish—a behavior he’s never seen before. He calls for his wife, Margee, to come take a look: “There’s this really interesting phenomenon going on with the buffleheads!”

[Thunderhaw Decorah]

Living room shelves hold things the couple has found nearby: beach glass, a basketful of minerals, and fossilized barnacles, coral and great white shark teeth. A 15-million-year-old whale jawbone, discovered on the beach at low tide, is spread out in pieces on the dining room table, where Hazen is cleaning it. “It was part of a living, breathing whale when this was a tropical paradise,” he says.

Hazen traces his interest in prehistory to his Cleveland childhood, growing up not far from a fossil quarry. “I collected my first trilobite when I was 9 or 10,” he says. “I just thought they were cool,” he says of the marine arthropods that went extinct millions of years ago. After his family moved to New Jersey, his eighth-grade science teacher encouraged him to check out the minerals in nearby towns. “He gave me maps and he gave me directions and he gave me specimens, and my parents would take me to these places,” says Hazen. “So I just got hooked.”

After taking a paleontology class together at the Massachusetts Institute of Technology, Hazen and Margee Hindle, his future wife, started collecting trilobites. They now have thousands. “Some of them are incredibly cute,” says Hazen. “This bulbous nose—you want to hug them.”

There are trilobites all over Hazen’s office and a basement guest room at the Hazens’ Bethesda, Maryland, home—they cover shelves and fill desk drawers and cabinets. There’s even trilobite art by his now grown children, Ben, 34, who is studying to be an art therapist, and Liz, 32, a teacher. “This is the ultimate cute trilobite,” he says, reaching into a cabinet and taking out a Paralejurus. “How can you not love that?”

Hazen calls himself a “natural collector.” After he and Margee bought a picture frame that just happened to hold a photograph of a brass band, they started buying other pictures of brass bands; eventually they wrote a history of brass bands—Music Men—and a time in America when almost every town had its own. (Bob has played trumpet professionally since 1966.) He has also published a collection of 18th-and 19th-century poems about geology, most of which, he says, are pretty bad (“And O ye rocks! schist, gneiss, whate’er ye be/Ye varied strata, names too hard for me”). But the couple tend not to hold on to things. “As weird as this sounds, as a collector, I’ve never been acquisitive,” Bob says. “To have been able to hold them and study them up close is really a privilege. But they shouldn’t be in private hands.” Which is why the Hazen Collection of Band Photographs and Ephemera, ca. 1818-1931, is now at the National Museum of American History. Harvard has the mineral collection he started in eighth grade, and the Hazens are in the process of donating their trilobites to the National Museum of Natural History.

After considering, for some time, how minerals may have helped life evolve, Hazen is now investigating the other side of the equation: how life spurred the development of minerals. He explains that there were only about a dozen different minerals—including diamonds and graphite—in dust grains that pre-date the solar system. Another 50 or so formed as the sun ignited. On earth, volcanoes emitted basalt, and plate tectonics made ores of copper, lead and zinc. “The minerals become players in this sort of epic story of exploding stars and planetary formation and the triggering of plate tectonics,” he says. “And then life plays a key role.” By introducing oxygen into the atmosphere, photosynthesis made possible new kinds of minerals—turquoise, azurite and malachite, for example. Mosses and algae climbed onto land, breaking down rock and making clay, which made bigger plants possible, which made deeper soil, and so on. Today there are about 4,400 known minerals—more than two-thirds of which came into being only because of the way life changed the planet. Some of them were created exclusively by living organisms.

Everywhere he looks, Hazen says, he sees the same fascinating process: increasing complexity. “You see the same phenomena over and over, in languages and in material culture—in life itself. Stuff gets more complicated.” It’s the complexity of the hydrothermal vent environment—gushing hot water mixing with cold water near rocks, and ore deposits providing hard surfaces where newly formed amino acids could congregate—that makes it such a good candidate as a cradle of life. “Organic chemists have long used test tubes,” he says, “but the origin of life uses rocks, it uses water, it uses atmosphere. Once life gets a foothold, the fact that the environment is so variable is what drives evolution.” Minerals evolve, life arises and diversifies, and along come trilobites, whales, primates and, before you know it, brass bands.

Helen Fields has written about snakehead fish and the discovery of soft tissue in dinosaur fossils for Smithsonian. Amanda Lucidon is based in Washington, D.C.

A hilly green campus in Washington, D.C. houses two departments of the Carnegie Institution for Science: the Geophysical Laboratory and the quaintly named Department of Terrestrial Magnetism. When the institution was founded, in 1902, measuring the earth’s magnetic field was a pressing scientific need for makers of nautical maps. Now, the people who work here—people like Bob Hazen—have more fundamental concerns. Hazen and his colleagues are using the institution’s “pressure bombs”—breadbox-size metal cylinders that squeeze and heat minerals to the insanely high temperatures and pressures found inside the earth—to decipher nothing less than the origins of life.

Hazen, a mineralogist, is investigating how the first organic chemicals—the kind found in living things—formed and then found each other nearly four billion years ago. He began this research in 1996, about two decades after scientists discovered hydrothermal vents—cracks in the deep ocean floor where water is heated to hundreds of degrees Fahrenheit by molten rock. The vents fuel strange underwater ecosystems inhabited by giant worms, blind shrimp and sulfur-eating bacteria. Hazen and his colleagues believed the complex, high-pressure vent environment—with rich mineral deposits and fissures spewing hot water into cold—might be where life began.

Hazen realized he could use the pressure bomb to test this theory. The device (technically known as an “internally heated, gas media pressure vessel”) is like a super-high-powered kitchen pressure cooker, producing temperatures exceeding 1,800 degrees and pressures up to 10,000 times that of the atmosphere at sea level. (If something were to go wrong, the ensuing explosion could take out a good part of the lab building; the operator runs the pressure bomb from behind an armored barrier.)

In his first experiment with the device, Hazen encased a few milligrams of water, an organic chemical called pyruvate and a powder that produces carbon dioxide all in a tiny capsule made of gold (which does not react with the chemicals inside) that he had welded himself. He put three capsules into the pressure bomb at 480 degrees and 2,000 atmospheres. And then he went to lunch. When he took the capsules out two hours later, the contents had turned into tens of thousands of different compounds. In later experiments, he combined nitrogen, ammonia and other molecules plausibly present on the early earth. In these experiments, Hazen and his colleagues created all sorts of organic molecules, including amino acids and sugars—the stuff of life.

Hazen’s experiments marked a turning point. Before them, origins-of-life research had been guided by a scenario scripted in 1871 by Charles Darwin himself: “But if (and oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present, that a proteine compound was chemically formed ready to undergo still more complex changes....”

In 1952, Stanley Miller, a graduate student in chemistry at the University of Chicago, attempted to create Darwin’s dream. Miller set up a container holding water (representing the early ocean) connected by glass tubes to one containing ammonia, methane and hydrogen—a mixture scientists of the day thought approximated the early atmosphere. A flame heated the water, sending vapor upward. In the atmosphere flask, electric sparks simulated lightning. The experiment was such a long shot that Miller’s adviser, Harold Urey, thought it a waste of time. But over the next few days, the water turned deep red. Miller had created a broth of amino acids.

Forty-four years later, Bob Hazen’s pressure bomb experiments would show that not just lightning storms but also hydrothermal vents potentially could have sparked life. His work soon led him to a more surprising conclusion: the basic molecules of life, it turns out, are able to form in all sorts of places: near hydrothermal vents, volcanoes, even on meteorites. Cracking open space rocks, astrobiologists have discovered amino acids, compounds similar to sugars and fatty acids, and nucleobases found in RNA and DNA. So it’s even possible that some of the first building blocks of life on earth came from outer space.

Hazen’s findings came at an auspicious time. “A few years before, we would have been laughed out of the origins-of-life community,” he says. But NASA, then starting up its astrobiology program, was looking for evidence that life could have evolved in odd environments—such as on other planets or their moons. “NASA [wanted] justification for going to Europa, to Titan, to Ganymede, to Callisto, to Mars,” says Hazen. If life does exist there, it’s likely to be under the surface, in warm, high-pressure environments.

Back on earth, Hazen says that by 2000 he had concluded that “making the basic building blocks of life is easy.” A harder question: How did the right building blocks get incorporated? Amino acids come in multiple forms, but only some are used by living things to form proteins. How did they find each other?

In a windowed corner of a lab building at the Carnegie Institution, Hazen is drawing molecules on a notepad and sketching the earliest steps on the road to life. “We’ve got a prebiotic ocean and down in the ocean floor, you’ve got rocks,” he says. “And basically there’s molecules here that are floating around in solution, but it’s a very dilute soup.” For a newly formed amino acid in the early ocean, it must have been a lonely life indeed. The familiar phrase “primordial soup” sounds rich and thick, but it was no beef stew. It was probably just a few molecules here and there in a vast ocean. “So the chances of a molecule over here bumping into this one, and then actually a chemical reaction going on to form some kind of larger structure, is just infinitesimally small,” Hazen continues. He thinks that rocks—whether the ore deposits that pile up around hydrothermal vents or those that line a tide pool on the surface—may have been the matchmakers that helped lonely amino acids find each other.

Rocks have texture, whether shiny and smooth or craggy and rough. Molecules on the surface of minerals have texture, too. Hydrogen atoms wander on and off a mineral’s surface, while electrons react with various molecules in the vicinity. An amino acid that drifts near a mineral could be attracted to its surface. Bits of amino acids might form a bond; form enough bonds and you’ve got a protein.

Back at the Carnegie lab, Hazen’s colleagues are looking into the first step in that courtship: Kateryna Klochko is preparing an experiment that—when combined with other experiments and a lot of math—should show how certain molecules stick to minerals. Do they adhere tightly to the mineral, or does a molecule attach in just one place, leaving the rest of it mobile and thereby increasing the chances it will link up to other molecules?

Klochko gets out a rack, plastic tubes and the liquids she needs. “It’s going to be very boring and tedious,” she warns. She puts a tiny dab of a powdered mineral in a four-inch plastic tube, then adds arginine, an amino acid, and a liquid to adjust the acidity. Then, while a gas bubbles through the solution, she waits...for eight minutes. The work may seem tedious indeed, but it takes concentration. “That’s the thing, each step is critical,” she says. “Each of them, if you make a mistake, the data will look weird, but you won’t know where you made a mistake.” She mixes the ingredients seven times, in seven tubes. As she works, “The Scientist” comes on the radio: “Nooooobody saaaaid it was easyyyy,” sings Coldplay vocalist Chris Martin.

After two hours, the samples go into a rotator, a kind of fast Ferris wheel for test tubes, to mix all night. In the morning, Klochko will measure how much arginine remains in the liquid; the rest of the amino acid will have stuck to the mineral powder’s tiny surfaces.

She and other researchers will repeat the same experiment with different minerals and different molecules, over and over in various combinations. The goal is for Hazen and his colleagues to be able to predict more complex interactions, like those that may have taken place in the earth’s early oceans.

How long will it take to go from studying how molecules interact with minerals to understanding how life began? No one knows. For one thing, scientists have never settled on a definition of life. Everyone has a general idea of what it is and that self-replication and passing information from generation to generation are key. Gerald Joyce, of the Scripps Research Institute in La Jolla, California, jokes that the definition should be “something like ‘that which is squishy.’”

Hazen’s work has implications beyond the origins of life. “Amino-acids-sticking-to-crystals is everywhere in the environment,” he says. Amino acids in your body stick to titanium joints; films of bacteria grow inside pipes; everywhere proteins and minerals meet, amino acids are interacting with crystals. “It’s every rock, it’s every soil, it’s the walls of the building, it’s microbes that interact with your teeth and bones, it’s everywhere,” Hazen says.

At his weekend retreat overlooking the Chesapeake Bay, Hazen, 61, peers through binoculars at some black-and-white ducks bobbing around in circles and stirring the otherwise still water. He thinks they’re herding fish—a behavior he’s never seen before. He calls for his wife, Margee, to come take a look: “There’s this really interesting phenomenon going on with the buffleheads!”

Living room shelves hold things the couple has found nearby: beach glass, a basketful of minerals, and fossilized barnacles, coral and great white shark teeth. A 15-million-year-old whale jawbone, discovered on the beach at low tide, is spread out in pieces on the dining room table, where Hazen is cleaning it. “It was part of a living, breathing whale when this was a tropical paradise,” he says.

Hazen traces his interest in prehistory to his Cleveland childhood, growing up not far from a fossil quarry. “I collected my first trilobite when I was 9 or 10,” he says. “I just thought they were cool,” he says of the marine arthropods that went extinct millions of years ago. After his family moved to New Jersey, his eighth-grade science teacher encouraged him to check out the minerals in nearby towns. “He gave me maps and he gave me directions and he gave me specimens, and my parents would take me to these places,” says Hazen. “So I just got hooked.”

After taking a paleontology class together at the Massachusetts Institute of Technology, Hazen and Margee Hindle, his future wife, started collecting trilobites. They now have thousands. “Some of them are incredibly cute,” says Hazen. “This bulbous nose—you want to hug them.”

There are trilobites all over Hazen’s office and a basement guest room at the Hazens’ Bethesda, Maryland, home—they cover shelves and fill desk drawers and cabinets. There’s even trilobite art by his now grown children, Ben, 34, who is studying to be an art therapist, and Liz, 32, a teacher. “This is the ultimate cute trilobite,” he says, reaching into a cabinet and taking out a Paralejurus. “How can you not love that?”

Hazen calls himself a “natural collector.” After he and Margee bought a picture frame that just happened to hold a photograph of a brass band, they started buying other pictures of brass bands; eventually they wrote a history of brass bands—Music Men—and a time in America when almost every town had its own. (Bob has played trumpet professionally since 1966.) He has also published a collection of 18th-and 19th-century poems about geology, most of which, he says, are pretty bad (“And O ye rocks! schist, gneiss, whate’er ye be/Ye varied strata, names too hard for me”). But the couple tend not to hold on to things. “As weird as this sounds, as a collector, I’ve never been acquisitive,” Bob says. “To have been able to hold them and study them up close is really a privilege. But they shouldn’t be in private hands.” Which is why the Hazen Collection of Band Photographs and Ephemera, ca. 1818-1931, is now at the National Museum of American History. Harvard has the mineral collection he started in eighth grade, and the Hazens are in the process of donating their trilobites to the National Museum of Natural History.

After considering, for some time, how minerals may have helped life evolve, Hazen is now investigating the other side of the equation: how life spurred the development of minerals. He explains that there were only about a dozen different minerals—including diamonds and graphite—in dust grains that pre-date the solar system. Another 50 or so formed as the sun ignited. On earth, volcanoes emitted basalt, and plate tectonics made ores of copper, lead and zinc. “The minerals become players in this sort of epic story of exploding stars and planetary formation and the triggering of plate tectonics,” he says. “And then life plays a key role.” By introducing oxygen into the atmosphere, photosynthesis made possible new kinds of minerals—turquoise, azurite and malachite, for example. Mosses and algae climbed onto land, breaking down rock and making clay, which made bigger plants possible, which made deeper soil, and so on. Today there are about 4,400 known minerals—more than two-thirds of which came into being only because of the way life changed the planet. Some of them were created exclusively by living organisms.

Everywhere he looks, Hazen says, he sees the same fascinating process: increasing complexity. “You see the same phenomena over and over, in languages and in material culture—in life itself. Stuff gets more complicated.” It’s the complexity of the hydrothermal vent environment—gushing hot water mixing with cold water near rocks, and ore deposits providing hard surfaces where newly formed amino acids could congregate—that makes it such a good candidate as a cradle of life. “Organic chemists have long used test tubes,” he says, “but the origin of life uses rocks, it uses water, it uses atmosphere. Once life gets a foothold, the fact that the environment is so variable is what drives evolution.” Minerals evolve, life arises and diversifies, and along come trilobites, whales, primates and, before you know it, brass bands.

Helen Fields has written about snakehead fish and the discovery of soft tissue in dinosaur fossils for Smithsonian. Amanda Lucidon is based in Washington, D.C.

[archaeologist]

the problem is 1. he will never be able to verify if his method is correct; 2. he is involved and manipulated the experiment; 3. he will never know if his ingredients are the correct ones.

i already know he is wrong and is chasing an illusion.

After considering, for some time, how minerals may have helped life evolve, Hazen is now investigating the other side of the equation: how life spurred the development of minerals. He explains that there were only about a dozen different minerals—including diamonds and graphite—in dust grains that pre-date the solar system. Another 50 or so formed as the sun ignited. On earth, volcanoes emitted basalt, and plate tectonics made ores of copper, lead and zinc. “The minerals become players in this sort of epic story of exploding stars and planetary formation and the triggering of plate tectonics,” he says. “And then life plays a key role.” By introducing oxygen into the atmosphere, photosynthesis made possible new kinds of minerals—turquoise, azurite and malachite, for example. Mosses and algae climbed onto land, breaking down rock and making clay, which made bigger plants possible, which made deeper soil, and so on. Today there are about 4,400 known minerals—more than two-thirds of which came into being only because of the way life changed the planet. Some of them were created exclusively by living organisms.

he cannot prove any of this and it is tiresome to read these articles as modern scientists and humans were not at creation thus they can never say what took place in the beginning without the Bible. everything is merely his subjective opinion which means squat.

[Rebecca]

he cannot prove any of this and it is tiresome to read these articles as modern scientists and humans were not at creation thus they can never say what took place in the beginning without the Bible.

Neither were the very human beings who wrote the Bible and were simply passing on regional folk tales at the time. You keep forgetting that.  Interesting how you have a much lower standard of proof for the ancient scribes.

[Robert0326]

Archeologist is bitter about science because science takes away the need to believe in god.

[Andrew Waters]

Robert0326 writes:

''Archeologist is bitter about science because science takes away the need to believe in god.''

No, science doesn't take away the need to believe in God. Atheists may believe that. Some scientists do believe that a creator exists. It's just that it's outside the realm of human understanding and will always be.

My view tells me it is much easier to say some super intelligences with thousands, maybe hundreds of thousands of years of advanced genetics behind them accomplished the feat of ''assembling'' life on this planet. What evolutionists call adapting to their environment and natural selection is putting the cart before the horse. Life didn't need to adapt, it was always programmed to do so from the very beginning.

[Robert0326]

So you think little green or gray men started life on this planet?  I really don't know which is more far-fetched...  God or aliens. 


Evolutionary Adaptation in the Human Lineage

By: Stephen F. Schaffner, Ph.D. (Broad Institute of MIT and Harvard, Cambridge, MA, USA) & Pardis C. Sabeti M.D., D.Phil.  (Harvard University, Cambridge, MA) © 2008 Nature Education
Citation: Schaffner, S. & Sabeti, P. (2008) Evolutionary adaptation in the human lineage. Nature Education 1(1)
Are you lactose intolerant? Many people are. In fact, the ability to digest lactose may be an example of adaptive evolution in the human lineage.

   1. 1Introduction
   2. 2 Advantageous Alleles and Selective Sweep
   3. 3 Evidence of Positive Selection in Humans
         1. 3.1 Lactose Tolerance
         2. 3.2 Malaria Resistance
         3. 3.3 Pigmentation
   4. 4 Signals for Positive Selection Mark the First Step to Understanding the Story of These Loci
   5. 5References and Recommended Reading

 

Positive natural selection, or the tendency of beneficial traits to increase in prevalence (frequency) in a population, is the driving force behind adaptive evolution. For a trait to undergo positive selection, it must have two characteristics. First, the trait must be beneficial; in other words, it must increase the organism's probability of surviving and reproducing. Second, the trait must be heritable so that it can be passed to an organism's offspring. Beneficial traits are extremely varied and may include anything from protective coloration, to the ability to utilize a new food source, to a change in size or shape that might be useful in a particular environment. If a trait results in more offspring who share the trait, then that trait is more likely to become common in the population than a trait that arises randomly. At the molecular level, selection occurs when a particular DNA variant becomes more common because of its effect on the organisms that carry it.

Charles Darwin and Alfred Wallace (1858) famously proposed that positive selection could explain the many marvelous adaptations that suit organisms to their environments and lifestyles, and this simple process remains the central explanation for all evolutionary adaptation yet today. Positive selection is by no means the only component of evolution, however. In humans, at least, the great majority of mutations are thought to be selectively neutral, conferring neither benefit nor cost on their bearers (Hellmann et al., 2003). The frequency of some of these neutral genetic variants (alleles) increases simply by chance, and the resulting "genetic drift" is thought to be the most common process in human evolution (Kimura, 1968). Moreover, when selection does occur, it is most often in the form of negative, or purifying, selection, which removes new deleterious mutations as they arise, rather than promoting the spread of new traits (Kreitman, 2000).
Advantageous Alleles and Selective Sweep
A selective sweep.
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Figure 1

As advantageous alleles that are under positive selection increase in prevalence, these alleles leave distinctive signatures, or patterns of genetic variation, in the DNA sequence. Consider a population of individuals for which, before selection, there are hundreds of thousands of varied chromosomes in the population, all with different combinations of genetic variants. Now, say that an advantageous allele arises as a mutation on one copy of a chromosome. Through succeeding generations, the descendants of this copy, including the selected allele and nearby "hitchhiking" alleles, become more and more common through a process called a "selective sweep" (Figure 1). Note that the entire chromosome is not passed down as a unit, however; rather, because of recombination, segments of the chromosome are inherited. Thus, while the selected allele and hitchhiking alleles increase in prevalence in a selective sweep, at the same time, the segment that includes the selected allele is slowly reduced in size by recombination. Investigators are interested in the types of signals that can be detected in a selective sweep, as well as their properties and technical challenges (Nielsen, 2005; Sabeti et al., 2006).
Evidence of Positive Selection in Humans

Within the last decade, our ability to probe our own species for evidence of selection has increased dramatically due to the flood of genetic data that have been generated. Starting with the complete sequence of the human genome (Lander et al., 2001), which provides a framework and standard reference for all human genetics, key data sets include the completed or near-completed genomes of several related species (e.g., chimpanzee, macaque, gorilla, and orangutan), a public database of known genetic variants in humans, and surveys of genetic variation in hundreds of individuals in multiple populations (Chimpanzee Sequencing and Analysis Consortium, 2005; Gibbs et al., 2007; Sherry et al., 2001; International HapMap Consortium, 2007). With these new data, it is now possible to scan the entire human genome in search of signals of natural selection.

Although the study of natural selection in humans is still in an early stage, the new data, building on decades of earlier work, are beginning to reveal some of the landscape of selection in our species. In fact, researchers have identified many genetic loci at which selection has likely occurred, and some of the selective pressures involved have been elucidated. Three significant forces that have been identified thus far include changes in diet, changes in climate, and infectious disease.
Lactose Tolerance

The domestication of plants and animals roughly 10,000 years ago profoundly changed human diets, and it gave those individuals who could best digest the new foods a selective advantage. The best understood of these adaptations is lactose tolerance (Sabeti et al., 2006; Bersaglieri et al., 2004). The ability to digest lactose, a sugar found in milk, usually disappears before adulthood in mammals, and the same is true in most human populations. However, for some people, including a large fraction of individuals of European descent, the ability to break down lactose persists because of a mutation in the lactase gene (LCT). This suggests that the allele became common in Europe because of increased nutrition from cow's milk, which became available after the domestication of cattle. This hypothesis was eventually confirmed by Todd Bersaglieri and his colleagues, who demonstrated that the lactase persistence allele is common in Europeans (nearly 80% of people of European descent carry this allele), and it has evidence of a selective sweep spanning roughly 1 million base pairs (1 megabase). Indeed, lactose tolerance is one of the strongest signals of selection seen anywhere in the genome. Sarah Tishkoff and colleagues subsequently found a distinct LCT mutation also conferring lactose tolerance, in this case in African pastoralist populations, suggesting the action of convergent evolution (Tishkoff et al., 2007).
Malaria Resistance

The development of agriculture also changed the selective pressures on humans in another way: Increased population density made the transmission of infectious diseases easier, and it probably expanded the already substantial role of pathogens as agents of natural selection. That role is reflected in the traces left by selection in human genetic diversity; multiple loci associated with disease resistance have been identified as probable sites of selection. In most cases, the resistance is to the same disease—malaria (Kwiatkowski, 2005).

Malaria's power to drive selection is not surprising, as it is one of the human population's oldest diseases and remains one of the greatest causes of morbidity and mortality in the world today, infecting hundreds of millions of people and killing 1 to 2 million children in Africa each year. In fact, malaria was responsible for the first case of positive selection demonstrated genetically in humans. In the 1940s and 1950s, J. B. S. Haldane and A. C. Allison demonstrated that the geographical distribution of the sickle-cell mutation (Glu6Val) in the beta hemoglobin gene (HBB) was limited to Africa and correlated with malaria endemicity, and that individuals who carry the sickle-cell trait are resistant to malaria (Allison, 1954). Since then, many more alleles for malaria resistance have shown evidence of selection, including more mutations in HBB, as well as mutations causing other red blood cell disorders (e.g., a-thalassemia, G6PD deficiency, and ovalocytosis) (Kwiatkowski, 2005).

Malaria also drove one of the most striking genetic differences between populations. This difference involves the Duffy antigen gene (FY), which encodes a membrane protein used by the Plasmodium vivax malaria parasite to enter red blood cells, a critical first step in its life cycle. A mutation in FY that disrupts the protein, thus conferring protection against P. vivax malaria, is at a frequency of 100% throughout most of sub-Saharan Africa and virtually absent elsewhere; such an extreme difference in allele frequency is very rare for humans.
Pigmentation

As proto-Europeans and Asians moved northward out of Africa, they experienced less sunlight and colder temperature, new environmental forces that exerted selective pressure on the migrants. Exactly why reduced sunlight should be a potent selective force is still debated, but it has become clear that humans have experienced positive selection at numerous genes to finely tune the amount of skin pigment they produce, depending on the amount of sunlight exposure.

The role of selection in controlling human pigmentation is not a new idea; in fact, it was first advanced by William Wells in 1813, long before Darwin's formulation of natural selection (Wells, 1818). In recent years, signals of positive selection have been identified in many genes, with some signals solely in Europeans, some solely in Asians, and some shared across both continents (Lao et al., 2007; McEvoy et al., 2006; Williamson et al., 2007). Evidence for purifying selection has also been found to maintain dark skin color in Africa, where sunlight exposure is great.

A good example of selection for lighter pigmentation is the gene SLC24A5, which was one of the first to be characterized. Rebecca Lamason and her colleagues identified a mutation in the zebrafish homologue of this gene that is responsible for pigmentation phenotype. The investigators then demonstrated that a human variant in the gene explains roughly one-third of the variation in pigmentation between Europeans and West Africans, and that the European variant had likely been a target of selection (Lamason et al., 2005). In related work, Angela Hancock and her colleagues examined many genes involved in metabolism, and they showed that alleles of these genes show evidence of positive selection and correlate strongly with climate, suggesting that humans adapted to cooler climates by changing their metabolic rates (Hancock et al., 2008).
Signals for Positive Selection Mark the First Step to Understanding the Story of These Loci
Characterizing signals of selection in humans.
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Figure 2

While these instances of selection illustrate the power this line of research has to answer important biological and historical questions, in most cases, little or nothing of the underlying story is understood. For the great majority of selective sweeps, the pressure that drove selection, the trait selected for, and even the specific gene involved are unknown. Understanding these will require case-by-case study, identifying the possible causal mutations within each region based on strength of signal and function (e.g., mutations that alter amino acids or gene regulatory regions), and then finding the biological effects of each.

Such detailed investigations are underway, and they are intriguing. For example, a strong signal of selection in Asia localizes to amino acid substitution in the gene EDAR Sabeti et al., 2007). Mutations in EDAR cause defects in the development of hair, teeth, and exocrine glands in both mice and humans. Meanwhile, there is also evidence for selection at other genes in the same pathway in humans, as well as in stickleback fish (Colosimo et al., 2005), where the pathway regulates scale development. The phenotypic variation for this mutation is only just being elucidated, but it has already been linked to thicker head hair in Asia and has been shown to affect gene activity in the molecular pathway (Bryk et al., 2008; Fujimoto et al., 2008), although what trait was actually under selection is not yet clear. In another case, Scott Williamson and his colleagues found the strongest signal of selection in Europe and Asia at the gene DTNA, a component of the dystrophin complex (Williamson et al., 2007). While the target polymorphism and genetic variation have yet to be elucidated, the dystrophin complex is known to be important in the architecture of muscle tissue, as well as in the pathogenesis of many infectious agents, including arenaviruses and mycobacterium leprae. Another candidate gene for selection, LARGE, is also important for dystrophin function, and it has been shown to be critical for entry of various arenaviruses, including Lassa virus (Sabeti et al., 2007).

Understanding the biology behind these cases, and the many others like them, will not be easy, and it will require contributions from diverse fields, including genetics, molecular biology, developmental biology, and the study of model organisms (Figure 2). Nevertheless, the potential rewards are high. Through the study of natural selection in humans, researchers hope to learn more about how our species has changed over time, about the challenges the species has faced and how it has overcome them, and about past and present causes of disease.

[Andrew Waters]

Robert0326 asks and says:
''So you think little green or gray men started life on this planet? I really don't know which is more far-fetched... God or aliens.''

A creator or two or three is posited here. That  makes it an intelligence.Your little green or gray men is best suited for your explanation of evolution in some important areas. Speaking of which astronomers will take issue with you calling their favorite extraterrestrial search as little green or gray men. I'm sure I told you this a few months back.)

If astronomers find extraterrestials somewhere what do you think evolutionists will make of all that?  The religious folks will say God created all that stuff out there and the evolutionists will say no, evolution did it; without telling anyone how this feat was accomplished...just like the religious folks. Yes Robert that makes you a fundamentalist; not the churchgoing kind but the scientific kind.

By the way I see you didn't read enough of your posted article to see what they don't know?  Keep trying dude, you may pick up on it one of these days...unless of course you refuse to rid yourself of your dogmatism. In which case... .

[Robert0326]

Are you saying astronomers believe aliens started life here?  What dogmatism are you speaking of?  I guess if we find aliens on other worlds we could just ask them.  No need for conjecture on our end.  But of course the religious wouldn't believe them if they didn't mention some supernatural being.  If they were more advanced than we are, which is likely, they probably wouldn't even consider a supernatural being responsible for their creation.  They may have given up such foolishness ages ago.

[Andrew Waters]

Robert0326:

''Are you saying astronomers believe aliens started life here?''

Not saying that at all Robert. However there are a few scientists who believe in panspermia; i.e., that life came here horseback-riding on a comet. That certainly doesn't stretch credulity to the breaking point in the way that evolutionists say life started here on this planet from scratch.

If evolution started life from scratch then doesn't it follow evolutionists have their God but don't call it that. That's some of that dogmatic naturalism I'm talking about.

  ''I guess if we find aliens on other worlds we could just ask them.  No need for conjecture on our end. But of course the religious wouldn't believe them if they didn't mention some supernatural being.''

Yes, science from a thousand centuries from now, maybe much less, will make today's religious and materialists believers: that is there will be no need for the religionists to affix themselves to the supernatural and the evolutonists will also abandon their supernatural way of thinking that life is an accident of nature.