Tag Archives: origin of life


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A spring outflow pouring into another pool. These small streams are home to rich communities of microbes.

These hot springs—often as clear as swimming pools, as though methodically poisoned to kill algae and small plants—are chocked with life. Even pools of boiling sulfuric acid have diverse communities of microbes. They drift invisibly in the crystal-clear center, down to depths of many meters. They can live without light or oxygen. Around the rims, colored bands of brown, red, yellow, and green are national borders. On one side, one kind of life thrives and repels its enemies; on the other, one of those enemies has found the tangy land of sour milk and rancid honey.

“There’s more diversity in these pools,” Everett Shock tells me, than all the macroscopic life you can see here at Yellowstone–pine trees, bison, bears, elk, shrubs, grass…all of it.”

The springs runneth over. The outflow finds the lowest point of exit from the pool and winds down the hill, where it braids with many others to form Geyser Creek. To the untrained eye, these outflows are unspectacular, compared to the pools. But Shock helps me learn to see. These outflows are rich with life and form laboratories for microbe hunters.

They present a wealth of different environments. At one spot that I’d been inclined to hop across, Shock pulled me close and made me look. Two outflows merged. One was acidic, the other basic. In a little wedge just above the confluence, was a patch of green, where photosynthetic bacteria thrived. “This boundary may represent the beginning of conditions under which photosynthesis is viable,” he said. “Looking at the bands is like going back in time.”

Two outflows merge, with a wedge of photosynthesis between them.

Two outflows merge, with a wedge of photosynthesis between them.

Here, you can often see the microbes—or at least their cities. The scientists call them “streamers.” The tiny bugs build ribbons of minerals that undulate like hair in the current. Some are pink, some green, others a nearly colorless grayish. The least pretty are some of the most interesting. Even though plenty of sunlight and oxygen is available to them, they don’t use it. They are anaerobic and draw their energy from hydrogen produced in the Earth’s mantle. I was not the first to think the colorless streamers looked like mucous; one pool particularly rich with them was called “Spent Kleenex.”

Let’s say you arrived on Earth to take samples, and you took an enormous bite out of a skyscraper—a couple hundred cubic feet, say. You load it onto your ship for analysis. Your instruments would record a lot of steel, glass, and plastic…and a small proportion of living material. Perhaps your scoop grabbed an administrator and a middle manager—no more than a few percent of the total mass of the sample. Would you taste it?

Nom nom nom.

Nom nom nom.

On an earlier field trip, apparently at a moment of boredom and certainly out of Shock’s earshot, one student pointed to some streamers and said to another, “I’ll give you a quarter if you eat one of those.” To the surprise and delight of the group, she plucked one out, blew on it a few times, and popped it into her mouth. Peals of laughter rang out through the field site. “How does it taste?” they asked, wanting to know.

“It’s flavorless,” she replied, “But it’s crunchy.”

When, several years later Shock’s group performed a chemical analysis on the streamers, they found that they contained only about two percent organic carbon. The streamer is unquestionably a product of biological processes, but almost all of the carbon in it comes from inorganic sources. It’s a mineral structure built by the community; it is their skyscraper.

What are the streamers for? The paleontologist Stephen Jay Gould was fond of pointing out the dangers of thinking that every biological structure must have a purpose, but it’s worth asking the question, judiciously. One possibility is that the streamer is simply sandy poop—not functional but merely a waste product resulting from their metabolism. The underlying geology in this region is heavily based on silica. If, for example, you needed to get rid of a lot of silica, it might stick together and remain bound up with the sticky, mucousy microbes.

Another possibility is that the streamer is a fishing net, a matrix that captures nutrients as they float past. Life and mineral could be inseparable; without their sandy sieve, the microbial community might not survive in the stream, which must feel a bit like a Himalayan peak to microbes accustomed to living in dark, toasty, anoxic pools of boiling sulfuric acid.

Streamers thus lead us to think of life as many astrobiologists do. We are all geo-biological systems. We are suffused with minerals, from the salt in our tears to the iron in our blood. The most ancient biological catalysts have metal centers, probably acquired from the surrounding rock in an undersea geothermal vent four billion years ago. Since then, ground rock and metal have cycled constantly through our bodies.

We are streamers, we are iron, and we’ve got to get ourselves back to the geothermal garden.

Microbe Safari II: Geyser Creek


The Geyser Creek field of thermal pools, from a rise above.

This microbe safari is risky business. We are an hour’s bush-whacking off the trail, in the Yellowstone back-country, amid a field of geothermal pools. Most of the pools are at or near the boiling point. Some are alkaline, while others are as sour and corrosive as stomach acid. There was danger in nearly every step. The whole district is shot through with potholes, each one potentially deadly. Some are gurgle with boiling water. Some belch steam. To put a foot in one could mean vicious burns. To break the thin crust of silica and fall through would be deadly. (Someone died not far from here a month ago, straying off the boardwalk unguided. Fell into a pool. There were no remains to recover.) The place also smells like farts.


Note the dangerous shelf on the far side. Approaching from that side, the ground appears solid right up to the thin, brittle edge.

After nearly twenty years of working around geothermal springs, Professor Everett Shock has developed a remarkable eye for reading these treacherous landscapes. Holes a few inches wide could be twenty or more feet deep and indicate thin ground. A particular kind of crusty formation on one side of a pool indicates danger, although similar crusts can be perfectly safe. One rule of thumb is to keep on the grass. Typically, as one approaches a pool, the soil becomes too harsh and hot to support macroscopic plants; a small, barren rock “beach” surrounds the pool. However, in some instances, grass may grow near the water while a barren but solid patch nearby is more secure. Shock can tell the difference. Soon we had all fallen into the habit of carefully checking each step before we took it. While moving, we kept our eyes down, scanning a radius of two yards or so around us for hazards. As we moved through the landscape, the ground burbled, glugged, steamed, spewed, belched, and boiled. It looked like a world out of Star Trek. Traversing it felt like crossing a minefield.

The pay-off for a microbe-hunter here, though, is huge. In this remote bit of the park, an area the size of a couple of football fields, one can find, Shock says, “a little bit of everything.” “This pool is acid,” he said, pointing as we gazed over the hot spring field, “that one right next to it is basic. One is spitting out iron, another is bright blue.” Some are as clear and inviting as a swimming pool, others are turbid and tinted, others are “mudpots,” boiling mud-puddles meters deep. One student, Melody, is doing her thesis on them. Melody judges the value of a site by its mudpots. IMG_2125 sm

“When we started,” Shock said, “we gave the pools simple names. Pool 1, pool 2, pool 3. But we found we couldn’t keep track of which was which. So we started giving them stupid names.” By “stupid” he means silly. Some are actually quite clever. A good name is mnemonic and funny–either witty or vulgar. Today we were sampling seven pools: Jackhammer boils violently and is surrounded by loose rocks the size of footballs. Bat Pool is vaguely bat-shaped. As we approached it, it shot up a burst of gas and water. “Hello, Bat Pool,” Shock said. “It’s nice to see you too.” St. Blucia is a milky blue. Spitting Croissant is crescent-shaped and harbors great colonies of mucousy microbes. Over the years, the pH and conductivity in Spitting Croissant have fluctuated wildly. Evolutionary theory would suggest that different species would flourish under the different conditions; physiology, however, offers the possibility that Spitting Croissant microbes are selected to tolerate a wide range of conditions. One of the students is working on finding an answer. The landscape here changes year to year. Last year, Dirty Donut was in fact donut-shaped. This year, we find the water has breached one of the walls, creating a wide outflow. Corner Thing I imagine being named at the end of a long day. Finally, lording over the other pools on the hill above, is the majestic Empress Pool.

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As inviting as a spa…but deadly.

The technician, Vince—6’4”, about 220, decked out in a flannel shirt, aviator glasses, and a broad-brim hat with a jaunty long feather in the hatband—is integral to the operation. He carries the heaviest pack, keeps track of logistics, and watches over the group. Shock calls him “Uncle Vince.” Uncle Vince also had the painstaking job of collecting dissolved gases in the water samples. As the dry, thin mountain air warmed, sleeves rolled up, shirts came unbuttoned. Uncle Vince revealed a “Led Zeppelin Tour 1977” t-shirt. When I commented on it, Shock began singing “Whole Lotta Love” in a Robert Plant falsetto, playing air guitar as he puttered around, checking on the students’ progress. “Oohh baby, I ain’t foolin’/Gonna send you, back for schoolin’/Waaaay down inside…”

The sampling itself is simple enough, but it’s a delicate task. Many pools are undercut, leaving thin, treacherous ledges around part or all of the rim. Shock ensures that the students collect from a safe distance; the scoops have six-foot handles and can be extended to twelve feet. Usually one side of a pool is determined to be the sturdiest. Then the researchers have to work out a safe path across the minefield between camp and the pool. “Do you know the way to Jackhammer?” a student may ask, though the pool is in sight, as far away as a ten-year-old can throw a stone. Frequently, the answer is “Ask Everett.”

Shock’s students and technician, men and women alike dressed in variations of Early Indiana Jones, set up a field lab in a grassy spot with a bit of shade. Each member of the team got right to work on his or her designated task. One measured temperature, pH, and conductivity. Another collected water samples, which would be divvied up for later analysis: sulfur, hydrogen, various minerals, trace metals, organic and inorganic carbon, and small organic acids such as formate and acetate, which can be “bio-signatures”—characteristic products of life. Another student collected samples of the sediment in each pool. In the muck live microbes that don’t need oxygen or food. Sometimes the students shared samples. “Is there any leftover Spitting Croissant water?” is a question that makes sense here.

A typical biology lab is like a factory. The students are lined up at benches organized into “bays,” long tables jutting out from the walls with two student stations on each side. They work independently, bantering and listening to music as they carry out their often-repetitious tasks and shuttle between their bench and the instruments around the lab. Out in the field, the students arrayed themselves into a lumpy version of the lab, tucking themselves into niches, shady ones if possible, and often with bushes or scruffy trees demarcating the boundaries. They bantered as they carried out their repetitive tasks, while some picked their way carefully out to the next pool to collect their sample. Jokes and teasing were lobbed over the bushes like playful water balloons. The group killed about an hour seeing if they could name a mythical animal for each letter of the alphabet. Impressively, they could.

Shock presided over the operation like an orchestra conductor, keeping track of and checking in on each project, cueing the entrances and exits as necessary and then glancing out over the minefield and grabbing his walkie-talkie to warn a student of a hazard and suggest a safer route. Oddly, the group settles in a kind of normalcy, everyone at his or her task, the day ticking away. It’s just like being in the lab, except if you stray by a couple of steps you could literally melt on your way to getting a drink of water.

[next: Streamers]

Microbe Safari

We were an eleven-person ant-line marching down the boardwalk, laden with oversized, overstuffed backpacks, coolers, and tiny buckets on six-foot handles. The path to Artists’ Paintpot bore left, preparing to ascend. Steam plumed out of the Earth ahead on the right. Our leader veered left and stepped off onto spongy moss and plunged into scrubby pine forest. For the next hour, we bushwhacked our way around the mountain and up the adjacent valley. We pushed through the “green blizzard,” a limb-scratching forest of young pines. We scrambled over fields of fallen and rotting logs, as though we’d wandered into an over-sized game of pick-up-sticks. We crossed a laughing, bathtub-warm mountain stream and followed it through bogs and uphill. At last, we emerged into a primordial landscape—a barren field pocked with bubbling pools, steaming potholes, and boiling mud. One would not be surprised to see a Triceratops make its way gingerly across it. As we entered the field site, steam and water blasted out of a pile of rocks, a hundred feet into the air, as if saluting. “Hello, Avalanche Geyser,” said our leader, Dr. Everett Shock. “Nice to see you, too.”

Avalanche Geyser, Yellowstone National Park

Avalanche Geyser, Yellowstone National Park

I am trying to get a handle on the origin of life. One way to do that is to study organisms and environments in our world that approximate features of that ancient one. So I tagged along with Shock, to the back country of Yellowstone National Park. Its geothermal pools and springs are among the harshest habitable conditions on the planet. But in them life indeed thrives: diverse communities of microbes that most scientists place on the shortest, deepest branches of the tree of life. From them, Shock gleans clues to how early life may have coped with similar conditions. He goes to Yellowstone every summer with his group “GEOPIG,” the Group Exploring Organic Processes in Geochemistry.” The GEOPIGs’ motto is, “The biochemistry we have is the biochemistry Earth allows.”

Barring a time machine, anyone trying to think about the origin of life has to make assumptions. Everyone has their own model, which stresses certain variables and ignores others. In recent years, something approaching consensus has emerged that life probably arose in or around an undersea geothermal vent, about four billion years ago. Such vents still exist, at sites such as Lost City, a warm alkaline vent system in the mid-Atlantic. Some researchers study Lost City itself; others make model Lost Cities in the lab (see my previous piece about my visit to the lab of Laurie Barge and Mike Russell).

Hot springs provide another point of attack. Every summer, Shock comes to Yellowstone for two weeks to gather samples from about sixty pools in remote corners of the park. One pool is basic (high pH) while a few feet away lies one that is essentially boiling sulfuric acid. Temperatures range from the forties (centigrade) to the nineties. Conductivity, sulfur, chloride, metals, organic vs. inorganic carbon, dissolved hydrogen and oxygen, amount and quality of sediment, and other factors also vary widely. All of this data goes into a database that characterizes each pool in seventy-four-dimensional space. Analyzing the samples gathered during these two weeks keeps Shock’s team busy the other fifty.

[DO NOT try this at home, kids. Even with a back-country permit, it is foolish to go poking around these pools unless you know what you’re doing. Last month, a young man wandered off-trail and fell into a Yellowstone hot springThere were no remains to recover.]

While not identical to the early Earth, Yellowstone hot springs share some qualities with what many scientists believe were life’s initial conditions. Besides being high in temperature—similar to the “warm” hydrothermal vents that many think were the cradle of life—they are rich in the elements of the “Fe-S-C-H-O-N” system; iron, sulfur, carbon, hydrogen, oxygen, and nitrogen.

“What we’re doing is looking at the geochemical conditions that provide materials that life can take advantage of,” Shock told me, as the beautiful but deadly pools bubbled around us. “Maybe that can help us think clearly,” he said, about how some of the first organisms coped with similar environments. Life needs a carbon source, a constant source of energy, plenty of hydrogen, and important minerals such as iron, sulfur, and phosphorus. Good evidence exists that life emerged in water close to the boiling point, without free oxygen, and that it derived its energy by reducing CO2 to methane (CH4). After it became free-living, some microbes developed the ability to capture energy from sunlight rather than geothermal heat. The emergence of photosynthesis, about two billion years ago, was a huge game-changer: the oxygen that is a waste product of photosynthesis is poisonous to anaerobes. But life that could tolerate and then exploit oxygen survived the so-called Great Oxidation Event. Our modern world was off and running.

Much of this process is recapitulated in the Yellowstone pools. “There is more [genomic] diversity in these pools than in all the life you can see around us,” Shock said with an implicit sweep of the hand across the horizon. “Bison, Grizzlies, wolves, trees, grass, us,…everything.” (Indeed, one 1998 study found that none of 31 unique 16S ribosomal RNA sequences found in one pool matched that of any known organism.) Many microbes look similar under a microscope—they are the usual balls and rods and filaments. But in the 1970s, Carl Woese and George Fox showed that what used to be called the “Monera” in fact comprised two fundamentally different forms of life. Through a painstaking analysis of the RNA in ribosomes, Woese and Fox designated a new kingdom—later upgraded to a new category: domain—they called Archaea.[1] Although both a bacterium and an archaean are prokaryotic microbes, lacking a membrane-bound nucleus, they differ in the genes that encode and the proteins that compose some of life’s most ancient, fundamental structures. Among them are the various components of the ribosome itself, as well as membrane proteins key to metabolism and other cellular molecules present in some form in all organisms.

Shock’s approach, like every other in origin-of-life research, has its critics. How can you study the origin of life in an environment that’s already full of life?, some ask. How can you understand the early, oxygen-free world in pools with substantial levels of dissolved oxygen? Life has terraformed Earth almost beyond recognition. Just before the emergence of life, the Earth would have been mostly if not entirely ocean. There was little or no free oxygen, so the first life would have made its living anaerobically.

Shock doesn’t pretend that these pools and their inhabitants are identical to those at the dawn of life—he bristles at terms such as “primitive” or “living fossil.” Darwinism does not say that humans descended from chimpanzees; it says that we share a common ancestor that lived more recently than primates’ common ancestor with birds. Similarly, the microbes in Yellowstone hot springs are living very much in the present, but their lineage branched off the tree of life down close to the root. Studying them and their environments can help us understand how these deep lineages respond to particular conditions of heat, pH, mineral concentrations, and so forth, that were important in early evolution. This information can then inform models of how life’s basic biochemistry emerged.

Octopus spring, home of Thermus aquaticus.

The work would yield dividends even if it didn’t shed light on the origin of life. Our first day in Yellowstone, Shock took us to see Octopus Spring. Located just a few miles from Old Faithful, Octopus was the first pool where microbes were discovered living above the temperature at which life was thought to be sustainable, by the great microbiologist Thomas Brock, in 1966. Soon thereafter, and nearby at Mushroom Spring, Brock discovered Thermus aquaticus[2] In the early 1980s, the brilliant but eccentric chemist Kary Mullis, then working at Cetus, one of the early California biotech companies, used the DNA polymerase from T. aquaticus in developing one of the most potent tools in the history of biotechnology. Because it is adapted to high temperatures, the so-called taq (for “T. aquaticus”) polymerase was ideal for Mullis’s polymerase chain reaction, or PCR—one of the principal tools for amplifying a small sample of DNA up to billions of copies for analysis. Mullis received a Nobel Prize in Chemistry in 1993 for the invention.

[next: the pools at Geyser Creek]

[1] For a history of Woese’s work, see Jan Sapp’s The New Foundations of Evolution (2009).

[2] Brock, T. D., & Freeze, H. (1969). Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J Bacteriol, 98(1), 289-297. See also Brock’s “The value of basic research: discovery of Thermus aquaticus and other extreme thermophiles” (1997).

Bison trouble

Just returned from a trip to Yellowstone National Park, where I tagged along with scientists as they bushwhacked into the back country to study geothermal pools and their microbial communities. It’s dangerous work; one of the hazards is hiking into a remote site, only to find that it’s overrun with bison. Or, maybe one is simply walking up the road in front of you, holding up traffic.

What can hot springs tell us about the origin of life? Stay tuned to find out…

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Wait, there’s a fly in my soup

My new piece in Nautilus Magazine is up. It’s on some exciting research going on at NASA’s Jet Propulsion Lab in Pasadena, on the origin of life. Most of us grew up with the “primordial soup.” Forget all that–hydrothermal vents are where it’s at. No one knows how life really started, of course, but this theory is pretty persuasive, because it obeys one of the central laws of the universe: entropy, the tendency for energy to go “downhill.” Take a look. 

Also, Nautilus Editor-in-Chief Michael Segal did an interview with me that’s now online. It’s a wide-ranging conversation, in which we talked about the history of science as a discipline, women in science, the Nobel Prize, and more. And it’s broken into nice, bite-sized pieces, perfect for brief lunch breaks and short attention spans.