CU Boulder researchers investigate what glaciers could tell you about your tummy

Don’t worry; glaciers get acne too.

When seen from high above, small blemishes dot Antarctic glaciers. Like acne, they come and go. And like acne, they’re full of tiny bacteria.

A team of CU Boulder researchers leaves for Antarctica’s Taylor Valley in October to investigate exactly what these pockmarks, called cryoconite holes, could teach us about microbial life in extreme environments — and in our own bodies.

“No one’s ever really documented the microbes that live in these sorts of ecosystems,” Steve Schmidt, professor of ecology and evolutionary biology, said to a group of CU Boulder students.

The ingredients for glacier acne are simple: wind, sun, ice and dirt. And the recipe is pretty easy too: sediment blows from the ice-free valley floor and onto the glaciers flowing down over steep mountain slopes. The dark dirt heats up faster than surrounding ice and melts into pits of varying size. Over time, vibrant mats of this wind-blown sediment layer the bottom of the holes.

Microscopic organisms blow in with the dust, creating an infinitesimal ecosystem at the bottom of each hole. These biomes are active during the warmer months of the austral summer, and also manage to survive the harsh Antarctic winters in states of suspended animation.

Cryoconite holes pepper about 10 to 15 percent of Antarctic glaciers, but they aren’t isolated to the deep, cold south. They sprinkle the glaciers of the high Himalaya and Alaska, freckle the ice sheets of Greenland and stud other frozen environments around the world.

The team decided to study cryoconite holes in Antarctica instead of in more easy-to-access locales like Montana or Alaska due to the Antarctic’s relative purity. The area has seen little direct human impact or development, post-doctoral researcher Pacifica Sommers said.

“It’s an unusual place of incredible beauty,” Research Associate Dorota Porazinska said.

Each hole preserves a petri dish of tiny life — including nematodes, tardigrades (or water bears) and rotifers. Through a microscope, they look like miniscule peas, squiggles and apostrophes.

These diminutive life forms are notoriously difficult to culture in a laboratory environment. The microbial ecosystem of even a patch of soil houses a dazzling diversity of life.

The wind-blown pimples of Antarctica offer a natural laboratory teeming with enough life to stimulate scientific inquiry, Schmidt said. But the frigid environment limits what can survive inside so that scientists aren’t overwhelmed by data. The ice even creates its own lids.

“So if we’re sitting here thinking, ‘If only we could do these kinds of test-tube experiments somewhere with evolutionary history,’ there’s a place down in Antarctica where these types of ecosystems might actually exist,” Sommers said. 

The researchers will drill cylinders of ice from the cryoconite holes, and examine the layers of dirt at the bottom. Called “sediment patties” — and not entirely unlike burger patties — thick glops of Antarctic muck stick to the bottom of the cores.

In these patties, layers of dirt represent years of wind-blown dirt and life. The layers come in a variety of colors — red, orange, green and black. The researchers will test how the order of these colorful layers affects the overall ecosystem of the holes.

These layers represent a simplified model of the critters that live in human guts and other microbial ecosystems.

“We’re thinking about things like wetlands or re-vegetating old mining sites,” Sommers said. “You might get radically different communities where a beaver showed up and built a dam versus where it didn’t. Same thing might happen in your gut if some microbes start exuding waste products that are more important than others.”

The team will also create its own holes on the ice sheets of Antarctica. In some they’ll put, say, an orange layer of sediment before a black layer. In others, they’ll put a black layer before the orange. Then, they’ll test for similarities and differences in the holes’ overall microbial makeups.

Sommers said that these tests of “priority effect” might eventually inform procedures such as fecal transplants and the scientific understanding of the ecosystems of the human gut. This potential, she said, comes from the mysterious world of microbes.

Microbes run the planet unseen, Schmidt said. These tiny bacteria govern our guts and our gums, the oxygen we breathe, the soil on which we tread, the plants and animals and metabolic processes around us.

“As an aggregate, they’re more metabolically complex than you or me or anything else,” Jack Darcy, a Ph.D. student in ecology and evolutionary biology, said, “ They actually do more things than we do, and they’re responsible for everything from the tiny scale to the large scale.”

Darcy stressed that these studies represent only the first steps on a long road of microbial discovery. However, it could provide a means of building theory that illuminates much more than the Antarctic ice.

“You turn up the complexity a bit and change the tool a little bit, and turn up the complexity a little more, and eventually we’re at a stage where the tool works in a complicated system,” he said.

A system, perhaps, as complicated as the human gut.

“It’s really hard to drill cores in someone’s butt,” Darcy said. “But it’s comparatively easier to go down to Antarctica and drill holes in a glacier.”

A time machine for endangered species: CRISPR, the Devils Hole pupfish and the future of conservation biology

March 20, 2012 — There’s a rumble and a shift in the earth near Oaxaca, Mexico. 30,000 homes crumble. The Mexican Stock Exchange shuts down. So does the airport. More than 2.5 million people lose power. More than 2,000 miles north, water in a tiny hole in the desert slurps up and down, surges one way, then the other. About a hundred tiny pupfish bob up and down with the waves, unperturbed.

This is Devils Hole, a 6-by-18-foot pool in the desert floor. And it’s connected to everything.

Devils Hole is home to the rarest and loneliest species in the world, the Devils Hole pupfish. Listen close, and these tiny critters tell a story about the controversial future of conservation in an age of highly technologized biology.

The hole lies in the Amargosa — meaning “bitter” — desert. It’s a fitting name for a place that lies next to Death Valley and the Funeral Mountains. The landscape in the area seems to collapse in on itself. The rocky cliffs and buttes and bluffs formed about 3 million years ago; yesterday, in terms of geology.

Even though the hole sits on Ash Meadows National Wildlife Refuge land, it’s technically part of Death Valley National Park. The towering Sierra Nevada and the rugged Panamint mountains block incoming rain. It’s one of the hottest and driest places on earth.

Before gold-diggers dubbed the place Death Valley in the mid-1800s, the local Shoshones called it Timbisha. The term referred to a reddish pigment, sometimes used as body paint, derived from the desert soils. To these desert dwellers, the area was one of life, not death. Tribesmen cultivated corn, squash, wheat, beans and mesquite seeds. They lived in the lower elevations to stay warm in the winter months, and moved to cooler, mountainous ground in the summertime.

It was possibly these inhabitants who first saw the pupfish in the springs of Ash Meadows, and in Devils Hole itself. Shoshone lore speaks of “water babies” that arose from the depths of the hole. Some scientists theorize that they might have even transported the pupfish themselves, or their eggs, from the springs downhill.

For decades, scientists and passersby have been entranced by the little critters.

“It’s this outstanding, charismatic little endangered species,” Chris Martin, assistant professor of biology at UNC-Chapel Hill, said.

Although they’ve numbered as high as the 400s since scientists started keeping track, their numbers reached an all-time low of 38 in 2013. They’ve since rebounded slightly, to about 115. They were among the first species listed as endangered on the 1967 Endangered Species Preservation Act, which later became the Endangered Species Act. They live in the 92-degree waters of the upper shelf of Devils Hole — and only there. It’s a space about half the size of a living room

The pupfish themselves are cute little things. They’re smaller and less bright than other desert pupfish in the region — on average, shorter than your thumb. Males are almost fluorescent blue; they even have their own mating dance. From above, the male appears to press itself against the female, and spasms, its tail firing rapidly against the water.

Look close, and you’ll see a fishy underbite – 16 tiny teeth on both the upper and lower portions of the creature’s jaw. Their rounded fins fade to dark stripes at their ends. All the pupfish in Devils Hole lack pelvic fins, that are found in other species of pupfish. It’s a curious and obvious case of the environment shaping the species.

And they’re also nearly terminally chill. Many populations of desert pupfishes are territorial. Males fight each other, and court females. But in Devils Hole, the males don’t seem to exhibit the same brutishness over territory. Because there’s barely any territory to begin with.

Andy Martin, professor of ecology and evolutionary biology at the University of Colorado Boulder, thinks the pupfish’s lethargy and low numbers might be due to basic defects in their DNA. Years of pressure on their water supply, human interference, flash floods and a rising climate have created a “mutational meltdown,” he said.

In the 1960s, a local rancher began pumping groundwater near the hole. The water level went down substantially, and the fish felt the consequences. Conservationists took the case to the Supreme Court. In 1975, the court ruled that the rancher had to stop pumping.

But Martin said groundwater use is still of paramount concern. Instead of a single straw sucking up water near the hole, the growth of the Las Vegas and local water use, such as the demands of solar energy farms, risks depleting the aquifer that feeds the hole.

“Now the straws are kind of all over the place,” he said. “So the effect of a single straw isn’t super great, but the problem is there’s a bunch more straws.”

The National Park Service has concentrated efforts on isolating environmental problems that have led to the fish’s demise. They’ve spent millions constructing a titanic tank that simulates the conditions of the hole to breed a reserve stock of the species in captivity. Thus far, their efforts have spawned [nice! ;-)] little success.

Martin said such efforts come from the right intention, but are rooted in human hubris.

“I understand the desire to make it better and engineer restoration, but sometimes the best restoration is just to let nature take its course,” he said.

Chris Martin, who primarily studies pupfish in the Caribbean, theorizes that a different sort of engineering could pave the way for the pupfish’s salvation. The gene-editing technology CRISPR-Cas9 offers a radical new way to preserve the species, he said. Pupfish, in particular, may be a cheap and expedient means to explore the technology’s promise in the world of conservation.

CRISPR-Cas9 is a relatively new and inexpensive technology that allows scientists to manipulate the genetic makeup of any living being.

For the technology to work, you need two plugins: the CRISPR enzyme, and Cas9. CRISPR — or “clustered regularly interspaced short palindromic repeats” — refers to a recurring genetic code that appears in just about all living things. CRISPR segments locate particular sections of DNA that scientists wish to delete. Cas9 grabs hold of these segments and chops them off.

CRISPR is the map; Cas9 is the scissors.

Scientists can inject “good genes” near the chopped section of DNA. Repair enzymes naturally replace the broken sequence with the good section of DNA.

Devils Hole pupfish actually dwell across the nation, not just in the hole, Chris Martin said. They’re just long dead, dried out, and in the dusty basements of museums. These specimens, Martin said, serve as time machines.

By analyzing the genetic makeup of pupfish before human activity stressed the population, scientists could isolate genetic “defects,” and fix them.

“Museum collections are extremely valuable right now,” Martin said. “There’s no other way to restore genetic diversity.”

Martin first heard of CRISPR over lunch in 2014. A year later, he was practicing it in a lab. CRISPR is easy, cheap, and in many ways uniquely suited to externally-fertilized creatures like fish, Martin said. To scientists like Martin, CRISPR could engineer the future of conservation biology.

With this technology, researchers are trying to develop hypoallergenic chicken eggs, mosquitos unable to reproduce, revive the wooly mammoth, make tiny pigs perfect for pets, save the black-footed ferret from extinction and bring back the passenger pigeon.

However, the technique is controversial. It means humans become the architects that construct the natural world.

In November, researchers in China tested the potential of CRISPR on a human for the first time. Scientists at Sichuan University injected extra-strength, CRISPR-modified white blood cells into a patient with lung cancer.

But Martin said CRISPR-engineered animals shouldn’t draw the same ethical controversy as would CRISPR-modified humans. The problems with pupfish stem from human activity, so it takes human intervention to solve them, he said.

“I mean you can get very philosophical about it I guess if you want,” Martin said, and sighed. “In reality, you wouldn’t be able to detect any difference between a CRISPR engineered fish versus one you collected in the 1940s, presumably.”

Anthony Echelle, Emeritus Regents Professor of biology at Oklahoma State University, said protecting the species means the preservation of a symbol. If you have to ask why we should preserve the fish, Echelle said, you wouldn’t understand in the first place.

“In some ways, it’s the protection of an ideal, a romantic ideal,” he said. “It’s nature untouched. Nature that looks as untouched as possible by humans. Humans have a way of screwing things up.”

Andy Martin and Echelle advocate hybridizing the creatures with pupfish from nearby. But then, Andy Martin said, nature should take its course.

“I think they need to address the issue of genetic diversity in the hole,” he said. “But then I would just let everything go. Let everything do its thing.”

The park service could remove the fencing, and open the hole to the public, Andy Martin said. It could serve as the symbol it is, and a tool for education. A symbol of the interconnection of the natural realm, of the romanticism and wonder of biology, and a window into the world of water in the west.

Those waves in Devils Hole are called “seismic seiches” (pronounced say-shiz). Seiches themselves aren’t particularly uncommon. They’ve been recorded as early as 1755, and in areas as diverse as Portugal and Norway and Alaska and Montana. But most seiches stay at least somewhat localized. In Devils Hole, scientists recorded ripples even after the 2011 earthquake that devastated Japan, more than 5,000 miles away.

Somehow, this tiny hole in the middle of the desert is connected to the rest of the world.

“We as humans are altering every biosphere on the planet and every single population,” Chris Martin said. “You do the best you can and you try not to get too philosophical about it.”


Motion Graphic Critique: The Dawn Wall

Shan Carter, Wilson Andrews, Derek Watkins and Joe Ward’s “The Dawn Wall: El Capitan’s Most Unwelcoming Route” ran for the New York Times in January of 2015. The story features a combination of text, photos and graphics. At first, the reader sees a brief introduction to Tommy Caldwell and Kevin’s Jorgeson’s achievement — free-climbing the nearly 3,000 foot Dawn Wall of El Capitan. The route is potentially the most difficult route of its size in the world — it goes at 5.14d, and features pitch after pitch of 5.14 and 5.13 climbing. Hard as nails, in climbing terms. Next to the text, there is a large graphic of El Cap, a 3,000 foot cliff in Yosemite National Park. The graphic highlights key sections, including the scale of a single person, and includes a key to gain a sense of scale.

As the user scrolls through the text and images, the graphic zooms in and navigates to appropriate sections of the route. This allows the user to effectively experience aspects of the climb as they learn about Tommy and Kevin’s achievement.

I remember watching Tommy and Kevin approach the summit live on YouTube as I crossed the border back into the U.S. from Potrero Chico, a climbing area in Mexico (in which Tommy’s established numerous first ascents). To me, as a climber, it really was a remarkable achievement. But I already knew the grandeur of El Cap, and the slippery smoothness of its sheer walls.

The graphic is a valiant effort but fails to do justice to the complexity and boldness of the climb. The user never understands what it feels like to free climb El Cap. Tommy and Kevin put more than seven years of work into the route. Tommy’s responsible for some of the most cutting edge and difficult routes in Yosemite, and the article never touches on their history there, or on the experience of spending that much time on the wall. A graphic of a port-a-ledge, dangling 2,000 feet above the void could have added to the feeling of this story.

Google Maps, for example, features a full “Street View” adventure of Alex Honnold and Lynn Hill climbing “The Nose” of El Cap — perhaps the feature’s most famous route. At first glance, the images aren’t particularly engaging. However, you can navigate key parts of the route in 3 dimensions. This shows the scale and tenuous nature of the climb. Even this doesn’t do justice to the cliff itself. Perhaps nothing can, except for being there. A more compelling venue would utilize virtual reality. Immersed in the climb, a VR user would see the tremendous distance to the valley floor below him or her, and the towering walls of granite ahead.

Tommy and Kevin’s climb took 19 days on a final push, after more than seven years of work. Last month, Adam Ondra, a young, Czech climber completed the Dawn Wall during his first outing in Yosemite National Park. He worked the route for a couple weeks before his final push, which took him eight days.

The trippy science of hallucinogens

Turn on, tune in, turn out.

It was a mantra of the sixties, when psychedelics were all the rage. Even scientists — most famously, Tim Leary — were fascinated.

For decades, this research went out of fashion. But new research on the therapeutic value of psychedelics is emerging. And the results are surprising.

These studies looked at the death-related anxieties of cancer patients. Could mushrooms help patients overcome the anxiety and depression that comes with terminal illness?

It’s quite likely, researchers at Johns Hopkins and New York University found. About 80 percent of study participants said their sojourn with psilocybin had been one of the most meaningful experiences of their lives, one of the head researchers reported to NPR.

In the studies, patients were given a “guide” to assist with their experience, along with light-blocking shades and headphones playing a carefully-selected playlist of music. Participants reported journeys from the ocean and into space, and images of bright colors, shapes and characters.

The researchers emphasized that these studies shouldn’t be treated as advocacy for the recreational use of psychedelics. Patients received only one dose of psychedelics, in highly controlled circumstances. Benefits of personal use “evaporates like water running through their hands,” a researcher told the New York Times.

The beer archaeologist


You are a Roman soldier, and you’ve had a long day. In the heat, the leather and metal of your armor feel welded to your skin. So you sit down with your comrades and do what you do most nights. You have a beer.

It was likely tart, flat and not very alcoholic.

Based on the available evidence, that’s the suspicion of Travis Rupp, a ‘beer archaeologist,’ and Avery Brewing Company’s research and development project manager.

We don’t know very much about Roman beer, or beer in the ancient world generally. But a handful of beer archaeologists around the country like Rupp are dedicated to learning what an ancient Roman soldier and Egyptian worker may have tossed back after a hard day on the job.

From archaeological excavations and the literary record, Rupp, who also serves as an adjunct instructor of classics, anthropology, art history and continuing education at CU Boulder, searches for traces of beer production in the ancient world. And then he actually brews it for anyone to try.

“I think it wasn’t all that different than what beer is for us today,” Rupp said. “It was a main means of socialization.”

At Avery, Rupp helped launch a series of ancient-inspired ales in September. Avery is partnering with the Denver Museum of Nature and Science to release beers in conjunction with exhibits on mummies in the ancient world and, eventually, Vikings.

Rupp said Avery will begin brewing an ancient Incan chicha, or corn-based beer, and also some ancient Egyptian suds, next week.

Rupp, 36, is the only ‘beer archaeologist’ in the U.S. who is a brewer as well as an academic. He said this enables him to view ancient brewing from a unique perspective.

Ancient brews devised by others in his field — like Dogfish Head’s Midas Touch — rely on chemical analyses of pottery shards and other ancient paraphernalia to find traces of herbs and spices, and other hints of recipes from thousands of years ago.

Rupp’s research looks even deeper.

Pots were reused over and over again in the ancient world. Chemical traces of extravagant spices may not have been from beer ingredients at all, he explained.

“I’m trying to look at what was readily available for the common man and what would have been plausible ingredients to be in a beer,” he said. “And then looking at the actual brewing process under which they made that beer and then recreating it here.”

Nestor’s Cup, the first of Avery’s ancient-inspired series, fizzes deep pink, with hints einkorn wheat, acorn flour, figs and elderberry — unique additions to the brewing process.

Rupp said there’s a tension inherent in the process of brewing these ancient concoctions. At Avery, brewing ancient beer is a difficult process of letting go, of losing control.

Modern brewing arose from a drive for cleanliness, predictability and uniformity.

“Sanitation is probably the biggest advancement in the last thousand years,” Avery staff microbiologist Dan Driscoll said. “It allows people to actually control the environment in fermentation, to control what’s in there.”

Since ancient brewers couldn’t use impenetrable steel vessels, their brews utilized open-air or “spontaneous” fermentation. Lactobacillus and pediococcus, bacteria in the air around us would have soured the beers during brewing.

The lack of technologies and scientific understanding — the “wild” nature of ancient beer — gave it its unique flavor and character.

The Peruvian chicha entering Avery’s tanks next week, for example, is based on a brew that required chewing corn and spitting it in a vessel. During chewing, alpha amylase converted the corn’s starches and sugars into something fermentable.

“Because of the scale of this brew, we can’t all sit around and chew corn all day,” Rupp said.

Instead, they’ll fill the tanks by hand with 50-pound bags of enzymes that simulate the natural outcome of corn-chewing.

“A lot of this is experimentation,” Rupp said. “We’re making it up as we go and we’re making our own data on it that didn’t exist prior.”

Ancient beer was likely tart and flat, and only one to three percent alcohol. It wouldn’t have had the bitterness of hops, which came into usage around the 12th century AD. Taste and the alcohol content would have varied based on travel time, temperature and other factors.

Ancient peoples didn’t have the same understanding of microbiology as do modern brewers. However, they were far from naïve, Rupp said.

The archaeological record suggests Ancient Egyptians and Romans mass-produced beer— in some cases up to 200 gallons a day. Rupp thinks the ancients had a grasp on the techniques of brewing, even without knowledge of the microbiology that drives it.

For example, brewing might have emerged as the first purely Egyptian industry, he said.

Ancient Egyptians used papyri straws — sometimes with makeshift filters — to drink straight out of beer vessels, while leaving the important yeast intact for future brewing.

“They didn’t understand what yeast were,” Rupp said. “But they did understand there was something beyond what they understood was going on.”

When brewing, ancient peoples would have seen krausen form at the top of the beer. Krausen, Rupp said, is basically “yeast poop.” As yeast consume complex sugar chains to produce alcohol in the mush of mashed grain — otherwise known as wort — they spit matter back out, and it sticks to the top of the brewing vessel.

Pliny the Elder, a Roman historian and general, even wrote that krausen was good for the skin. So Romans likely rubbed the stuff on their faces, Rupp said.

Nicole Garneau, curator and department chair of health sciences at the Denver Museum of Natural Sciences, said using beer with the exhibit makes science less scary and more compelling to everyone.

“It makes the science personally relevant,” she said. “It allows you to experience it in a way that’s completely accessible to everyone — taste. Because everyone has it.”

Where’s all that oceanic methane come from?


A Woods Hole Oceanographic Institute study published this week in the journal Nature Geoscience reports to unravel a longstanding oceanic mystery, known as the “marine methane paradox.”

About 4 percent of our atmospheric methane comes from the ocean. However, most methane-generating species of microbe can’t survive in the high-oxygen water near the surface of the sea.

As a greenhouse gas, methane is about 20 times as strong as carbon dioxide. Understanding this mysterious source of emissions may be crucial to understanding the complexities of our atmosphere in a changing climate.

So, how’d all that methane get there?

Initially, scientists sought answers in ocean-bound guts and feces, but research failed to reveal a substantial methane-producing mechanism.

The answer, the research team theorized, lies in the way oceanic bacteria break down organic matter in the depths of the seas.

A great deal of the dissolved matter in the surface waters of the ocean are made up of long chains of sugars, called polysaccharides. As bacteria break down these polysaccharide chains, they rip out pairs of carbon and phosphorus atoms — or C-P bonds — their molecular makeups.

In this tearing process, the microbes generate methane, ethylene and propylene gases. This methane escapes into the atmosphere.

To confirm this notion, the WHOI team simulated seawater in a variety of conditions, including high amounts of nitrates and glucose. But the seawater only began producing methane when they dropped pure polysaccharide chains into the mix.

However, the research paints only part of the picture. Oceanic bacteria only consume organic phosphorus in the upper ocean as a last resort. If that’s the case, then methane production shouldn’t be all that common.

“There’s a really interesting story there if we can figure it out,” Dan Repeta, a lead author of the study, said.

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