Science Writing

How do dams affect downstream river ecology?

Study on two southwestern Colorado rivers provides answers


The San Miguel and Dolores rivers are both southwestern Colorado waterways that begin high in the San Juan Mountains near Telluride. Both carve through narrow, red sandstone canyons and eventually merge with the Colorado River in eastern Utah. But there is one major difference: the Dolores is dammed at McPhee Reservoir near Cortez while the San Miguel is one of the last free-flowing rivers in the West.

A study of plant traits on these two rivers may provide clues about how riparian habitats respond to climate change. Researchers from Colorado State University recently completed a two-year study on the Dolores and San Miguel rivers, the results of which were presented at the Upper Colorado River Basin Forum in Grand Junction in early November.

The study compared two sites on the Dolores (Rico and Bedrock) with two sites on the San Miguel (Placerville and Uravan) by documenting different plant traits at each of the four sites. A “trait” is simply a measureable feature of a plant, like leaf area, root depth and height. The more diverse these traits are, the higher something called “functional diversity.” For both of the upstream sites, Placerville and Rico, functional diversity was higher than it was at the downstream sites, which scientist expected because the downstream sites receive less rainfall. But the Bedrock site, because it is downstream from McPhee Reservoir, had a much lower functional diversity than Uravan.


San Miguel River

“Dams really do have a huge impact on the downstream ecosystem and it’s not always talked about,” said Erin Cubley, one of the researchers on the project and a PhD candidate in ecology at Colorado State University. “Dams hold sediments and seeds, they change the flow, they change the processes that are essential in maintaining these ecosystems.”

The McPhee dam near the town of Dolores is the fifth biggest reservoir in the state and holds back about 381,000 acre feet of water from the Dolores River. McPhee Reservoir supplies the agricultural irrigation needs of farmers and ranchers in the area. The resulting decreased flow below the dam has big impacts on the downstream ecology, Cubley said. A smaller river channel cuts deeper, not wider, and this lowers the groundwater that riparian plants depend on to survive.


Dolores River

“Riparian species have a big taproot and can access water a few feet down, but if they can’t access groundwater they die,” Cubley said. “That is what we are seeing at Bedrock.”

Another way dams alter the natural flow of the river has to do with spring runoff. Many dams are managed solely with maximum storage capacity in mind, says David M. Merritt, a riparian ecologist with the U.S. Forest Service National Stream and Aquatic Ecology Center. There are easy tweaks water managers can make that will not compromise the power or storage needs of the dam that can also improve the ecological functioning downstream.

For example: one of the most important components of river health is peak flows and flooding with spring runoff. Some species, like the cottonwood tree, time the release of their seeds to coincide with peak flows. The fluffy white fibers use the river to carry them downstream to hopefully take root in the riverbank. But when dams control the river and don’t allow for this peak flow to happen, it can have a negative effect on the whole downstream ecosystem.

“If you are a dam operator, it might be easy for you to time a spike that coincides with that historic timing,” Merritt said. “The timing of peak flow is reliant on temperatures with a little variability annually. A dam operator would have tremendous flexibility on when that would occur.”


And how does Cubley and Merritt’s research translate into predicting what the future ecosystem will look like with the effects of climate change? Assuming that the future of the American West will be warmer and drier than it currently is, the research team can model what a future ecosystem might look like: At what point will more drought-resistant plants move in? If you change the flows of a river how will the vegetation respond? What would happen if water managers changed dam operations?

“What if climate change is twice as bad or what if it’s not as bad?” Merritt said. “We are scientists who predict change… We will be able to show predictions of what the vegetation will look like. It’s a model and a technique that can be used on any river anywhere.”


Do cryo holes hold the secret to ecosystem restoration?


In three weeks, a team of scientists from CU Boulder will set out on the second of three annual expeditions to the polar deserts of Antarctica to conduct research that could have implications for how many types of ecosystems assemble, including the human gut microbiome.

Last winter, researchers Dorota Porazinska and Pacifica Sommers visited three glaciers in the Taylor Valley collecting samples from cryoconite holes. And what exactly is a cryoconite hole? (Called a cryo hole for short.) They are created when a tiny bit of airborne material made up of dirt, dust, soot and microbes blows onto a glacier. The dirt is dark-colored and absorbs solar radiation, warming and melting the snow beneath it. The microbe-laden dirk sinks down into the hole and creates a puddle at the bottom. In a feature that is unique to Antarctica, an ice lid usually freezes over the hole, creating a test tube of dirt and microbes sealed off from the rest of the world.

The McMurdo Dry Valleys are simplified systems in which to conduct research. There is no plant cover, no vertebrates, very low humidity and a lack of human disturbance. Some scientists consider the region’s environment to be close to that of Mars.

Last year’s research, conducted at a camp near Lake Hoare, focused on a survey of the holes and DNA sequencing of the bacteria in the holes. This year, researchers will create a grid of 250-300 artificial cryo holes, drop in some dirt containing fungi, microbes and algae collected from the glacial streams and sit back and wait.


“We drill down maybe a centimeter deep and just make a little divot in the ice,” Sommers explained. “We add 20 grams of sediment, just a pinch of dirt because you want it to melt, not insulate.”

The experimental holes will be divided into two groups to test two different hypotheses about how microbial communities assemble. The first will try to determine whether the order in which different bacteria arrive matters for the overall composition of the ecosystem. The second will test whether the amount of bacteria matters. Scientists will use two different types of dirt and bacterial mixtures, called algal mats, collected from the streams around the glacier. There are black mats from Green Creek and orange mats from Aiken Stream.

“The idea is that if the order of arrival matters, we would expect that those started with black will just end up black and those started with orange will just end up orange,” Porazinska said. “We won’t know exactly why, but it will be indicative that the order is really important. Or we could see a really different outcome. It could develop into some kind of third state.”

Sommers says getting a handle on assembling microbiomes can help scientists get a better handle on everything from ecosystems to human health.

Researchers will resample the holes about a month after they are created and again the next month and then a year later. The holes are meticulously marked with GPS so researchers can find them if it snows. Snow shuts down the cryoholes’ development and last year researchers had to sweep the glacier after a storm before they could get to its surface and start working.

Sommers and Porazinska think the results of this research could have implications for many different areas of science. By understanding how ecosystems are formed, it could provide insight into how to rebuild a forest after the invasion of a non-native plant or how to restore the human microbiome after a course of antibiotics.

“The general idea is that we don’t really know how certain communities are the way they are,” Porazinska said. “Now these (cryoconite hole) communities can become experimental test communities so we can see what’s going on and extrapolate those ideas to bigger organisms and longer time scales… We don’t really know exactly what is important in the process of restoration.”

The science of beer

Avery Brewing in Boulder has been making beer since 1993 (Avery’s IPA is my all-time favorite IPA in the whole world!) and in 2015 moved into its current location on Nautilus Drive.


Beer starts out with just four simple ingredients: water, grains, yeast and hops. From there, the process gets a little more complicated. Avery moves the malt and wheat from its silos inside to a wet mill, where the kernels are steeped in hot water to start the enzymatic process. The mixture then goes into something called a mash tun to be converted into simple sugars and fermented. The ratios of grain and water and temperature differ depending on the beer recipe. The hot, sugary liquid called wort is then put into the lauter to be rinsed and strained.


The wort is boiled with hops, which add bitterness and aroma. Most of Avery’s hops are from Oregon’s Yakima Valley. At this stage, depending on the beer, hops are added up to three more times. Avery’s beers tend to be hoppy and have a high alcohol content. Then, the yeast is added, the fermentation process begins, followed by clarification and filtration, canning and bottling.

Throughout the time the beer is fermenting until it is packaged, a team of scientists are constantly checking and chemically analyzing it, making sure it tastes just right. But nothing compares to the human senses. So the batches of beer also have to pass a taste test by a team of tasters in a control room.


“Through modern sensory science, we can really fine tune our beer,” said Avery Process Analyst Dan Strevey. “The taste, smell and visual components are huge.”

Antibiotics are a life saver

Antibiotics are now a common and lifesaving treatment for all kinds of infections. But they were first discovered less than a century ago – 1928 to be exact. Researcher Alexander Fleming came back to his lab after the weekend and found that a mold, penicillin, had stopped the growth of staph bacteria in his petri dishes. Voila! Antibiotics were born.


I’m pretty happy I live in a time where antibiotics are a widely available treatment. Two weeks ago, I needed a course of Azithromycin to knock out a case of bronchitis. I had a painful cough, a fever of 103 and felt generally terrible for five days. I couldn’t do anything (not even study!) except lay on the couch and mindlessly watch TV. But just 12 hours after I took the first dose of the Z pack, the tightness in my chest had loosened its grip on my lungs.

I guess back in the day before antibiotics, you just sat around and waited to see whether you were going to die or not. Given all the times I’ve taken antibiotics in my life, there’s a good chance I wouldn’t have made it this far in a pre-antibiotic world. Any of the silly little infections I’ve had could have killed me.

Antibiotics work by either interfering with the bacteria’s ability to repair itself, stopping it from growing new cells or weakening the cell’s walls until it bursts. Azithromycin works by stopping the production of protein and stopping bacteria growth. It hasn’t been around that long – the medicine was discovered 37 years ago in 1980.

Proprioception is a trail runner’s friend

I got this nasty scrape from a fall when I was running down the Bear Peak trail. I also got a scrape on my upper arm because I fell into a tree. A TREE. Turns out bark is abrasive.


The trails around Boulder are really technical. By technical, I mean rocky and rugged and fancy footwork is needed just to remain upright and not sprain an ankle. I could improve my trail running here, if I work on my proprioception.

What is proprioception? It’s like a sixth sense of the relative position of your body in space and the strength of effort being applied in motion without having to look. Also known as kinesthetic awareness, it’s an instinctive, spatial reaction to stimuli. Law enforcement uses proprioception tests in roadside maneuvers to determine if a driver is impaired by alcohol. When you’re sober, you should be able to close your eyes and touch your finger to your nose with pretty good accuracy. Drunk, not so much.

Barefoot runners say they have more proprioception than when their feet are covered by shoes. You can work on improving proprioception by doing balancing exercises, plyometrics and certain balancing exercises with the eyes closed. Accident-prone and clumsy people can improve proprioception so maybe there’s hope for me yet!

I made rice!


This might not seem like an accomplishment, but it is. Brown rice. Not that easy-to-cook white rice, BROWN RICE.

I lived for the past five years in Telluride, which sits at 8,750 feet above sea level. While high altitude is great for growing extra red blood cells and escaping the horrific heat of the Front Range where it’s 70 degrees in December and a million degrees in summer, it’s not great for cooking. At sea level, water boils at 100C, but at 8,750 feet, water boils at about 91C due to the reduced atmospheric pressure. This means things take longer to cook because the temperature is lower. No matter how long I cooked brown rice or how much extra water I added, I invariably ended up with crunchy rice. It took hours to produce something edible so I basically gave up on rice and didn’t cook it for the five years I lived in the mountains. Maybe I should have invested in a rice cooker or used a pressure cooker. Pasta takes about forever to cook as well, but it’s doable.

Then I moved to Boulder. While 5,000 feet might not seem like low altitude, it makes all the difference for rice cooking. First attempt was a success and it didn’t even take all night. I was amazed when I fluffed it with a fork after cooking for only THE AMOUNT OF TIME THE PACKAGE SAID. No crunchy rice here.


Back from the brink: A species twice thought extinct is beginning to see a comeback in the wild


For 10 nights this fall, scientists prowled the grasslands of the Rocky Mountain Arsenal Wildlife Refuge, shining lights on prairie dog holes and looking for the telltale green, glowing eyes of one of the most endangered mammals in North America.

The scientists were looking for the black-footed ferret, which was reintroduced in 2015 to the 15,000-acre expanse just northeast of Denver. Since the animals are nocturnal but more active during a full moon, researchers split their 10 p.m. to 7 a.m. shifts over two months: six nights in September and four in October. The black-footed ferrets were captured in small, metal, boxy traps, checked for a micro-chip or given one under their skin if they didn’t yet have one, and vaccinated against the deadly canine distemper virus and sylvatic plague.

This year’s nighttime ferret survey counted 57 animals, up from last year’s tally of 50. That’s an indication that the reintroduction program is so far a success, said Rocky Mountain Arsenal National Wildlife Refuge Manager David Lucas.

“I think we are very happy with that number,” Lucas said. “The first night out your fingers are crossed that you’re going to find something.”

The black-footed ferret, which is one of three ferret species in the world and the only one native to North America, was written off twice as extinct in the wild. It was brought back from the brink by captive breeding programs by the U.S. Fish and Wildlife Service and partners, and then reintroduced back into its native habitat: the Great Plains of the North American West. Thirty-two black-footed ferrets were reintroduced to the refuge in 2015 and 22 more were added in 2016. Although just 57 were counted this year, Lucas estimates there are at least 70 out there. That would make the refuge home to nearly one-third of the estimated 300 animals that exist in the North American wild.


Nineteenth-century naturalist John James Audubon, best known for his work with birds, once painted a picture of a black-footed ferret hunting a nest full of eggs. This depiction was a huge mistake. With their forward-facing eyes, long canines relative to their skulls and slinky bodies that can contort inside narrow burrows, the black-footed ferret is a deadly predator. And it’s near-exclusive prey is prairie dogs.

“They spend their whole life on the prairie dog colony; they move into an abandoned burrow,” said Kimberly Fraser, outreach specialist with the National Black-footed Ferret Conservation Center in Wellington, CO. “They cannot live without the prairie dog. I like to say it’s evolution at its finest hour. They have really evolved with that elongated body so they can hunt prairie dogs in the burrow system.”

With their room and board so dependent on the prairie dog, that means the fate of predator and prey are intertwined as well. When an outbreak of plague sweeps across a prairie dog colony, ferrets are often the first to be affected, Fraser said. Not only are the ferrets susceptible to plague themselves, the disease also kills off their food source – a double-whammy for a species with an already-tenuous hold on the landscape due to historic habitat loss as humans have plowed up the plains. Plague management through vaccines is the reason the black-footed ferret reintroduction at the Rocky Mountain Arsenal has been so successful, Fraser said.

Lucas has a theory about why the vaccination program has worked: adaptation on the part of humans. Researchers carried out the first ferret count during frigid weather in winter while riding utility vehicles. Those conditions made it difficult to get an accurate count, Lucas said. So they moved the count to the warmer temperatures of fall. Scientists also used to transport captured ferrets to a building 20 minutes away to implant the microchip and administer the vaccine. This year, they converted a camper trailer to a mobile field lab to cut in half the amount of time the animal is stressed.

“I think the key to where we are now is this realization of what works and what doesn’t work,” Lucas said. “That learning part of science is really important. There are a million little process improvements you can do to optimize results better for the whole program.”

Why do leaves change color in the fall?


First, we must understand a bit about photosynthesis and chlorophyll. During the summer, the leaves use sunlight to make its food. Chlorophyll, which gives leaves its green color, absorbs the sunlight, which is used to turn water and carbon dioxide into sugars. As the days get shorter and the nights colder, trees stop their food-making process and the chlorophyll breaks down. What’s left behind are the other leaf pigments, like yellow, orange and red.


When I was in Telluride a month ago (where fall comes about six weeks earlier than the Front Range) I noticed the aspens on the hillsides were not that bright. They seemed drab. Kind of blah compared to previous years. Why do some year’s colors seem more vibrant than others? According to the Colorado State Forest Service, a wet growing season with a dry sunny fall with cool (but not freezing) nights are the best conditions for brilliant fall colors. Telluride had a wet late summer and early fall. Maybe that had something to do with it?

It’s a bird! It’s a plane! It’s a … UFO?


No, it’s a lenticular cloud. This stacked lens or saucer-shaped formation appeared over the foothills west of Boulder early the morning of Tuesday, Oct. 17. Illuminated by a spectacular sunrise, this particular lenticular even made the Boulder Daily Camera. 

Lenticular clouds are formed when air moves over mountains and cooling (and therefore condensation) take place. These clouds don’t move with the breeze like regular clouds, but hang out in the same place as they are continually reformed by the rising air. They usually form on the downwind side of a mountain (like Boulder!)

Hot air: NOAA’s Pieter Tans is certain about CO2


Although his ultimate boss, the President of the United States, might deny it, a Boulder climate scientist has no doubts at all that humans are causing climate change.

Pieter Tans, chief of the Carbon Cycle Greenhouse Gases Group at Boulder’s National Oceanic and Atmospheric Administration has a three-part message for climate change doubters and deniers. Human actions are 100 percent responsible for the increase in greenhouse gases. Greenhouse gases retain in the atmosphere 100 times more energy than all the energy humans produce. And some greenhouses gases will remain in the atmosphere for thousands of years, even after emissions stop.

“More CO2 will cause more warming – it’s a fact,” Tans said.


Tans can say these things with such certainty because he has spent his career measuring and analyzing greenhouse gases (primarily carbon dioxide, but also methane, water vapor and others) in the atmosphere. The Boulder lab is also home to a global reference network, which monitors air samples from around the world. The lab calibrates all the air collection canisters and measuring devices, which are subject to stringent quality control methods.


In 1972 Pieter Tans was a physics student in the Netherlands. Reading a book on humans’ impact on climate was enough to make him change his studies to earth science. More than 40 years later, Tans still cites that experience as life-changing.

“That was my conversion,” he said. “I’ve never doubted since then that mankind had a big impact on climate.”

Tans says he and his colleagues have three main goals. First is to meticulously document their methods and findings as a defense against climate change deniers.

“We have nothing to hide,” Tans said.

Second is to understand where greenhouse gases come from, where they are absorbed and how they cause the climate to respond.

And lastly, to help policy makers from different countries understand how effective their efforts are (or are not) at reducing greenhouse gas emissions.

“We need to keep more records than we did before,” Tans said. “We see that as our contribution we can make to get the world off carbon fuels.”

There is another thing Tans knows for sure: A particular sub type of carbon, known as isotope carbon 14, can enable scientists to much more accurately pinpoint the sources of CO2 from fossil fuel burning. And that could help cities and countries know whether they are meeting emissions reduction goals.

Tans’ number one scientific goal is to add carbon 14 measuring as a standard component of the global reference network. This could provide a number of additional valuable benefits, he says. This isotope, decays pretty quickly over time. Half will decay in 5,730 years. This means all the prehistoric dead plant matter we burn as fossil fuels does not contain any carbon 14 – because it has decayed and is long gone. As a result, the carbon in the CO2 produced from the burning of those fossil fuels consists of other isotopes, not carbon 14.

The upshot: If CO2 in the atmosphere is increasing due to emissions from fossil fuel burning, then we should see a decrease in the ration of carbon 14 to overall carbon. According to Tans, this is, in fact, just what’s happening. But a rigorous monitoring program would provide much more information.

It would make fossil fuel CO2 measurable and in Tans’ words “visible” in a sense. Among other things, scientists could monitor trends of emissions of fossil fuel CO2 from cities and states that have set reduction targets and thereby confirm whether they are meeting those goals.

The carbon 14 monitoring plan has been in the lab’s requested budget since 2012, Tans said. But Congress has always removed the funding. According to Tans, it would cost about $5 million a year, a seemingly paltry sum in the scope of the federal budget.

Tans is sure about many climate-related things, but he refuses to speculate about climate change impacts, saying these kinds of predictions are a form of “hubris.” He prefers to stick to the facts. For example, for every one-degree Celsius increase, the air holds seven percent more water vapor, creating the potential for stronger storms with more rain. Facts like it will take the atmosphere 100,000 years to return to the way it was before humans.

But these things don’t get him down.

“This is very painful for our future,” Tans said. “But I’m not really discouraged. I’ll just do the best I can.”

A skiable laccolith


I snapped this picture of Mount Crested Butte from my campsite in Washington Gulch. Yes, this was a beautiful sunset. But that’s not the point. See how the mountain (which kind of stands alone and is home to 1,547 skiable acres) is a pointy, dome-shape? That’s a laccolith. And Colorado has a lot of them.

Laccoliths are formed when magma intrudes up into sedimentary rock layers and creates a mountain with a domed top and flat bottom. According to the Colorado Geological Survey, the laccolith triangle extends from Carbondale in the north to Crested Butte in the south and is one of the best places to view the unique geologic formations. Other well-known mountains in the area are also laccoliths: Mount Sopris, Marcellina Mountain and Gothic Mountain to name a few.

The area around these laccoliths is also known for its high-grade coal. The heat from the intrusions baked the bituminous coal into anthracite coal. (Crested Butte was founded as a coal mining town!)

Study finds traffic is main cause of small airborne particles that contribute to climate change

A recent study has found that urban traffic is a major source of the smallest airborne aerosol particles, which could pose health risks and are a factor in human causes of climate change.

Up until now, the source of these tiny particles, known as nanocluster aerosol particles or NCAs, has not been studied extensively. It was thought that the natural atmosphere, (namely, cloud formation) was a primary source of these particles. But the study found that in urban air, these tiny aerosol particles make up a significant part of the total number of particles and are a direct result of traffic emissions.

Researchers from Tampere University of Technology in Finland conducted the study, which took place in Helsinki and other parts of Europe. Scientists measured the particles in three locations: next to a road, in a street canyon and with a mobile laboratory — a van that took measurements as it drove on highways from northern Spain, through France, Luxembourg, Belgium, the The Netherlands, Germany, Denmark, Sweden and to Finland via ferry.

The highest concentrations of NCAs were found in tunnels and the concentrations matched the daily traffic patterns at the measurement sites. The study also implies that atmospheric processes, like cloud formation, are not necessary for the formation of a large number of NCAs.

These findings help to understand the atmospheric processes that affect climate change, urban air quality and public health. The full text of the study can be found at