Coevolution and Darwin's 'abominable mystery'

A Joshua tree wields serrated blades to repel invaders. But the yucca moth is undeterred. Seduced by a succulent flower, the moth flits by hedgerows of sword-like leaves. She shrouds herself in white petals, and the ancient ritual begins.

The dusty grey insect follows ancestral instructions imprinted in her genetic code. Stakes are high: Her children’s lives are on the line.

Complex relationships among flowering plants and pollinators shape nearly every aspect of modern terrestrial life. Flowering plants are our food, shelter, clothing and medicine, yet fundamental questions remain about their sudden diversification 100 million years ago.

Charles Darwin recognized that his theory of gradual evolution was threatened by this fossilized bloom, describing it as an “abominable mystery.”

New research into the Joshua tree genome suggests that evolutionary pressures among pollinators and plants may be part of the answer to Darwin's mystery.

Coevolutionary Clues

Coevolution occurs when one species’ evolution affects the evolution of another species, which, in turn, affects the evolution of the original species.

By eating slower gazelles, cheetahs reduce the overall number of “slow” genes in gazelles’ gene pool. Fast gazelles put pressure on cheetahs to speed up, which, in turn, puts pressure on gazelles once again. The cheetah’s explosive sprint and gazelle’s nimble leap were shaped by a coevolutionary arms race over millennia.

Unlike the evolutionary footrace between cheetahs and gazelles, yucca moths and Joshua trees have a special type of coevolutionary relationship known as an obligate mutualism. Each partner depends on the other for survival. Only yucca moths pollinate Joshua trees; in turn, Joshua trees serve as nurseries for moth larvae, which feed on the plant’s seeds. But there is a twist — two of them, actually. There are two species of Joshua tree and two corresponding species of yucca moth. The pairs live in different Southwest neighborhoods, but their territories overlap in a 60-mile stretch of desert in Tikaboo Valley, Nevada.

A few hours drive from Las Vegas, the remote desert ecosystem serves as an outdoor laboratory for Chris Smith, an evolutionary biologist and professor at Willamette University. With funding from the National Science Foundation, Smith has collaborated for nearly a decade with other researchers, undergraduate science students and citizen-scientist volunteers to gather and analyze field measurements, to decode the Joshua tree’s genome, and to look for genetic signatures of coevolution between Joshua tree and yucca moth.

“Darwin described this as ‘the most wonderful case of fertilization ever published,’” said Smith. “I think it’s our best shot at solving his ‘abominable mystery.’”

Darwin’s “Abominable Mystery”

Biologists have circumstantial evidence that pollinators may be part of the answer. “Not only do flowering plants, or angiosperms, and pollinating insects proliferate in the fossil record at the same moment in deep time,” says Smith, “Four of every five plants are angiosperms; most have specialist pollinators.”

Darwin’s contemporary, French paleobotanist Gaston de Saporta, also thought pollinators were a part of the solution. He wrote to Darwin in 1877 describing a mechanism — a biological feedback loop — that could explain the rapid rise of flowering plants:

“Insects and plants have therefore been simultaneously cause and effect through their connection with each other, plants not being able to diversify without insects and the latter not being able to provide many pollen and nectar feeders so long as the plant kingdom remained poor in arrangements and was composed almost exclusively of [non-flowering] plants.” 

Unsatisfied with his own supposition — that some isolated, lost continent served as an evolutionary incubator for flowering plants — Darwin recognized the power of Saporta’s idea and immediately wrote back:

“Your idea that [flowering] plants were not developed in force until sucking insects had been evolved seems to me a splendid one. I am surprised that the idea never occurred to me, but this is always the case when one first hears a new and simple explanation of some mysterious phenomenon.”

While speculation goes back to Darwin’s time about insects’ role in arranging Earth’s flowering bouquet, major challenges have stymied efforts to demonstrate that pollinators drive speciation — a notion that’s inconsistent with the prevailing theory.

“Evolutionary theory predicts a stable relationship, or stasis, between Joshua tree and yucca moth. Their interactions shouldn’t spark evolutionary change,” says Smith. “But that’s not what our research suggests is going on.”

Evolutionary Arms Race

Because changes occur over many generations, observing evolution is particularly challenging for long-lived organisms like the Joshua Tree that might not reproduce or reach maturity for decades. Likewise, systems with multiple pollinators can confound scientists trying to determine the effect any one pollinator species has on a particular plant species.

“Many plant-pollinator interactions are among generalists, where both parties have other choices,” says Anne Royer, an evolutionary ecologist and postdoctoral researcher responsible for genomic analyses. Royer relies on Joshua trees’ exclusive pollinator relationship and hybrid zone to winnow the potential field of genetic influences and to identify snippets of Joshua tree DNA associated with a particular trait.

Researchers hypothesized that physical differences between Joshua tree flowers were related to a key feature of the yucca moth: the length of the moth’s ovipositor. Moths unfurl this needle-like organ to inject their larvae into the flower’s style – a small tube connecting the plant’s flower and ovules, or unfertilized seeds. One species of Joshua tree produces flowers with a short style. It’s pollinated by a moth with a short ovipositor. The other tree species has a longer style and is pollinated by a moth with a long ovipositor.

Smith believes that a cold war between pollinator and plant is pushing the two Joshua tree species further apart. He suspects that some Joshua trees evolved longer styles to make it harder for moth larvae to reach and eat as many seeds. Some moths evolved longer ovipositors in response.

The partners avoided mutually assured destruction for millennia through natural selection. Then a million years ago, the genetic seas parted. One species became two.

DivergenceSmith and Royer are looking in the flower’s DNA for clues to Darwin’s mystery. “If the flower is involved in speciation, we should find signs of genetic and structural variations,” says Smith.

The team relied on big data tools to track down genetic variations associated with the floral style. To see if those genes were under positive selection pressure from a particular pollinator, Smith and Royer looked for Joshua tree gene variants associated with one moth’s territory and not the other’s. They also looked for gene variants that are rare among hybrids, which suggests selection against those traits.

While these powerful tools can uncover relationships in enormous data sets, they don’t show whether a particular genetic variant actually causes the flower to develop a longer style, for example, only that plants with this genetic variant tend to have longer styles.

“When we compare across these three tests, we find a startling overlap,” says Smith. “Genetic variants that are associated with style length also appear to be under selection pressure. In fact, these genes show some of the strongest signs in the Joshua tree genome of being under selection pressure.”

Not only do the Joshua tree and yucca moth offer a clear physical target for coevolutionary influence — length of the style — the exclusive plant-pollinator relationship allow scientists to have more confidence in attributing genetic variation to the pollinator’s influence.

“There appears to be strong disruptive selection pressure on the Joshua tree flower,” says Smith, who is quick to add that his team’s research hasn’t fully resolved Darwin’s “abominable mystery.” “Our study suggests that natural selection driven by pollinators plays an important role in fostering diversity among angiosperms such as the Joshua tree and—perhaps—all flowering plants.”

Looking Under the Hood

Physicist David Altman is moved by myosin. We all are.

Myosin is a motor protein. Responsible for every conscious and unconscious flex of our muscles, it beats our hearts.

Altman wants to understand how the molecular motor works — how the roiling action inside of a cell affects myosin's function. In 2012, Altman spent his junior sabbatical at McGill University in Montreal, Canada, performing an experiment that tested competing theories about muscle fibers’ unusual mechanical properties. The results of his experiment were published April 16 in PLoS ONE.

Muscles and Motors

Muscles have an odd and poorly understand behavior. Normally, an active muscle is stiff, because its proteins interact and form connections. But when an active muscle is used in a cyclic fashion — think of your heart beating or leg muscles when you’re running — the muscle temporarily becomes softer. When the cyclic motion stops, the muscle stiffens again.

This temporary softening, called thixotropy, may be connected to our posture. Stiff muscles provide support when you sit in class, but become less stiff and more limber when you run. The mechanism of thixotropy in muscles is not well understood, though Altman suspected that myosin was the key.

At the heart of muscle fibers are two types of interlocking filaments: myosin filaments — which contain hundreds of myosin motors that tie themselves together — and actin filaments. In active muscle, myosins bind to actin. Myosins make muscles contract by pulling themselves, stroke by stroke, along the actin filament.

Loosening Up

Altman wanted to test whether the interaction between actin and myosin was responsible for muscle’s thixotropy. According to this model, muscles’ cyclic motion breaks the actin-myosin attachments and makes the muscle fiber softer. Once motion stops, it takes a little while for myosin to re-bind to actin and make the fiber stiff again.

Altman’s experiment involved disrupting actin-myosin interactions and vibrating the muscle fiber at different frequencies to measure its stiffness. Using two chemicals that prevent myosin binding to actin, Altman then tested the muscle. The loosening effect vanished.

“To people who study muscle, it was a debate as to what was responsible for thixotropy,” says Altman. ”The experiment indicates that muscles’ stiffness depends on myosin’s grip.”

Next Steps

The experiment revealed another, unknown process at work. When the cyclic motion was slow enough, Altman was surprised to find that the muscle fiber no longer softened; it became stiffer, or rheopectic. Altman suspects thixotropy depends on forces from molecules jostling within the crowded cellular environment, but no one knows how or why muscles would stiffen when subjected to low frequency vibration.

Through Willamette’s Senior Research Seminar course and through the Science Collaborative Research Program, students work with Altman to learn more about myosins’ cellular function. “In my lab, we study myosins inside cells as opposed to just purified myosins, because we want to understand physiologically relevant conditions and how they affect the motor,” says Altman.

Over the summer, he’ll move his myosin-trapping laser lab to the basement of Collins Science Center. In the fall, Altman will continue working with physics majors on their theses, while looking for more collaborative research opportunities to explore the enigmatic muscular motor protein.

Unmasking a Researcher

Kaeli Swift ’09 wears a mask as she uncovers the corpse. She knows she’s being watched.

Eerie and emotionless, the mask does its job. Swift’s hazel eyes meet obsidian stares, and her experiment begins.

Swift studies crow funerals, raucous avian flash mobs that form when a dead crow is spotted.

Crows are smart. They remember faces of threatening people and warn others to be on the lookout. To avoid being recognized and affecting the birds’ behavior, Swift and her colleagues wear masks when unwrapping the stuffed crow used in their research.

While staying undetected by the birds, Swift’s work is earning visibility of a different sort. She was recently featured on the PBS program “IN Close.”

Researchers at the University of Washington have discovered that crows might hold funerals, and sophisticated brain scans might tell why. IN Close airs Thursdays at 7pm on KCTS 9. ___________________________ Connect with IN Close: Visit the IN Close webpage: http://KCTS9.org/in-close Like IN Close on Facebook: https://www.facebook.com/KCTS9INClose Follow IN Close on Twitter: https://twitter.com/KCTS9INClose Subscribe to IN Close on YouTube: http://www.youtube.com/user/KCTS9InClose This current affairs series was made possible by viewers like you.

The Nest

Swift netted her mentors at Willamette before earning a National Science Foundation fellowship to pursue crow research at the University of Washington.

When she landed as a freshman, Swift knew she wanted to study birds. It didn’t take long to track down her undergraduate advisor, Dave Craig.

“One thing I knew that I was especially good at—for all of the other things that I felt doubt about—was networking,” Swift says. “I like birds,” she told Craig. ”I’ve been told you like birds. I want you to be my advisor.”

As a biologist who studies bird behavior, Craig says he couldn’t pass up a student named “Swift,” a nimble species of bird that targets insects mid-flight.

Swift first became a masked crow menace through collaborative work with Craig. They investigated crows’ ability to recognize individual human faces. She found another mentor in Emma Coddington, a neuroethologist who studies the effects of stress on behavior and the brain.

“She was like a laser beam,” says Coddington, smiling as she remembered meeting Swift before the start of a tough physiology class. “She stood out because she was genuinely curious and kept asking questions that indicated she was constantly integrating, thinking about how this fits in her life.”

A key part of Swift’s undergraduate life was her work with Saturday Explorations and Willamette Academy. She describes teaching through the university’s youth programs as among her most meaningful personal and most valuable professional experiences. “It’s important that students see there are all kinds of people that do science,” she says.

The Leap

Graduation came and went. Though an important chapter in her story, it’s hard to picture Swift as a recent graduate unsure if she was cut out for academia.

As someone who also struggled to imagine herself as a scientist and professor, Coddington understood such self-doubt but had no question about Swift’s ability. Coddington hired her to help set up a new physiology lab in Olin Science Center, and Swift’s mentors encouraged her to apply for an NSF fellowship. Grad school was a way to explore how her passions for teaching, fieldwork and research could fit together in her life.

Swift credits Craig and Coddington for giving her the space and the encouragement she needed, when she needed it.

“They were there to support me when I said, ‘I don’t know if I’m the kind of person who could do this,’” Swift says. They told her, “You are. Do this.”

She did.

The Ascent

Her experience with animal behavior and physiology proved invaluable to her research into crow funerals. But Swift took off for graduate school with something more: She earned the respect and admiration of her professors, especially her mentors.

“Their role as advisors wasn’t this discrete four-year period when I was an undergrad,” she says. “They’re still the people I call when I’m most ‘done’ and when I have awesome triumphs. Having the support of people who understand what it’s like to be in this profession—and what it’s like to be in this profession as woman—is really important.

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Photo, left to right: Coddington, Ramona Flatz (biology research assistant), Swift and Craig

“I knew that I picked Willamette because I could get more one-on-one attention, but I never expected to have faculty that I would invite to my wedding—and who would show up! But they did.”

Swift’s relationship with her mentors is evolving. She’s more colleague than advisee now, visiting campus in December to teach Craig’s "Behavioral Ecology" class and again in January for a biology colloquium.

As her career takes flight, crows and the NSF won’t be the only ones watching Swift. Like the birds she studies, her friends and colleagues at Willamette will be on the lookout.

“She’s amazing, and it’s been a privilege to watch her,” says Coddington. “I’m excited to see who she continues to grow into.”

Lunar eclipse video

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The total lunar eclipse from Brainard Lake, in Colorado's Indian Peaks wilderness

My passion: Understanding science

I shared the following column, which ran on March 11, 2013, as part of the "My Passion" series in our local newspaper. 

Growing up in Las Vegas with parents that insisted I venture out into summer’s sandy oven, I spent a lot of time catching scorpions, vinegaroons and all kinds of reptiles. I marveled at the way each creature seemed perfectly suited for its place — and its prey. 

I’ve seen blood squirt from the eyes of a horned lizard, and I’ve dropped a desert iguana when distracted by the whip of its separated, writhing tail. One of my best friends can attest to the wallop a small sidewinder packs.  

Despite all the time I spent exploring and experiencing the desert, it wasn’t until a college trip with friends to Zion National Park, far from the electric skies of Las Vegas, that I looked up and saw the Milky Way - the band of stars that form the “backbone of night.” I felt the bewildering immensity of nature for the first time.

I still wonder what our ancestors thought as they gathered around a fire pit and looked to the sky. Some of their answers became myths that shaped and were shaped by society, but what of the countless millions who weren’t satisfied by such explanations? Among the everyday struggle for survival, there must have been people like me — people for whom the echoing question, “What are stars?” would never be silenced.

Human nature is to seek understanding. Our minds are powerful, complex but imperfect pattern detectors. When we look at clouds, we see shapes. We impose meaning on randomness. We confuse correlation and causality. We infer intent by default, and because we are biased to reinforce our own beliefs, it takes effort to overcome an incorrect idea that has taken root. 

These biases served us well through millennia. We survived. 

Through science, we’ve opened a window to the heavens, and we’ve looked back in time to discover much about how we came to be. 

I was stunned to learn that nearly half of Americans don’t know how long it takes our planet to revolve around the sun. I cringe when politicians deny evolution. My heart breaks when children die from easily preventable or treatable conditions because parents decide against vaccines or choose prayer over medicine.

Though science has certainly demonstrated its value to our health, economy and quality of life, it is more than advanced technology or medical treatments. The scientific method is humanity’s best tool to discover truth.

I started the local Science Pub series in conjunction with OMSI, and I collaborate with scientists to help share their work with the public. I’m passionate about the public understanding of science not just because I love the mysteries of quantum mechanics, neuroscience and cosmology, but because scientific literacy affects our ability to evaluate important issues facing our society.

With our growing population, its commensurate impact, our advancing technological sophistication and proliferation of ideas and claims, we need decision makers who understand the value and methods of science. We need a scientifically literate electorate that is able to face with open eyes our economic, environmental and geopolitical challenges.

I’m passionate about the public understanding of science not only because it answers the question, “What are stars?” but because I believe that the truth is the best foundation upon which to build our future.

Professor's journey shapes student experience

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Photo by Frank Miller

David Altman described his first year teaching as more exciting than he could have imagined. It was punctuated by two nationally competitive grants to study the protein myosin, a family of motor proteins that are core pieces of cellular machinery.

When you clicked on the link to read this story, myosin was at work. It is the cell’s motor, responsible for muscular contraction among many other cellular functions.

“Myosin’s got this elegant simplicity,” Altman said. “I want to understand how the motor works.”

Collaborative research

As part of Willamette’s Science Collaborative Research Program, Altman works with Jared Green ’11 and Jesse Sant ’12. The team spent the summer building an optical trap in Collins Science Center, using a laser to examine myosin’s behavior. They will analyze the motor’s range of motion and perform experiments to study its function in retinal cells.

“I’m really excited to use the lab for my senior project,” said Green. “David and I sat down and came up with a really cool idea. We’re going to look at how the molecular motor works in endocytosis within eye cells.” Endocytosis is how cells absorb molecules from outside the cell.

“Jesse will use the lab for his junior year ATEP, Advanced Techniques in Experimental Physics, which I’ll be teaching next semester,” Altman said.

The research he and his students are doing now will act as the springboard for future projects, continuing to study myosin not just in its original form but also working to engineer specific behavior. Likewise, Altman would like to see Green’s work become the framework for a model of myosin function within eye cells.

Altman’s journey

Altman’s own intellectual voyage mirrors many students’ college journeys. “I like exploring as many things that I don’t understand as possible,” he said.

“I started working with optical traps as an undergraduate in Chicago, where we studied the dynamics of colloids – the dispersion of small particles in liquids,” Altman said. His optical trap experience paid off in graduate school at Stanford, when he was asked to be part of a biochemistry team. Ultimately his work led to collaboration with a group in India, beginning Altman’s focus on molecular motors in cellular systems.

Altman’s passion for intellectual exploration has influenced his students. The team visited Stanford to create motor proteins using the university’s specialized equipment, and the trip was transformative. “Just sitting in on some of David’s conversations with his colleagues and seeing the immersion you get in grad school where you’re constantly talking and reading about all of these subjects was really cool,” Green said.

Green’s goal is to become an educator, a goal which was well-served by working with Altman through SCRP. “Having a research background and being able to bring a lab to a department would be an advantage,” he said.

Outside the lab

Even the staunchest researchers need a break from the darkened laboratory space required for such optical trap experiments. Altman often meets with students outside of the Collins Science Center to discuss the team’s work or occasionally to jam.

“Willamette has been fun in that you get to form really close relationships with a lot of professors,” Green said. “I first got to know David when we played in a band last semester at Wulapalooza. It was called ‘Dr. Altman’s Bird Refinery,’ and we had a really good time.”

Altman is a percussionist. “We’re looking at playing bluegrass this year,” he said.

When not in the lab or teaching, you might see Altman downtown at Governor’s Cup, Venti’s or Tangled Pearls, a new knitting shop. “Our lab in general has become a big fan of Clockworks Café,” Altman said. “That’s become a regular meeting spot.”

Whether in class, working in a lab or chatting over coffee, Altman appreciates the opportunity to get to know students personally. “The interactions in the small classes at Willamette were so wonderful,” he said. “I definitely ended my first year thinking I’m in the right place.”

Watkins' research presents a challenge for current cosmological model

According to Richard Watkins’ latest research, nearby galaxies have an enigmatic “flow,” like billiard balls rolling on a slightly tilted table – motion that challenges the current cosmological model.

Watkins, a physics professor at Willamette University in Salem, Ore., is at the leading edge of research into the movement of galaxies. He works with Hume Feldman from the University of Kansas and Michael Hudson from the University of Waterloo to use satellite data to draw conclusions about how galaxies flow.

In 2001, NASA launched the Wilkinson Microwave Anisotropy Probe (WMAP), which measures remnant light from the Big Bang. This light loses energy as the universe itself expands. By measuring tiny differences in the resultant low-frequency microwave radiation, WMAP’s precise scans define parameters of mathematical models of the universe.

WMAP image of the universe's matter density at 380,000 years

According to the prevailing model, the expansion of space causes all galaxies to recede from each other. Galaxies also flow towards areas of higher concentrations of mass because of gravity. The model makes very specific predictions about how galaxies should move based on expansion and gravity. Scientists refer to any additional movement as “peculiar velocity.”

Watkins’ team measures this peculiar velocity by directly comparing previous surveys of differing volumes of space from “nearby” galaxies – within 163 million light-years of Earth.

His team calculated that nearby galaxies are flowing quickly, at the very edge of consistency with the prevailing model. “What’s the likelihood that a universe with the WMAP parameters could give us this big of flow?” Watkins asked. “It’s less than 2 percent.”

The simplest explanation for the flow found by Watkins’ team is that we live in a statistically unlikely volume of space. “If you had a hundred volumes, you’d expect one or two out of a hundred to be moving with this velocity,” Watkins said.

A researcher from NASA’s Goddard Space Flight Center, Alexander Kashlinsky, takes Watkins’ results much further. Kashinlisky cites Watkins’ work in a recent article as potential support for Kashlinsky’s notion of “dark flow.”

Kashlinsky’s team uses a different technique to look much further away on a much larger scale. In their latest paper, the team claims to have found evidence of a large flow of galaxies that is in roughly the same direction as the much smaller flow measured by Watkins’ team in nearby space.

While Watkins’ measured flow is improbable but within the bounds of the prevailing model, Kashlinsky’s results would require a major revision. Kashlinsky suggests the flow “might provide an indirect probe of the Multiverse,” a theory that suggests that our universe may be part of a higher dimensional space in which there are many – or even and infinite number of – other universes, potentially with different physical laws.

His results have met with some skepticism in the scientific community. Several physicists have taken aim at Kashlinksy’s conclusions, specifically the way he computes the level of uncertainty in his calculations.

According to Watkins, figuring out uncertainty on such extreme scales is difficult, and his next step is to use computer simulations to test his team’s assumptions. Watkins also expresses some reservations about tying his team’s results to Kashlinksy’s conclusions.

“There may be some process that we don’t understand. Perhaps something that occurred between the Big Bang and now to cause this peculiar velocity, but you don’t need something radical to explain our flow.”

Scientists remain conflicted about the extent, direction and cause of the flow. “We need more data,” Watkins said. “This is an indication that something is not quite right. Right now, it’s just a hint.”