Category Archives: Uncategorized

It’s a Bird Eat Bird World

Female sage-grouse in eastern Oregon, 2017. Photo credit: Hannah White

Over the last half century, populations of Greater Sage-grouse – a relative of pheasants and chickens – have declined throughout their range. Habitat loss and degradation from wildfires is regarded as a primary threat to the future of sage-grouse in Oregon. This threat is exacerbated by the spread of invasive annual grasses (read: fuel for fires). In addition, raven populations, a predator of sage-grouse nests, are exploding. But how does all of this relate? PhD student Terrah Owens of Dr. Jonathan Dinkins lab in the Department of Animal and Rangeland Sciences at Oregon State University and her colleagues are trying to find out.

Specifically, Terrah’s research is focused on the impact of wildfire burn areas – the burn footprint and edge – on sage-grouse predation pressure and how this influences habitat selection,

Terrah Owens with a radio-collared female sage-grouse in Nevada, 2015.

survival, and reproductive success. To do this work Terrah is characterizing six sites in Baker and Malheur counties, Oregon, based on their burn history, abundance of avian predators, shrub and flowering plant cover, as well as invasive annual grasses. To monitor sage-grouse populations, Terrah captures and radio-marks female sage-grouse to identify where the birds are nesting and if they are producing offspring. Additionally, Terrah conducts point counts to determine the density and abundance of avian predators (ravens, hawks, and eagles) in the area. Burn areas generally provide less protective cover for prey, making it an ideal hunting location for predators. Ultimately, Terrah hopes her work will help determine the best ways to allocate restoration funds through proactive, rather than reactive measures.

An encounter with a Bengal tiger at a petting zoo as a young girl inspired Terrah’s lifelong interest in wildlife conservation. As an undergraduate, Terrah studied Zoology at Humboldt State University in Arcata, CA. She then interned at Bonneville

Banding a juvenile California spotted owl, 2016.

Dam on the Columbia River for the California sea lion and salmon project. After this she went on to work for the U.S. Forest Service in northern California as a wildlife crew leader working with spotted owls, northern goshawk, fisher, and marten, among other species. She eventually moved on to work with sage-grouse in Nevada with the U.S Geological Survey.

After graduate school, Terrah would like to head a wildlife service research unit and apply her wealth of knowledge and government experience to bridge the gap between scientists and policymakers.

Join us on Sunday, December 10, at 7 PM on KBVR Corvallis 88.7 FM or stream live to learn more about Terrah’s research, how she captures sage-grouse, and her journey to graduate school.

Ocean basins are like trumpets– no, really.

We’re all familiar with waves when we go to the coast and see them wash onto the beach. But since ocean waters are usually stratified by density, with warmer fresher waters on top of colder, saltier ones, waves can occur between water layers of different densities at depths up to hundreds of meters. These are called internal waves. They often have frequencies that are synched with the tides and can be pretty big–up to 200 meters in amplitude! Because of their immense size, these waves help transfer heat and nutrients from deep waters, meaning they have an impact on ocean current circulation and the growth of phytoplankton.

The line of foam on the surface of the ocean indicates the presence of an internal wave.

We still don’t understand a lot about how these waves work. Jenny Thomas is a PhD student working with Jim Lerczak in Physical Oceanography in CEOAS (OSU’s College of Earth, Ocean, and Atmospheric Sciences). Jenny studies the behavior of internal waves whose frequencies correspond with the tides (called internal tides) in ocean basins. This requires a bit of mathematical theory about how waves work, and some modeling of the dimensions of the basin and how it could affect the height of tides onshore.

Picture a bathtub with water in it. Say you push it back and forth at a certain rate until all the water sloshes up on one side while the water is low on the other side. In physics terms, you have pushed the water in the bathtub at one of its resonant frequencies to make all of it behave as a single wave. This is called being in a normal mode of motion. Jenny’s work on the normal modes of ocean basins suggests that the length-to-width ratio and the bathymetry of an ocean basin influence the structure of internal tides along the coast. Basically, if the tidal forcing and the shape of the basin coincide just right, they can excite a normal mode. The internal wave can then act like water in a bathtub sloshing up the side, pushing up on the lower-density water above it.

It turns out that water isn’t the only thing that can have normal modes. The air column in a wind instrument is another example. Jenny grew up a child of two musicians and earned a degree in trumpet performance from the University of Iowa, and she occasionally uses her trumpet to demonstrate the concept of normal modes. She can change pitches by buzzing her lips at different resonant frequencies of the trumpet–the pitch is not just controlled by the valves.

Jenny uses her trumpet to explain normal modes.

Near the end of her undergraduate degree at the University of Iowa, Jenny discovered that she had a condition called fibrous dysplasia that could potentially cause her mouth to become paralyzed. Deciding a career as a musician would be too risky, and realizing her aptitude for math and physics, she went back to school and earned a second undergraduate degree in physical oceanography at Old Dominion University. After a summer internship at Woods Hole Oceanographic Institution conducting fieldwork for the US Geological Survey, she decided to pursue a graduate degree at OSU to further examine the behavior of internal waves.

Tune in to 88.7 KBVR Corvallis to hear more about Jenny’s research and background (with a trumpet demo!) or stream the show live right here.

Jenny helps prepare an instrument that will be lowered into the water to determine the density of ocean layers.

Jenny isn’t fishing. The instrument she is deploying is called a CTD for Conductivity, Temperature, and Depth–the three things it measures when in the water.

Secrets of the Black Cottonwood

Ryan cultivated his interest in plants at a young age while checking wheat fields with his dad on the family farm near Beltrami, MN.

Growing up on a family farm in North Dakota, Ryan Lenz loved learning about wheat – specifically the things that made wheat varieties different. Why were some taller or shorter than others? Why did some have more protein? After gaining skills in molecular biology at North Dakota State University with a Bachelor of Science in Biotechnology, Ryan interned with a biotech company where he was finally able to make the connection between wheat varieties and the genes that make them different. This experience sparked his interest and led him to earn a Master’s degree in Plant Sciences at his alma mater and eventually brought him to OSU’s Department of Botany & Plant Pathology to study host-pathogen interactions as a PhD student with Dr. Jared LeBoldus.

Using black cottonwood (Populus trichocarpa) – a native tree to the western US – Ryan is working to reveal the genes responsible for making woody plants susceptible to fungal disease and those that give the fungus the ability to infect trees. The fungus of interest, Sphaerulina musiva, causes leaf spot and stem canker on cottonwood trees – the latter disease being more severe as it girdles the trees and causes the tops to break off.

Ryan tending to his tissue culture plants in the LeBoldus Lab.

The fungal pathogen was first found in the eastern United States in association with the more resistant eastern cottonwood (Populus deltoides), but has worked its way westward putting the susceptible black cottonwood at risk. This fast-growing cottonwood is a foundation species in riparian areas and provides erosion control. Not only are these trees important ecologically, they are also important in forest agriculture for their uses in making pulp for paper, biofuels, building materials, windbreaks, and for providing shade.

Ryan and his wife, Rebecca, enjoying the beautiful Pacific Northwest.

To learn how the tree and fungus interact, Ryan employs advanced molecular techniques like the CRISPR-Cas9 system to edit genes. To put it simply, he tries to find the important information in the plant and fungus by making changes in the genetic code and then seeing if it has a downstream effect. The implication of his work has two sides. On one hand, Ryan is trying to provide cottonwood breeders with insight to make a more resistant tree to be grown in the western US. While on the other hand, he is working to establish the black cottonwood as a model system for other woody hosts susceptible to necrotrophic fungi – those that feed on dead tissue. As a model system, the secrets of the black cottonwood would be unveiled, providing a blueprint of valuable information that could be applied to other woody trees.

 

One day, Ryan hopes to move back to the Midwest to be a plant researcher near his family’s farm.

Join us on Sunday, November 5, at 7 PM on KBVR Corvallis 88.7 FM or stream live to learn more about Ryan’s love for plant genetics and his journey to graduate school.

Tracing Goethe’s influence on botany and plant morphology

As a History of Science PhD student in the School of History, Philosophy, and Religion, Andy Hahn studies how botanists and plant morphologists in the 20th century were influenced by Goethe, a famed German writer and naturalist during the 19th century. Goethe is well known for his rendition of Faust, as well as his novel, The Sorrows of Young Werther. Although historians and philosophers have studied Goethe extensively, his influence on subsequent generations of botanists and plant morphologists has not been fully explored. Goethe wrote a book called Metamorphosis of Plants, which provided early foundational insight into morphology, the study of plant structure and appearance of plant features such as leaves and petals. For his PhD work, Andy has visited institutional archives in Switzerland, England, and Scotland to study the letters and writings of 20th century botanists and other scientists influenced by Goethe’s science.

Goethe’s science was characterized by taking account appearance and structure of plants as a whole entity, as opposed to focusing only specific parts of the plant, a method employed in the taxonomy of Linnaeus, a prominent 18th century natural historian. As the 19th century progressed, Goethe’s approach towards morphology was well-integrated in botanical science in Germany, France, and England. However, the rise of Darwinism, genetics, and experimental methods in the late 19th and early 20th centuries was accompanied by a decreased role for Goethe’s style of morphology. In the early 20th century, plant morphologist community split into two groups: new morphology based in Darwinian thought, and old morphology based in Goethe’s principles. The influence of Goethe’s writing can be seen among botanists in the 20th century, including Agnes Arber, a plant morphologist who translated Goethe’s Metamorphosis of Plants into English.

Andy was introduced to Goethe’s scientific work as he continued to follow his interests that arose from his as an undergraduate in philosophy. He appreciated Goethe’s and current Goethean scientists’ approach to plant morphology as a means to understand the natural world. By visualizing a plant through the course of its life, he was able to develop a stronger connection to the natural world, awakening his own senses by meditating on the form of plants. Andy found himself wondering what happened to the ideas of Goethe, and why Goethe’s ideas weren’t recognized more commonly in biological education. He became interested in philosophical questions surrounding why we think the way we do, as well as the accumulation of knowledge; in particular, how we produce scientific knowledge, and how we can be certain about it. During his Masters studies at OSU, Andy first began researching the botanical work of Goethe, and has continued to study the influence of Goethe on 20th century botanists for his PhD work. Following completion of his graduate studies, Andy would like to teach history of science at the university level and pursue science writing.

To hear more from Andy about the influence of Goethe’s science on botany and plant morphologists, tune in to Inspiration Dissemination on Sunday, October 22 at 7pm on 88.7 KBVR Corvallis. Or stream it online here!

The Breathing Seafloor

In the cold, dark depths of the seafloor across the world, microbes living in sediments and on rocks are quietly breaking down organic material and sucking dissolved oxygen out of the seawater. The continental shelf off of Oregon’s coasts, home to a fishing industry that brings in over a hundred million dollars of revenue per year, is no exception. Does oxygen consumption, and therefore carbon cycling, vary by location, or across seasons? Setting a baseline to investigate these patterns of oxygen drawdown is crucial to understanding habitats and distributions of fish stocks, but will also establish what “normal” oxygen consumption looks like off our shores. Measurements like these are also used by the Intergovernmental Panel on Climate Change (IPCC) to estimate global patterns of carbon burial. If any forces were to shift these patterns in the future, we’d at least have a baseline to allow us to diagnose any “abnormal” conditions.

Peter Chace is a third-year PhD student of Ocean Ecology and Biogeochemistry in the College of Earth, Ocean, and Atmospheric Sciences (CEOAS). Peter’s research focuses on developing a technique of measuring fluxes of oxygen across the seafloor called Eddy covariance. This technique takes high-resolution time measurements of three-dimensional velocities of water moving in turbulent whorls, or random circular patterns, within the boundary layer of a fluid like air or water. Eddy covariance has been employed to measure fluxes across air layers on land for decades, but has only recently been applied in marine systems. A point-source oxygen measurement within this turbulent layer is measured with a microelectrode and combined with the velocity data to develop a flux. Why go through all this trouble? Other ways to measure oxygen fluxes, like putting chambers over an area of seafloor and waiting to measure an oxygen drawdown, require a lot of work and give little temporal resolution.

Workers on the RV Oceanus, Oregon State’s largest research vessel, deploy a benthic (seafloor) oxygen sensor.

Peter can calibrate his microelectrodes to measure other chemicals and obtain their fluxes across the seabed, but he is mainly focused on oxygen. To measure fluxes off the Oregon coast, Pete and his advisor, Dr. Clare Reimers, will head to sea on the RV Oceanus several times this fall and winter to deploy their sensor on the seafloor for days at a time. The desk-sized seafloor lander and the microelectrode attached to it are fragile, and the rough seas offshore Oregon in fall and winter will make it a challenging endeavor. We hope they pack enough seasickness medication and barf bags!

You get right up close and personal with the ocean when you send down these instruments… and this is on a clear day with calm seas!

Since growing up as a child in New Jersey, Peter has always wanted to learn about the ocean. While studying chemistry and marine biology at Monmouth University (in New Jersey) as an undergraduate, he completed a summer REU (Research Experience as an Undergraduate) with his current advisor, Clare Reimers, here at Oregon State University. He also interned for NOAA (the National Oceanic and Atmospheric Association), analyzing the chemistry of hydrothermal vent fluids with Dr. David Butterfield. Pete revisited a hydrothermal system on a cruise to the East Pacific Rise off of Central America where he got a remarkable opportunity to dive in Alvin, the submersible that discovered the wreckage of the Titanic.

Here’s Pete in the submersible Alvin just before the dive, checking his microelectrodes.

To hear more about Peter’s research on sensor development and his seafaring expeditions, tune in to Inspiration Dissemination on Sunday, October 15th at 7pm on 88.7 KBVR Corvallis. Or stream it online here!

Breaking the Arctic ice

 

Thermal AVHRR image with land masked in black. Can see the lead coming off of Barrow Alaska very bright. The arrows are sea ice drift vectors.

Cascade over mossy rocks near Sol Duc Falls, Olympic National Park, WA.

When you hear about fractures in sea ice, you might visualize the enormous fissures that rupture ice shelves, which release massive icebergs to the sea. This is what happened back in July 2017 when a Delaware-sized iceberg broke off from the Larsen C ice shelf in Antarctica. However, there are other types of fractures occurring in sea ice that may be impacted by atmospheric conditions. Our guest this week, CEOAS Masters student Ben Lewis investigates how interactions between the atmosphere and sea ice in the Beaufort Sea (north of Alaska in the Canadian Archipelago) impact the formation of fractures. His research involves mapping atmospheric features, such as wind and pressure, at the point in time when the fractures occurred and provides insight into the effect of the atmosphere on the formation and propagation of fractures. Utilizing satellite imagery compiled by the Geographical Information Network of Alaska from 1993 to 2013, Ben has conducted a qualitative analysis to determine the location and time when these ice fractures occurred and what type of physical characteristics they possess.

Southern Alps from the summit of Avalanche Peak, New Zealand.

While fractures appear small on the satellite image, the smallest fractures that Ben can observe by are actually 250 meters wide. Fractures can span hundreds of kilometers, and the propagate very quickly; Ben cites one example of a fracture near Barrow, Alaska that grew to 500 kilometers within 6 hours!

Fractures are potentially deadly for people and animals hunting in the Arctic. As weather flux in the fragile Arctic ecosystem has become more erratic with climate change, it has been difficult for people to predict when it was safe to hunt on the ice based on patterns observed in prior seasons. Additionally, it has been problematic to track weather in the Arctic because of its harsh conditions and sparse population. A well-catalogued record of weather is not available for all locations. Modeling atmospheric conditions, such as pressure and wind, based on what has been captured by satelliteimagery, will facilitate better prediction of future fracture events.

Sunset over Sandfly Beach, New Zealand.

While pursuing an undergraduate degree in physics at the University of Arkansas, Ben was able to study abroad James Cook University in Australia, where he gravitated towards environmental physics, while taking advantage of incredible opportunities for nature photography. He also did a semester abroad in New Zealand, where he studied geophysical fluid dynamics and partial differential equations. Ben came to OSU as a post-baccalaureate student in climate science, and while at OSU, he became acquainted with his future PI, Jennifer Hutchings,  and his interest in Arctic research grew. He cites learning about snowball earth, glaciology, and the cryosphere, as providing the basis for his desire to pursue Arctic climate research. Eventually, Ben would like to pursue a PhD, but in the immediate future, he plans to keep his options open for teaching and research opportunities.

 

To code or not to code: the way forward for machine learning

In a rapidly changing word of technology and engineering advancements, we’re reminded of Charles Darwin’s words it’s not the strongest that survive, but the most adaptable. For humans this means learning from our errors, one painful mistake at a time, and fixing our approach so we do not stumble again. We’re limited by our personal experiences so we can only adapt once we approach a problem; but by then it may be too late. Imagine having the collective wisdom and understanding of everyone’s experiences so that you know how to solve problems you’ve never seen before. This is the beauty of machine learning.

 

Behrooz hanging out in front of the Magnolia’s in the MU

If you haven’t heard of machine learning, then it’s just a matter of time. These techniques are already involved in highly complex board games, advertising optimization, and especially self-driving cars. It’s difficult to say how impactful machine learning will be to our everyday lives because the applications of this field are still being discovered. One of the primary foundations of machine learning is researching how computers interpret visual information so computers can make on-the-fly adjustments to stop for a pedestrian or speed up to merge on the freeway.

Behrooz Mahasseni recently finished his Ph.D. in Electrical Engineering and Computer Science where his research focused on how computers interpret video recordings. As part of his research, he worked on a project to analyze football videos to identify specific patterns like huddles, punts, and special teams plays. This is specifically useful for football recruiters who don’t have time to watch 3.5-hour football games when they’re looking for a good wide-receiver for their team. Behrooz’s work helps the computer understand when passing plays occurred so the football recruiter can watch the ‘highlights’ reel for five minutes and get all the information they need to make a hiring decision. This seems rather easy, but Behrooz worked on this for high school football games where the video is not in high definition, from an oblique angle instead of a birds-eye-view, and probably has a very excited parent-videographers jumping up and down for major plays. Obviously teaching a computer to understand videos is easier said than done, but Behrooz was able to get all this accomplished with a high degree of accuracy that helped him land a job with Apple. He’s described this job as research and development using the skills he learned in graduate school (that’s about all he can say) but it took him many years of school to finally realize he had the skills to act as the spearhead of technological innovation.

Behrooz’s family including his wife Mitra and Behrad celebrating the Persian New Year March 2016

There is so much more to discuss with Behrooz, especially about where the field of machine learning and artificial intelligence is moving. We will also discuss his first experience with a robotic competition in Tehran, his decision to move to the United States, and his never-ending drive for finding and solving new problems. Be sure to listen in Sunday September 3rd at 7PM on 88.7 KBVR Corvallis!

Project CHOMPIN: Parrotfish, nutrients, and the coral microbiome

CHOMPIN comic.

Ecology is the study of the relationships among organisms and the relationships of organisms to their physical surroundings. The interactions of organisms can be described as a complex web with many junctions or relationships, and a single ecologist may focus on one or many relationships in a community or ecosystem. Our guest this week, Rebecca (Becca) Maher PhD student in the Department of Microbiology, is interested in the effect of environmental stressors on the coral microbiome. Let’s break this down by interaction:

  • Beneficial algae, bacteria, and viruses interact with coral by living in coral tissue and forming the coral microbiome
  • Corals interact with other organisms in the coral reef ecosystem, such as parrot fish
  • Corals are affected by their surrounding environment: water temperature, water nutrients, and pollution

Becca at the Newport aquarium for Scientific Diver Training through Oregon State University.

You may be familiar with coral bleaching and coral reef decline from our past episodes. Corals form a mutualistic relationship (both organisms benefit) with algae, where algae take shelter within coral tissue and provide the coral with food from photosynthesis. It is well known that high temperatures lead to coral bleaching, or a shift in the coral microbiome resulting from the loss of beneficial algae that live within the coral. Coral bleaching is often fatal.

Becca is interested in other aspects of the coral microbiome, such as differences in the symbiotic bacterial communities brought about by nutrient enrichment from agricultural run-off and overfishing. Do corals in nutrient rich water have a different microbiome than corals in nutrient poor water? Do corals in highly fished areas have a different microbiome than corals in fish-rich areas? In overfished areas, predatory fish (e.g. parrotfish) may bite coral (hence Project CHOMPIN), and so how does the coral microbiome respond after wounding by parrotfish?

Becca diving at the Flower Garden Banks National Marine Sanctuary in the Northwest Gulf of Mexico for her undergraduate thesis at Rice University.

These questions are relevant for our knowledge of environmental factors that threaten coral reef ecosystems. Corals are in decline globally and with them are the high diversity of marine species that gain shelter and substrate from the coral reef. The information gained from Becca’s research may be informative for policy makers concerned with agricultural practices near marine areas and fishing regulations.  Rebecca is traveling to Morrea, French Polynesia this August to set up her field and laboratory experiments at the Gump Biological Research Station.

This upcoming trip is highly anticipated for Becca, who has been pursuing research in marine ecosystems since her time at Rice University. After working with her undergraduate mentor Adrienne Correa at Rice, Becca’s general focus on Ecology shifted to a focus on Marine Ecology. For Becca, her project at Oregon State in the Vega Thurber Lab is a harmonious mix of field work, high-level experimental design, bioinformatics, and statistics—a nice capstone for a Marine Ecologist with aspirations for future research.

Hear more about Becca’s work with corals the Sunday at 7 PM on KBVR Corvallis 88.7FM. Not a local listener? Stream our broadcast live.

Seeing live animal exhibits can be a powerful experience, but do they change our behaviors?

Imagine you’re at the San Diego Zoo Safari Park cheetah run. You hear the sounds of awe and wonder as the cheetah demonstrates its amazing speed. The zookeeper tells you more about the cheetah and its ecosystem – an ecosystem that is being negatively impacted by humans. You walk away with tangible ways that you can do your part to reduce your impact – recycling, using less plastic. But when you exit the zoo gates and enter back into the hustle and bustle of life, do you actually make those changes?

Nicolette and Ebony, the raven, at Moorpark College in 2007.

Working under the advisership of Dr. Shawn Rowe in OSU’s College of Education, Nicolette Canzoneri is passionately pursing a Master of Science degree in Environmental Sciences with research centered around the idea of free-choice learning – or, the education that happens outside of a formal school environment. The menagerie of animals that zoos and aquariums have historically been known for has transitioned in recent years to conservation efforts. Instead of a spectacle, the animals – often rescued and unable to be re-entered into their natural environment – act as ambassadors for their ecosystems. This summer, Nicolette will be conducting a three-part project to get to the heart of human behavior changes based on interactions with live animal exhibits at zoos and aquariums.

First, Nicolette will be interviewing education directors and animal care supervisors to understand how the education programs are designed to target pro-environmental behavior. She will then observe the programs to determine the degree to which they align with the intended educational and behavioral goals. Despite the nuances of evaluation, Nicolette then plans to discover the if, how and why of evaluations being used to determine effectiveness of these educational programs. Ultimately, she hopes that her research can help to fill the knowledge gaps between theories and principles in applied behavioral studies and their implementation in free-choice learning.

Nicolette with her Animal Behavior students at Moorpark College in 2015.

Nicolette brings a wealth of experience in animal training and applied behavioral psychology to her research. As a teenager Nicolette knew that she wanted to work with animals, but it wasn’t until she found herself watching the Animal Planet reality TV show Moorpark 24/7 that she realized animal training was part of her calling. Nicolette went on to pursue her dream by obtaining her Exotic Animal Training & Management degree at the prestigious Moorpark College near Los Angeles, CA. Through the twists and turns of her career, Nicolette has since obtained a bachelor’s degree in Applied Behavioral Analysis at California State University, Sacramento and volunteered, interned, and worked in some interesting places along the way including as a dog trainer in Austria, an animal trainer at the Playboy Mansion, and most recently training dolphins for reconnaissance for the United States Navy.

Nicolette with her two dogs in San Diego, 2016.

Join us on Sunday, June 17 at 7 PM on KBVR Corvallis 88.7 FM or stream live to dive deeper into Nicolette’s free-choice learning research and journey to graduate school.