Wednesday, April 22, 2015

1000 Word Challenge: The dynasty of the Biology Department lives on!

      On April 9th the Forum on Science Ethics and Policy (FOSEP), the Young Naturalists' Society of the Pacific Northwest, and the Burke Museum hosted the 3rd Annual 1000 Word Challenge. The event challenges UW graduate students in STEM research and policy fields to explain their research using ONLY the 1000 most commonly used words in the English language, AKA no jargon. The event was a big success and Biology continued its track record of excellence. 
      2013: Yasmeen Hussain won overall, while Jonathan Calede and Brandon Peecook won style awards.
      2014: Dave Slager took home the gold.
      2015: Dave Slager begins a reign of his own as returning champion! Jen Day earned 2nd place. This was also the first year awards were given out by popular vote rather than by a panel of judges made up of science communication and public outreach experts.
      Biology entries below!

DAVID SLAGER (Klicka lab)

1000 Word Entry: On a nice summer day at our school, you can enjoy having lunch outside on the red rock-covered ground next to the pretty old building for getting books.  During lunch, you will see two types of big, loud, warm-blooded flying animals that like to eat pieces of left-over lunch.  One kind is white and grey and black and often spends time by the water.  I'm not talking about that kind.  I'm talking about the smaller black ones that have bright minds and sleep in trees together in groups of hundreds.  For many years now, people with nothing better to do have said that there are two different kinds of these black flying animals in our part of the world, even though the two kinds appear exactly the same. Looking at a picture of the land up on a wall, they say that one kind lives above where we are and the other kind lives under where we are. But can you see the problem?  Anyone who goes outside at our school knows that there is no clear line -- the flying black animals live here too.  What kind are the ones here?  Are they the above kind, the under kind, or a cross between the two kinds?  If the two "kinds" make babies with each other and those babies often go to other places to find love and make more babies, then can we even say there are really two "kinds" at all?  
      I study these questions by reading the letters on the very tiny stairs that wrap around each other inside all living things.  It is actually a pair of stairs, with one coming from the mother and one from the father.  The different letters on these stairs tell the baby's body what kind of grown animal to make.  I read the letters from the stairs into the computer, and ask the computer to tell me the answers to all my questions.  But it is a little harder than I am making it sound.  
      If there are really two different kinds of black flying animals, then I would expect to see signs of this in the letters on the stairs.  So far, the computer is telling me that there is only one kind of black flying animal here and that the people with nothing better to do were wrong about there being two kinds, but I'm still looking at other possible things to make sure this is the right answer.  
      Thanks for letting me tell you about what I do.  Now, next time you see a big black flying animal outside, you will have something new to wonder about.
Technical entry: A phylogenomic assessment of introgression and species limits in the American/Northwestern Crow complex.

                                                                                    JENNIFER DAY (Wasser lab)
1000 Word entry: Big cats are important to the world, they eat little food animals so there are not too many, which keeps trees, water, and air happy. Those are important things for humans too. Big cats move lots and do not like humans. Humans cut down trees where little food animals live, put bad things in the ground, and make lots of noise. Big cats hate that. When baby big cats grow up, they look for a home place where no other big cats live and where annoying humans are far away. If humans are in the way or there are no trees for little food animals to live in, then big cats have no home place and they die. If baby big cats do find a new home place, then they make more baby big cats. But how do we know where baby big cats go when they grow up? They are very hard to see, there aren't many of them, and they don't like us. So how do we learn about them???  We look for their shit! (We have dogs help, because they are really good at smelling cat shit) Big cat shit tells us all about their life - who their mom and dad are, what little food animals they ate, and if they are sad or scared. Using this, we can tell what humans are doing to the land that hurts big cats, and make better home places for big cats away from humans.  This makes the land a better place for both big cats and humans.
Technical entry: I use molecular ecology tools to answer conservation questions.  Specifically, I combine landscape genetics and endocrinology to investigate resource use and habitat connectivity of jaguars and puma in southern Mexico.

LEANDER LOVE-ANDEREGG (Hille Ris Lambers lab)
1000 Word entryWe are changing the things that a tree needs to grow. Trees die when they're dry and we're changing the rain. Some trees like it cold, and we're making it hot. What will trees do? Where will they go? How will they live and where will our children be able to find them? These are the questions I ask, because trees will need help dealing with shit that we're throwing at them. If our children and their children are to build tree houses and play in the woods after we check out, we have a lot of work to do.
Technical entry: I study the ecological impact of climate change on the forests of the western United States. Specifically, I explore how climate and species interactions constrain the geographic ranges of tree species in order to develop a mechanistic and predictive framework for understanding the ongoing restructuring of our forest communities.

                                                                                     JARED GRUMMER (Leaché lab)
1000 Word entryI study love between animals with cold red water stuff inside them. When mom and dad come from very different groups and can make babies, a new animal type might be made. Babies in this new group have some body parts from mom and some from dad. But remember, mom and dad are very different from each other! I am interested to know which parts of the important group of letters inside them, that all animals share, come from the mom group, and which come from the dad group. Then, I can begin to understand which parts of the important group of letters make it so some moms can't make babies with some dads, and how types of animals with cold red water stuff inside them stay the way they are over time.
Technical entry: I am interested in understanding the evolutionary processes that occur at the boundaries between species. In hybridizing taxa, two parental species may merge into a single (hybrid) population, or species boundaries may be reinforced through natural and/or sexual selection. I use genomics to understand particular traits that may be involved in maintaining species boundaries of South American lizards.

Sunday, April 12, 2015

Gideon Dunster: Outreach with Taf Academy and STEM OUT

At the beginning of the fall of last year I began working with a volunteer group called STEM OUT. This group, headed by a UW graduate student in the education department, is seeking to create mentoring relationships between graduate students and professionals with high school students from classically underrepresented groups in science. For the past 7 months, this small group of graduate student mentors have been making bi-monthly trips to TAF academy in Kent to meet with our "mentees" to talk science, college preparation, classwork, lab work, and the other general interests of life that are important to high schoolers.

TAF academy is a public school that was started in 2008 through a partnership between the nonprofit Technology Access Foundation and the Federal Way Public School district whose goal is to reach out to students from classically underrepresented minorities in STEM fields in order to help them succeed. STEM OUT was started as a partnership with TAF Academy to provide mentoring to students who wanted the opportunity to learn from individuals actively pursuing STEM careers in academia or the private sector.

There is no specific goal for this project, we are not supposed to ensure the students graduate on time or make it in a specific career. Rather, we have spent our time helping out with a myriad of questions, building a layer of support that the students can rely on, and providing an example of what you can do with a career in STEM if that is what they decide to do. We are there to make connections and, in some cases, settle important scientific questions like if toilet paper should be installed with the leading edge over or under (a topic which included a 10 minute formal debate with opposing sides and judges).

As an obvious extension of that work, on Friday March 27th the majority of STEM OUT students took a field trip to the UW in order to tour the labs of their mentors and participate in some awesome hands-on science. The timing was great because the university was out for Spring Break so no one minded 20-30 high school students poking their heads in labs. During the morning, I lead a group of 9 of our high schoolers around to two of our other mentors labs so the kids could see some science in action. In our first lab, the students used common berries to make photovoltaic solar cells and then got to measure their electrical output. In the second lab, the students were taught how bacteria can produce light and the ways that viruses can cause cancer. I was proud of how involved the students got into each project and the amount of really awesome questions they asked. 

The workspace. The black laser (top) shoots down into the muscle.

Finally, in the afternoon our groups broke up and I lead my "mentees" to the Daniel Lab in order to show them the work that I have been doing during my rotation. For those of you who don't know, I have been spending my time helping with a project investigating the physics of muscle contraction. In short, I have been stimulating frog leg muscles while passing a laser through in order to measure the cross-bridge interactions during contraction. This project is not only fun, but it results in some pretty cool pictures. Muscle proteins are so highly organized and regular, that when you pass a laser through it, it produces repeating lines (see photo below). How those lines move during contraction gives us a measure of how the proteins are interacting. After a quick demonstration to what I can only describe as a captive audience (the bus wasn't leaving for another half hour so they had nothing better to do than to listen to me yammer on) it was time to head back to the bus and send them on their way.
Muscle is made up of two main proteins: actin (thin filaments) and myosin (thick filaments). These two proteins slide along  each other during contraction, that's what causes the muscle to shorten. The z-disks are where the actin proteins come together and form a line, an anchor if you will. Muscle is so highly organized that these z-disks (and there are millions of them) line up even when we scale up to the size of a whole muscle. What we do when we shoot a laser through the muscle is bounce the light off of those repeating z-disks, resulting is the discrete lines you see in the picture. Those lines are for all intents and purposes, a real-time visualization of the z-disks. Thus, when we stimulate the muscle and those fibers slide past each other, the distance between the z-disks changes. The laser allows us to watch how those distances change and make conclusions about the physics of the muscle contraction. Top image credit

As many of you know, I am here in graduate school because I want to teach some day. I chose the UW because of the impeccable researchers and mentors, but also because this department provides it's graduate students with some amazing opportunities to help us define what it means to be a scientist. As we all know, some weeks the daily minutiae of the lab can pile up and cause us to question the intelligence of our decisions. After several hours, days, or weeks of an experiment not working we begin to tell ourselves that maybe the original question isn't THAT interesting after all and perhaps your parents were right, you should have gone into a more lucrative business like art history. Those are the times when I am the most thankful that I volunteer in STEM OUT. Not because it's a resume booster or good karma, but because through those interactions I am reminded why I love science. Teaching, like any career, is not for everyone. For me, however, it is a perfect way to help the next generation of scientists and recharge the soul.


Monday, April 6, 2015

Grad Publication: Will King

Let’s say you’re a bird (passerine). You’ve just noticed a potential predator (hungry). Alarmingly, the predator appears to have already detected you; it’s sizing you up for dinner. You might have noticed the predator earlier if you hadn’t been distracted by the jabbering of another bird (let’s call it Jamie).

But now that you’re aware of the predator, you will focus on monitoring its – wait, what is that ruckus? It’s loud, it’s attention-grabbing, it’s – whoa, whoa, when did the predator get so close?  Too dangerous. Time to flee!

Hopefully the thought exercise above demonstrated the idea that background noise can distract animals. Attention is limited, and being distracted can have important consequences on survival. The distracted prey hypothesis posits that animals may be distracted by any stimuli, inhibiting their ability to detect approaching predators.

While a student at UCLA, I obtained the opportunity to investigate this hypothesis in beautiful Moorea, French Polynesia. The findings of the study were recently published in Behavioral Ecology

A view of Morea, French Polynesia (photo credit).

My co-authors and I used playback experiments to simultaneously examine the relative effects of anthropogenic sounds, conspecific nonalarm sounds, and heterospecific nonalarm sounds as distractors for common mynas (Acridotheres tristis). We 1) compared myna behavior before and during playbacks and 2) measured the distances at which myna fled from an approaching predator during playbacks. We expected anthropogenic sounds (motorcycle noise) and conspecific nonalarm calls to distract mynas and for heterospecific nonalarm sounds to have little effect.

Our study species, the common myna.

Contrary to the distracted prey hypothesis, we found that mynas fled at greater distances when they heard heterospecific nonalarm sounds compared to a silent treatment. This suggests that some social sounds can enhance myna vigilance, even though the sounds come from a different species and should lack information about predatory threats. Our findings show that the effects of acoustic stimuli on prey are not necessarily straightforward. What seems distracting may increase antipredator response in certain contexts. Jamie’s jabbering may save your life yet.

– Will (primarily a marine ecologist)

You can read the paper here.

Tuesday, March 10, 2015

Snapshots from research

Pictures from grads while doing research. Sometimes the pictures are directly related to their research, sometimes the pictures are of cool things seen while doing research.

Sharp Shin Hawk by-catch during Gambel’s white-crowned sparrow field collection with mist netting in Eastern Washington. The Sharp Shin became caught while trying to catch a small song bird that had just flown into the mist net. The mist net is visible behind me. -Tracy Larson

A picture of "my office" in both the summer and fall...I study the phenology of those wildflowers! -Elli Theobald


On a walk through lion and zebra infested grassland I stumbled upon a bizarre femur in ~255 million year old rock. We found several more like it, but still don't know what it belongs to! -Brandon Peecook

I'm interested in the actin cytoskeleton of Giardia. Currently, I'm investigating the biochemical properties of this highly divergent molecule. My previous work focused on localizing the guanine activating proteins (GAP) in Giardia. Blue are the nuclei, red is actin, and green is the putative GAP. -Melissa Steele-Ogus

I spent the last quarter watching leaves grow! -Melissa Lacey

A photo of one of my summer neighbors. I was camping in western Montana for fieldwork. -Jonathan Calede

Ever wonder what it looks like when a virus infects bacteria? These charismatic plaques (holes in a bacterial lawn) were created by the bacteriophage Phi 6, which infects the bacterium Pseudomonas syringae which itself infects tomato plants. A pathogen of a pathogen! -Katrina van Raay

Thursday, March 5, 2015

Melissa Steele-Ogus: Immunity and Humanity

Probably the most controversial political issue right now is what should really be a non-issue: vaccination. Hot-button phrases are being thrown around–parental choice, bodily autonomy, personal responsibility. I am deeply troubled by the extremely vocal and fast-growing anti-vaccine (or anti-vax) movement.

This issue affects me personally. I am mildly immunocompromised, and while I do my civic and corporeal duty and routinely get my vaccinations, they aren’t always effective. My body doesn’t reliably react to them in the way it’s supposed to (N.B. this is not a failing of the vaccines themselves, but of my immune system). Additionally, there are others who are more severely immunocompromised and are unable to get vaccinated for medical reasons–most notably, those who have struggled with leukemia, lymphoma, or other cancers. These people rely on herd immunity to keep them safe. This means that those who choose not to get vaccinated are not only putting themselves at risk for preventable diseases, but also risking the lives and health of the immunocompromised population. These people are at a higher risk of catching preventable
This month's National Geographic explores why people doubt science. 
diseases, and are also more likely to suffer lasting, irreversible consequences from it. 

Even though any link between autism and vaccines has been dispelled multiple times, anti-vaxers have been desperately clinging to it as justification to not vaccinate their children. Although misguided, this impulse is understandable. Autistic spectrum disorders are, on the whole, misunderstood, and thus, feared. If people can find a scapegoat for autism, they can hold on to the hope that they can prevent their children from developing it. But this attitude is also incredibly problematic because it devalues the lives and experiences of those with autism. The act of risking the life of one’s child to “protect” them from autism has an unspoken, and terrible meaning: “I would rather my child die than be autistic.”

I can’t deny that I’m worried about my own personal safety, or that the spread of ableist attitude is disconcerting. But what is most distressing to me is the willful ignorance and rejection of technological advancement. As humans, we are incredibly fortunate to control our own destiny. Rational thought is our ecological niche. We have taken hold of our natural abilities and wielded them with such strength that we have eradicated some of the most terrible diseases in our history. We did this, with our own natural talents. To deny these talents, so flagrantly and unyieldingly, at the risk of the health and lives of others of our own kind, is an act that can only be described as inhuman.

When smallpox was eradicated, it was widely considered to be the greatest achievement of humankind. Polio is wiped out in the United States, thanks to vaccination. Before the anti-vaccine trend, measles, mumps, and rubella were on their way to being extinguished as well. We are at risk of losing the gift left to us by our forebears, a gift which belongs to all of us, through a disregard for truth and the safety of others. Shouldn’t we pass this legacy of health, and triumph of the mind, on to the next generation?

Many people are afraid to disturb the seemingly fragile-yet-perfect bodies of their children with foreign substances, like medication. But, vaccines aren't medication. They are technology that utilizes the body's own defenses. The reluctance to inject mysterious substances into the body of one's child is understandable. However, refusing to listen to the advice of pediatricians, immunologists, and other experts and instead placing trust in animal instinct is denying our humanity. It’s giving in to fear. But we aren’t prehistoric primates, huddled in a cave to insulate us from the world. We don’t have to do that anymore.

Wednesday, February 18, 2015

Jared Grummer: Studying hybrid zones between Argentinean lizard species with loads of DNA

At the end of every rainbow is a doctoral dissertation. Photo by Jared Grummer.

I often wonder what non-scientists think of my research: who cares about lizards that they will never see? When I say I study hybrids, do they think I mean hybrid cars? And no, there are no medical applications for my research. Hybridization, or interbreeding between distinct species, of lizards in Argentina is a very foreign idea for most, in more ways than one.

I am a fourth year PhD candidate and I have been interested in hybrid zones for a little while. Hybrid zones offer a unique view into the evolutionary processes that either generate or extinguish species. You see, “species” is a word that the non evolutionary biologist is certainly familiar with, but few know the incendiary debates that regularly occur on campuses worldwide that cover ideas of what defines a species. Just like species, the definition of a species is mutable and evolves over time, largely based on how data are collected. Before Darwin, species have been diagnosed based on morphological (physical/external) characteristics that separate different types of organisms; this lizard is green, and that one is yellow, therefore they are different species. Nowadays, species are mostly being defined based on something all organisms share: DNA.

DNA sequencing technologies that have recently been developed allow us to sequence a large portion of an organism’s genome, therefore shedding light on not only its past, but the past of its ancestors. I still, however, recognize the importance of morphology in determining species limits, those boundaries that separate species. When morphological variation within a “species” is high, it is suspect that more than one species may be present. This point brings us to the lizards!

I am studying a group of lizards in Argentina, the Liolaemus fitzingerii group, that belongs to a lizard genus (Liolaemus) that is confined to South America. This is an exceptional genus of lizards because some species exist at over 5,000m, whereas others are found at sea level; some are herbivorous, and some even give live birth. Furthermore, they are relatively poorly understood and between 10-15 new species are described each year! Regarding the L. fitzingerii group, approximately 15 species are currently recognized, but the geographic and biological boundaries that separate many of these species are not clear.

One of the first male Liolaemus melanops we found during this fieldwork! Photo by Jared Grummer.

I have awesome collaborators, Luciano Avila and Mariana Morando, who are researchers at the National Central Patagonia Institute and they have spent their careers trying to describe the diversity of Liolaemus species and understand their evolutionary history. They have studied the L. fitzingerii group for a number of years, mainly because it is a very difficult group to understand. A lot of morphological variation exists within some species in the group, such as L. melanops, where the males can go from having a completely black head, to no black on the head, and everything in between, in the same locality! This makes determining species solely with morphological data a very difficult task.

The governmental building of my collaborators Luciano Avila and Mariana Morando. Photo by Jared Grummer.
I have come to Argentina during their summer to sample some putative hybrid zones between some of the L. fitzingerii group “species”. We have sampled one area in Chubut province in particular because the extreme morphological variation seen in this species raises this question if this is a single species, or potentially a hybrid zone between two distinct species. Here is some of the variation in this area:

Variation in male dorsal patterning from individuals collected at the same locality. Photo by Jared Grummer.
Variation in male ventral patterning from individuals collected at the same locality. Photo by Jared Grummer.
Sometimes, hybrid zones are found in “ecotones”, where two distinct habitat types come together. However, in this area of Patagonia, the habitat appears to be homogeneous (at least to the human eye).

Liolaemus melanops habitat in Chubut Province. Photo by Jared Grummer.

It is fun to be doing science in an area where Darwin has been! Well, he wasn’t in this exact area, but he was close. In fact, there is a Liolaemus species with his name, L. darwinii, that we have seen a lot during this trip. It was not this species, but Darwin mentions in his notes from the Beagle voyage that he collected a viviparous lizard in Patagonia with a hammer (yikes!).

My collaborator Luciano and I have sampled ~10 sites in northern Chubut and southern Rio Negro provinces spanning an area over 100km that potentially represents a hybrid zone between 2-3 species in the L. fitzingerii group. Now that I have the lizards, the next step will be to collect and analyze DNA from across the genomes of these individuals to see the extent of gene flow between these various populations along a morphological gradient. Half of the vouchers, or physical specimens, will be sent to the Burke Museum of Natural History and Culture; the other half will remain with my collaborators at the National Central Patagonia Institute in Puerto Madryn. These specimens will be a critical reference when analyzing the DNA, as we will be looking for congruence or conflict between morphological and molecular data in this area of putative hybridization between species.

This is my working hypothesis of how hybrid zones have formed. Liolaemus fitzingerii taxa retreated eastward to the historic coastline during Pleistocene glaciation, then expanded westward following glacial retreat and warming temperatures. Species ranges have subsequently come into contact, and hybrid zones are shown in darker grey. Also shown is my hypothesis of genetic diversity as a function of longitude.
I will leave you with some photos of the other cool things that we have been seeing. Stay tuned with results of this research in the spring!

A gecko, Homonota darwinii, that is one of nine Homonota species in Argentina. Photo by Jared Grummer.

A male Liolaemus melanops. Photo by Jared Grummer.

The herpetology lab in CENPAT where we processed all of our samples. Photo by Jared Grummer.

Luciano overlooks a rocky outcrop and ranch in Chubut Province. Photo by Jared Grummer.
Flamingos leaving their laguna. Photo by Jared Grummer.

 A southern sea lion colony during breeding season at Punta Norte on the Valdez Peninsula. Photo by Jared Grummer.