Wednesday, July 1, 2015

Foen Peng: A winding journey to a conference

View from the conference center - once I finally arrived. The location was on an archipelago, and there were very beautiful views around the conference building. 

I went to the international conference for plant speciation in Stockholm, Sweden one week ago, which was organized by the European Molecular Biology Organization (EMBO). It was an important conference in this field and a lot of good researchers gave talks. It might have been just like any other good conference for most participants, but it was unusual for me - I started to prepare for it more than 6 months ago.

My first night in Sweden, at about midnight.
The sun rises about 2-3 hours later! Yes, you noticed
that this was the roof of my hostel. It looks cool, but
I did not appreciate it very much when I was trying to
adjust to jet lag.
As a Chinese student, I need Schengen visa to visit Sweden. Also, the Chinese US student visa has only one-year validity, which means I need to apply for a US visa every year if I need to go abroad. Since I wanted to go to Sweden this summer, I needed to get my US visa renewed beforehand so that I could come back without a problem. Of course, the official way for a Chinese person to renew US visa is to go back to China. In that case, I would have had to to travel around the earth: US - China – Sweden – US!

Lucky enough, Seattle is close to Vancouver, BC, which has a US embassy there. Although it is less likely for me to obtain a US visa in Canada than in China, it was worth a try. Easy? No! Chinese students also need a visa to visit Canada. So I started my “visa adventure” by applying for a Canadian visa. After that, I went to Vancouver, Canada to renew my US visa. After that, I went to San Francisco to apply for Schengen visa. It took me half a year to finally get all three visas (Canada, US and Schengen, which saved me from travelling around the globe) and be able to go to the conference. Hooray!

Stockholm city hall - where Nobel winners dine!
The conference in Stockholm itself was very good. It was a small conference (~100 attendees) and had a lot of opportunities to talk with people. I met with a lot of researchers who I had only seen their names on papers before, and also some professors who either worked in UW biology before or graduated from our Ph.D. program. I was proud to be a student from UW biology. It was very interesting to hear the stories alumni shared with me about their time at UW. And the big surprise to me is that the poster I made for this conference (the only poster I have ever made), won 2nd prize for best poster at the conference. It turned out that I was the only graduate student from US in this conference, and I really appreciate this opportunity.

At the Vasa Museum. This battle ship sank 300 years ago on the first day of its sailing.
Sad for ancient people, but good for us to have a chance to look at it

Thursday, June 11, 2015

SciPos Montage: Creatures Below

Stephanie Smith atop a Baird's Beaked Whale. Photo by Aaron Barna.
Cooper French flensing a Baird's Beaked Whale. Photo by Aaron Barna.
A couple of weeks ago Jeff Bradley brought a bunch of volunteers from the Burke (including Steph and Cooper!) to Grayland to flens (de-blubber) and clean the bones of a whale that washed up on the beach. We also had help from some cool people from Cascadia and Highline Community College. The whale was a Baird's Beaked Whale, which is a really super duper whale that looks like a big fat dolphin, and is pretty rare, with only 4 strandings ever recorded in Washington! Here are some neat facts about Baird's Beaked Whales:  It was a 38-foot long female and had recently given birth. We collected tissue samples from several organs, and I got to see a whale heart in real life, which is basically the size of a beach ball. Awesome. We buried the bones so they would get cleaned off, and then later we'll go dig them all up and hopefully mount the skeleton in the new Burke!! It was the best day ever.

On another note, Eliza Heery, who does a lot of scuba diving in Puget Sound for her research, made this beautiful underwater video documenting some of what she sees diving in Seattle. Check it out!


Wednesday, May 27, 2015

Introducing Washington's first dinosaur

The following article was originally published on the Burke Museum’s blog and is republished here with permission.

Brace yourselves, dino-lovers: Burke Museum paleontologists have discovered the first dinosaur fossil ever found in Washington state!

The fossil is a partial left thigh bone of a theropod dinosaur, the group of two-legged, meat-eating dinosaurs that includes Velociraptor, Tyrannosaurus rex and modern birds. It was found along the shores of Sucia Island State Park in the San Juan Islands.

The fossil is approximately 80 million years old and is from the Late Cretaceous period. During that time, the rocks that today form Sucia Island were likely further south. How much further south is a topic of scientific debate, with locations ranging between present day Baja California, Mexico, and northern California. Earthquakes and other geologic forces that constantly reshape our planet moved the rocks north to their present-day location.

Burke Museum Curator of Vertebrate Paleontology Dr. Christian Sidor and University of Washington graduate student Brandon Peecook describe the find in the journal PLOS ONE.

As the Washington State Museum of Natural History and Culture, we're so excited to display Washington's first dinosaur fossil in our lobby and share the discovery with you!

The road to discovering Washington’s first dinosaur fossil...
On April 10, 2012, two Burke Museum research associates were at Sucia Island State Park with a collecting permit for fossil ammonites—sea creatures with spiral-shaped shells that lived at the same time as dinosaurs.

The shore where the fossil was found on the southwest tip of Sucia Island State Park.
Photo courtesy of the Burke Museum.

While scanning the ground for ammonites, they spotted this.

The exposed bone sticks out of the rocky ground. 

Photo courtesy of the Burke Museum.

Most people would have walked right by it. But our keen-eyed paleontologists could tell it was a small section of exposed bone. Since it was embedded in rock, they took photos, recorded the location and contacted our partners at Washington State Parks.

Dr. Adam Huttenlocker, at the time a University of Washington
 graduate student,
examines the first dinosaur fossil found in Washington state.

Photo courtesy of the Burke Museum.

The following month, a crew of Burke paleontologists returned to Sucia Island with permits to excavate the fossil so it could be studied. The shoreline where the fossil was found is now covered by landslides, so it is very fortunate that the Washington State Parks and the Burke Museum were able to excavate the fossil when they did!

Burke Museum paleontologists carefully excavate a section 
of rock
containing the fossil to prepare back at the Burke Museum.

Photo courtesy of the Museum.

Over the next year, Burke paleontologists worked to carefully remove the extremely hard rock surrounding the fossil so they could get a better look at the specimen.

It took nearly a year to remove the extremely hard rock and glue the fossil back together.
Photo courtesy of the Burke Museum.

Dr. Sidor and Peecook compared the fossil to other museums’ specimens and identified it as a partial left femur (thigh bone) of a theropod dinosaur, the group of two-legged, meat-eating dinosaurs that includes Velociraptor and Tyrannosaurus rex, and even modern birds. “This fossil won’t win a beauty contest,” Sidor said. “But fortunately it preserves enough anatomy that we were able to compare it to other dinosaurs and be confident of its identification.”

Dr. Christian Sidor (right), Burke Museum curator of vertebrate paleontology,
and Brandon Peecook (left), University of Washington graduate student,
show the size and placement of the fossil fragment compared to the
cast of a Daspletosaurus femur. Photo courtesy of the Burke Museum.

Although incomplete, Sidor and Peecook were able to determine the femur is from a theropod dinosaur for two reasons: 1) The hollow middle cavity of the bone (where marrow was present) is unique to theropods during this time period, and 2) A feature on the surface of the bone (the fourth trochanter) is prominent and positioned relatively close to the hip, which is a combination of traits unique to some theropod dinosaurs.

The first dinosaur fossil described from Washington state is a portion
of the femur (thigh bone) from a theropod dinosaur. The detailed
illustration shows the fourth trochanter highlighted in blue.
Illustration courtesy of PLOS ONE, modified by the Burke Museum.

The fossil is 16.7 inches long and 8.7 inches wide. Because it is incomplete, they aren’t able to identify the exact family or species it belonged to. However, Dr. Sidor and Peecook were able to calculate that the complete femur would have been more than three feet long—slightly smaller than T. rex.

The first dinosaur fossil bone discovered in Washington
state (bottom) sits next to the cast of a complete Daspletosaurus femur.
Photo courtesy of the Burke Museum.

We also learned that the fossil is from the Late Cretaceous period and is approximately 80 million years old, based on the age of the marine sediment that surrounded the fossil. This rocky matrix was filled with the fossil remains of tiny sea creatures. So, how did this dinosaur end up in the ocean?

Tiny fossil shells are still attached to the first dinosaur fossil found
in Washington state. Photo courtesy of the Burke Museum.

These clams found with the bone held the answer. They’re so well preserved we can tell they’re a species that lived in shallow water. So it’s likely that after the dinosaur died, its carcass was tossed by the waves and eventually came to rest on the seafloor among these clams. The rest of the dinosaur was likely washed away or carried away by scavengers.

The accompanying fossilized clams are so well preserved
that Burke paleontologists were able to identify the species,
Crassatellites conradiana. These clams lived in relatively
shallow water (less than 300 feet deep). Photo by Burke Museum.

The ultimate test to confirm this was in fact Washington’s first dinosaur fossil was submission of a formal manuscript and the peer review process. Sidor and Peecook submitted the description of the dinosaur to the scientific journal PLOS ONE, where reviewers confirmed their identification.

In the end, all that hard work paid off. Washington is now the 37th state where dinosaurs have been found!

“The fossil record of the west coast is very spotty when compared to the rich record of the interior of North America,” said Peecook. “This specimen, though fragmentary, gives us insight into what the west coast was like 80 million years ago, plus it gets Washington into the dinosaur club!”

Why did it take so long to find a dinosaur in Washington state? Dinosaurs are found in rocks from the time periods in which they lived (240-66 million years ago). Much of Washington was underwater during this period, so Washington has very little rock of the right age and type. Because dinosaurs were land animals, it is very unusual to find dinosaur fossils in marine rocks—making this fossil a rare and lucky discovery.

You can see this lucky discovery in person! Washington’s first dinosaur fossil will be on display in the Burke Museum’s lobby beginning Thursday, May 21.

Washington's first dinosaur fossil is now on display in the Burke Museum lobby.


Learn more about Washington’s First Dinosaur fossil on the Burke website.

The Burke Museum is the Washington State Museum of Natural History and Culture. Burke Museum paleontologists were issued scientific collecting permits by Washington State Parks prior to excavating the fossil. Fossil exploration and collection on state land is legal only with proper permits issued for legitimate scientific research. Any items discovered in permitted scientific exploration are considered publicly owned and remain the property of Washington State Parks collections. The fossil is held in trust by the Burke Museum on behalf of State Parks.

Written by Cathy Morris, Digital Communications

Thursday, May 21, 2015

Octavio Campos: Fake flowers foster fantastic fortuity for further fact-finding

Fake flowers foster fantastic fortuity for further fact-finding - Or: a cool paper on 3D-printed flowers and what it means for the field of plant-pollinator interactions

A hawkmoth. Photo by Armin Hinterwirth.

A few weeks ago (on April 15th, to be exact), my first paper based on my PhD dissertation project came out for publication in the journal Functional Ecology!  The paper documents my early findings into how flower shape influences the ability of dark-adapted hawkmoths to find the nectar reservoir of a flower.

A 3D printed flower. Photo by Octavio Campos.
The data presented in the paper are interesting in their own right, but it's actually an aspect of my methods that has garnered lots of media attention in the past few weeks: I used a 3D-printer to manufacture the flowers that I used in my experiments. 

If you want to systematically manipulate flower shape in a series of experiments, using different varieties, cultivares, or species of real flowers is pretty much out of the question because of the uncontrollable variation found even among the various flowers of a single plant.  And what if you can't find a variety that displays the shape phenotype you're looking for?  And how do you control of all of the other confounding variables that are going to be present among different varieties or species of flowers?  It just makes things too messy from an experimental design point of view.  Making artificial flowers with prescribed shapes is the way to go.  But I wanted the ability to have extremely fine-scale quantitative control over my flower shapes, and I also wanted to be able to make precise duplicates quickly.

So, my advisers and I came up with a single mathematical equation that, depending on the numerical values of it parameters, specified a particular three-dimensional shape.  And we already had a 3D printer in the lab, so why not use that to quickly manufacture the mathematically-specified shapes?

Different 3D printed flower morphologies. Photo by Octavio Campos.
This is the first use of 3D-printing technology to study the nuances of plant-pollinator interactions (that we know of), and it could (we hope) set the stage for a whole new range of investigations that were previously prohibitively difficult to execute.  Perhaps that's why the paper has struck such a chord with various media outlets.  I'm thankful for the coverage, and I hope there is similar interest in my next paper (in prep), which will take the experimental setup in the current paper to a whole order of magnitude of increased sophistication and depth of available data!  Wait for it!!

These are some of the media coverage pieces that I have been made aware of so far:

Link to the original paper:

Link to the general-audiences description of the paper

From UW Today:

From the Annals of Botany:

From a 3D-printing industry channel:

From a newspaper in Switzerland:

From the research highlights of the prestigious Nature:

~ Octavio Campos

Monday, May 18, 2015

Sonia Singhal: Explain it to me like I’m a four-year-old.

This post was originally written for the BEACON Center blog.

How do you know that you understand a scientific concept?

When you can explain it to a four-year-old.

While this is not a situation I encounter in my day-to-day work, studying viral evolution in Dr. Ben Kerr’s lab at the University of Washington, I do face it frequently as a Science Communication Fellow with the Pacific Science Center. On a Saturday morning every couple of months, I take the bus down to Seattle Center, and in the bright, airy Ackerly Gallery of the Pacific Science Center, I set up a table with boxes of colored beads and sheaves of colored paper. These items form the backbone of the activities I am developing to teach visitors to the Pacific Science Center about evolution.

I run two activities. The first activity, which demonstrates mutation, is a drawing game. Visitors choose a simple line drawing and copy it as many times as they can in one minute. I then encourage them to tell me how their drawings compare to the original drawing. The second activity demonstrates selection. I set up boxes with colored beads, representing bacteria with different traits. Each box contains beads of predominantly one color, with a few beads of other colors mixed in. Visitors pour out the beads and notice the different colors. They then explore how the different colors – the different traits – are important by choosing colored paper backgrounds (antibiotics) that will “kill” beads with a matching color.

Biology grad students Sonia Singhal, Carrie Glenney, and post doc Brian Connelly in front of the activity table at the Pacific Science Center’s UW-centric “Paws-On-Science” event.
The activities have been designed so that any visitor to the Science Center, regardless of their age or background, could learn from them. However, I find that I get mostly 4- to 11-year-olds visiting my table. Interacting with them is demanding, hectic, frustrating, great fun, and incredibly rewarding, often all at once. Some of the children take their time copying a few pictures; some of them get into the game and make so many copies that they run out of room on the page. Some of them like to color-code their beads after pouring them out. Some of them want to pour out every bead from every box to make a multicolored bead soup. Some of them want to take home the boxes, or the beads, or the colored pieces of paper, or even the plush microbes that I bring in from my advisor’s office as props. But they all love making drawings and playing with the beads. Even when I don’t feel I’m getting my point across, I have fun watching them have fun.

The children teach me as much as – if not more than – I teach them. Working with them forces me to explain my research without jargon, and for a 4-year-old, this includes words like “bacteria” and “reproduce”. It stretches me to think of analogies between my research and the children’s everyday lives. For example, I will explain to them that bacteria copy themselves, and sometimes those copies look a little different from the parent, “just like you look a little different from your mom or your dad.” Most importantly, working with children challenges my assumptions. The media is rife with evolutionary stories involving antibiotic resistance and emerging diseases, so to those of us working in experimental evolution, viruses and bacteria are obvious examples of evolution in action. However, most of the children at the Pacific Science Center do not understand that viruses and bacteria replicate; they view germs as static forces rather than dynamic populations. And it turns out that this single point is a key hinge for explaining evolution. If the microbes are not copying themselves, they have very few avenues for dramatic changes.

The Pacific Science Center believes in giving its visitors freedom to explore. As in a typical museum, there are placards to read, but there are also levers to pull, wheels to spin, pressure pads to jump on, and water nozzles to aim at moving parts. In the same spirit, I let the visitors decide which activity they want to try. Usually they only choose one or the other, but sometimes I can take them through both and watch them fit the two activities together. One young girl decided that she wanted to draw, so we went through the drawing game; then she decided that she wanted to know what was going on with the colored boxes, so I had her choose one and pour out the beads. “Not all of them are pink,” she noticed. I told her, “That’s right. Just like you made copies of that drawing, these germs are making copies of themselves. And just like your copies were all a little different, the germ copies are a little different too.” “Oooohhh,” she said, with the intonation of a “eureka” moment.

The activities are flexible enough that I can layer in additional details. One boy liked the bead activity so much that he played it three times in a row. The fourth time, I asked if he wanted to try something a little different. “This time,” I said, “let’s give this person medicine before he gets sick, rather than after he gets sick.” I had him pour the beads directly onto the colored background, rather than adding the background afterwards. He immediately responded differently to the activity. Where before, he would dump out all the beads at once, now he shook them out a few at a time and stopped every four or five beads to remove the ones that matched the background color. He understood that, since the environment was different, the population of beads that were able to “survive” was also different.

My most interesting interactions, though, occur when the children bring their own questions to me. One girl, who already knew a little bit about disease-causing microbes (“Germs can infect people, or dogs, like parvo,” she told me.), asked a lot of detailed questions about how our bodies fight disease off, and how microbes can hide from immune cells. Another girl and her younger sister wanted to know whether mice were vertebrates or invertebrates. I had to shift gears abruptly to rack my microbe-centered brain for examples of common vertebrates and invertebrates. By the end of our conversation, I was explaining to them the difference between an endoskeleton (an internal skeleton, such as we have) and an exoskeleton (an external skeleton, such as insects have).

Working in an academic research lab requires understanding the minutiae of one’s question, organism, and experiments. At the same time, this fine focus can impede us from communicating the salient points to a non-scientific audience. My work with the Pacific Science Center gives me a way to step back, review the broader context of my research, and decide what is truly necessary for understanding. Although I’m still working out how best to present and explain evolution, I feel that every iteration of my activities brings me a little closer.

Thursday, May 7, 2015

GSS 2015!

Just a few weeks ago, UW Biology Graduate Students hosted the 12th Annual Graduate Student Symposium. Attendees were entertained and educated by grads sharing their past, present and future research in 15-minute presentations. If you weren't able to make it (or if you did come and want to relive #gss2015), some dedicated researchers, grads and postdocs live-tweeted the conference. Enjoy!

The much anticipated awardees from the talks:
Best dressed: Greg Golembeski and Katrina van Raay
Prettiest pictures: Hilary Hayford
Most appealing to a 3rd grader: Brandon Peecook
Best new artist: Camila Crifo and Hannah Jordt
Best Title: Myles Fenske
Best extemporaneous speaking: Leander LoveAnderegg and Yasmeen Hussain
Best overall talk (faculty pick): Brandon Peecook

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.