Monday, August 3, 2015

Beautiful Monsters

UW Grad Students participate in many different forms of outreach. John Chau, who studies evolutionary relationships among members of the genus Buddleia (Butterfly Bush), writes about "local color" for a popular neighborhood blog the Capitol Hill Seattle Blog. He contributes to the Pikes/Pines series, providing a natural history context for the urban jungle.

Read his recent post on Beautiful Monsters describing the genetic horrorshow that is the cultivated roses. 

YOU MONSTER! John explains the double rose in his Pikes/Pines post. Credit: J. Chau.

Friday, July 24, 2015

Ain't nothin better than the summer in the northwest

Our unusually warm weather this year brought all sorts of crazy phenomena: massive siphonophore strandings on the coast, Dungeness crab molting frenzies, algal blooms (also some things happened on land maybe?), but it also meant an early arrival of weather we typically don't get until July 5th, starting during a month locally renamed "Junuary".

Summer means we grad students don't get to keep as close of tabs on each other, often heading out to field sites, or into the lab for many hours straight. What are UW Biograds up to this summer?

Octavio Campos: I have already defended, so I have my "D"; now this summer I just have to work on finishing my written dissertation so that I can get my "r" to officially become... a Dr.

Jake Cooper: I'll be tracking evolution in my simulated populations, some of which can have sex and some of which can't.

Marie Clifford: This summer I am writing up my paper on floral scent so that the scientific community can WITNESS the convergent chemical evolution between plants with the same pollinator.

Marie's Passiflora Valhalla awaits...

Myles Fenske: Many plants require insects to facilitate their lovemaking, I'll be watching bugs in a windtunnel decide which plants they want to third-wheel for.

Emily Grason: Mud-truckin' again this summer, this time all over Puget Sound looking [hopefully in vain] for invasive European green crab - Carcinus maenas.

Jared Grummer: I am going to be doing a lot of genomic sequencing of frogs, lizards, and caiman, while writing manuscripts and preparing to be in Argentina for 5 months!

Hilary Hayford: I am sharing everything I know about invertebrates with a dedicated group of students, writing about radio-tracking marine snails, piecing together data on behavior, temperature, and performance to evaluate snail "decision-making," and letting my bike get some time in the sun.

Eliza Heery: I'm figuring out why sea urchins are currently taking over Seattle and studying the community of worms, clams, snails, and crustaceans that inhabit soft sediment habitats in the urban subtidal.

Yasmeen Hussain: This summer, I'll be banging on a keyboard and filling glass tubes with charcoal and alcohol. [aaah, science...]

Will King: This summer, I contemplate the metaphorical links between intertidal barnacle zonation on San Juan Island and my ever deepening tan lines.

Alex Lowe: I'm figuring out which marine adhesive is best for gluing oysters (thousands of oysters) to tile.

Brandon Peecook: I'll be an American in Paris (and Tübingen and Cambridge) scampering around in museum basements before returning to the US of A to dig up some OLD (and hopefully a few new) friends in the Petrified Forest of Arizona. "Je suis un paléontologue, uh huh huh".

Elli Theobald: I'll be looking into my crystal ball to look at what flowers will do in the future. I'm taking advantage of the early summer weather to explore what future climate conditions might mean for flowers and pollinators on Mt. Rainier. This summer, flower phenology is already 4-6 weeks earlier than usual, mimicking conditions predicted for the year 2080! Already we are seeing signs of community reassembly that we had predicted from climate models.

Katrina van Raay: This summer, I'll be evolving virus and bacteria mutants, and taking some breaks from lab to traipse around the beautiful Pacific Northwest.

Lauren Vandepas: I will be alternating between demanding that anemones reveal the secrets of their stinging cell harpoons and trying to watch jellies poop, in between sessions of sitting in an inner tube on a lake wearing a big floppy sun hat.

So that's the summer life of Biograds in a nutshell.  Hope your summer is just as ... interesting.

Thursday, July 16, 2015

Grad Publication: Ann Wen-Yang Lin

Ann (Parrish Lab) just had a paper published in Genes and Development about pathetic mutants! Below she describes the impetus and context for the paper, as well as the results.

The link to the full paper is found here.

A central question in growth control of multicellular organisms is how growing organisms maintain proportionality. For example, as animals grow, dendrite arbors of many neurons must expand proportionally to sustain proper connectivity and maintain coverage of their receptive field. However, different types of neurons have different growth requirements, depending on the size and complexity of their dendrite (and axon) arbors. We have been working to identify the cellular machinery that supports neuron growth with a focus on understanding whether neurons with large arbors have specialized mechanisms to support their extreme growth requirements.

From a genetic screen, we identified a mutant that selectively affects dendrite growth in neurons with large dendrite arbors without affecting dendrite growth in neurons with small dendrite arbors or the animal overall. This mutant disrupts a putative amino acid transporter, Pathetic (Path), that localizes to the cell surface and endolysosomal compartments in neurons. Although Path is broadly expressed in neurons and non-neuronal cells, mutation of path impinges on nutrient responses and protein homeostasis specifically in neurons with large dendrite arbors but not in other cells. Altogether, our results demonstrate that specialized molecular mechanisms exist to support growth demands in neurons with large dendrite arbors and define Path as a founding member of this growth program.
Figure 1: Role of the SLC36 Pathetic in
supporting extreme dendrite growth.

Shown here (Figure 1) is a confocal image of Drosophila Class IV da neurons (labeled by ppk-CD4-tdTomato) in a pathetic zygotic null mutant 3rd instar larva. Dendrite growth arrests at a fixed limit in pathetic mutant sensory neurons (cyan neurons), but in very rare cases (<0.5% of neu- rons), persistent maternal Pathetic protein rescue the mutant phenotype (red neuron), demonstrating that low levels of Pathetic are sufficient to support extreme dendrite growth in these neurons. Pathetic supports dendrite growth in part by increasing translational output, but is dispensable for growth and patterning of other larval tissues.
Figure 2: Specialized requirements for growth in neurons with large dendrite arbors. 

Shown here (Figure 2) are confocal images of Drosophila Class I (magenta) and Class IV da neurons (red), labeled by 98b-Gal4, UAS-CD4-tdGFP and ppk-CD4- tdTomato, respectively, in pathetic mutant (left) or wild type (right) 2nd instar larva (cyan). Dendrites of Drosophila dendrite arborization neurons grow continuously during larval development to maintain proportional body wall coverage, but Class IV da neurons have much larger and more elaborate dendrite arbors than Class I da neurons. Mutation of pathetic selectively affects dendrite growth in neurons with large dendrite arbors, including Class IV da neurons, doing so by affecting translational output of neurons. By contrast, pathetic is dispensable for dendrite growth in neurons with small dendrite arbors or the animal overall, demonstrating that growth of large dendrite arbors entails specialized molecular mechanisms.

Thursday, July 9, 2015

Laura Newcomb: Spidermen of the Sea

Washington State is a fantastic place to study shellfish – not only are they plentiful to study, the state is home to a productive shellfish industry which has enabled me to apply my results in the lab to real life problems.

This piece was originally prepared for FHL's Tide Bites:

As you walk past the Kings Market seafood aisle in Friday Harbor or browse at Costco, chances are that you will see fresh mussels harvested locally from Penn Cove Shellfish on Whidbey Island, WA. These mussels have been cleaned and washed to look enticing to buy, cook, and eat. What you do not see when you look at these mussels is one of the most important parts: the byssal threads that attached the mussels to the lines they grew on (Figure 1), enabling them to then progress from the ocean to your plate.

Figure 1. Mussels attached to each other by byssal threads.
Mussels are the Spidermen of the sea: they mold byssal threads to attach to a variety of surfaces, from rocks to aquaculture lines. These threads act as stretchy tethers to keep a mussel in place (Bell and Gosline 1996). The mussel aquaculture industry takes advantage of this characteristic in their farming practices. Adult mussels living along the shores of Penn Cove release egg and sperm into the water column, a process known as mass spawning. When egg and sperm collide, the egg is fertilized and the larva begins to grow. During this phase, larvae swim around in the currents, feeding and looking for a good home to settle and attach with their first adult byssal threads. Penn Cove Shellfish puts out collector lines in early spring (April May) to catch this mussel “seed.” Mussels then grow right on these collector lines for about one year, until they reach harvestable size (Figures 2 and 3).
Figure 2. Penn Cove Shellfish mussel harvesting boat tied up to a mussel raft.

Figure 3. Mussel aquaculture lines hanging in the water at Penn Cove.
The problem arises when the mussels fall off, leaving the lines bare. Mussel fall-off due to seasonally weak attachment and increased storm action is a process mussels encounter on rocky shores (Paine and Levin 1981). A mussel becomes weakly attached when it produces fewer or poor quality individual byssal threads, making the animal more likely to dislodge under waves and currents. Mussel fall-off cuts into a grower’s yield at harvest and is a problem for the industry worldwide.

With funding support from Washington Sea Grant and the National Science Foundation, a team led by Dr. Emily Carrington and including Dr. Carolyn Friedman, Dr. Michael (Moose) O’Donnell, Penn Cove Shellfish General Manager Ian Jefferds, Matt George, Molly Roberts, and myself have set out to address this problem. Our work seeks to identify what environmental factors may trigger weakened mussel attachment in farmed mussels. We started in the laboratory by identifying two potential culprits, ocean acidification and ocean warming, that weaken mussel byssal threads. Using controlled experimental mesocosms (aka fancy Igloo coolers) in Friday Harbor Laboratories’ Ocean Acidification Environmental Laboratory (FHL OAEL), we exposed mussels to a range of conditions to identify the threshold values for weakening: pH below 7.6 (O'Donnell et al. 2013) and temperature above 19˚C (66˚F). We also learned that elevated temperature reduces the number of threads a mussel makes, further weakening whole mussel attachment.

With the lab experiments identifying pH and temperature as possible weakening agents, we moved out to a mussel farm to ask if mussels ever encounter these threshold conditions and if so, do these events coincide with weak mussel attachment?

Partnering with Penn Cove Shellfish (the oldest and largest mussel farm in the nation), we installed multi-parameter instruments in Penn Cove on Whidbey Island to log hourly measurements of seawater temperature and pH, as well as salinity, dissolved oxygen, and chlorophyll. These data are uploaded onto the internet in real time ( so that we (and anyone else) can check in to see what the conditions are like at any time (Figure 4).

Figure 4. Grad Laura Newcomb with solar powered
telemetry units on a mussel harvesting raft.  Water
temperature and pH measurements are uploaded
to NVS and publicly available.
Growers hang mussel lines vertically in the water at depths from 1 to 7m, so we placed our sensor arrays at those depths to capture conditions throughout the water column. This equipment has been in place and logging since late summer 2014. So far, we have found summer water temperatures at 1m can surpass the 19˚C (66˚F) threshold for a few hours on warm days and pH dips below the threshold of 7.6, with especially prolonged periods from October February at both 1 and 7m. These measurements tell us that mussels do experience conditions that can weaken their attachment, and our concern is that these conditions are projected to get worse over the next 100 years.

At this point in the study, we don’t quite have enough monthly measurements of mussel attachment at 1 and 7m to fully evaluate how pH and high temperature may be affecting mussels in the field. However, we have observed that mussels are weaker in the months when the maximum temperature exceeds 18˚C. This observation suggests temperature may act as an environmental trigger for weak attachment. We are continuing to measure mussels and water conditions and will soon be able to firm up our conclusions about the effects of temperature and pH on mussels at the farm.

Moving our research from the lab to the field has allowed us to extend our results to an industry that stands to be affected by changing ocean conditions. By installing sensors that monitor the water in real time, we hope to give mussel farmers an early warning system for conditions that could threaten their mussels. Recently we have expanded our studies to include Penn Cove Shellfish’s farm in Quilcene Bay, WA, made possible by our partnership with Washington State Department of Natural Resources. We are excited our collaborative research can contribute to sustaining a culturally and economically important resource for Washington State and keep this popular seafood in grocery stores for years to come (Figure 5).

Figure 5. Biology Professor Emily Carrington meets with Governer Jay Inslee
to discuss the effects of ocean acidification.

Works Cited:
Bell E., and J. Gosline. 1996. Mechanical design of mussel byssus: material yield enhances attachment strength. Journal Exp Biol 199:10051017 (link)

Paine R.T., and S.A. Levin. 1981. Intertidal Landscapes: Disturbance and the Dynamics of Pattern. Ecol Monographs 51:145 (link)

O'Donnell M.J., George M. N., and E. Carrington. 2013. Mussel byssus attachment weakened by ocean acidification. Nature Climate Change 3:14 (link)

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