Hadly Lab blog

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A recent opinion piece by climatologist Michael Mann and a follow-up by environmental journalist Andy Revkin and environmental scientist Ken Caldiera raised the issue of how to tell the difference between communicating science, versus advocating for a cause. | Read more from this article co-written by Liz Hadly…

I spent last September and October in the Himalayas of Himachal Pradesh, India. This was my third field season and definitely the most productive. My amazing field assistant, Ania Wrona, and I spent 6 weeks in and around the villages of Kaza and Kibber in Spiti Valley, Himachal Pradesh. We trapped and sampled pikas, a small mammal related to rabbits, at three different altitudes (3,600m, 4,000m and 5,000m). We successfully sampled and released 24 individuals. From these samples we are currently sequencing the transcriptome of these individuals in order to see how gene sequence and expression are different across this elevation gradient. Both Ania and I can tell you that breathing at 5000m (16000ft) is anything but easy given that there is only a little more than half the oxygen at this altitude as there is at sea level. The lack of oxygen in this environment stresses organisms in many ways, and only a few species have evolved to live in such an extreme environment. Pikas are one such group of species, and we are hoping this genomic data will help us reveal how it is that they are able to live in such low oxygen conditions.

- Katie Solari

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I recently presented at “Eat. Talk. Teach. Run!”, a lunchtime series organized by the Stanford Center for Teaching and Learning that allows graduate students to share four minute flash talks about teaching. Check out the article (link) for a recap of the event!

- Jeremy

      Last quarter Alexis and I had the pleasure of TAing “Ecology” taught by Kabir Peay. It was a fun and exhausting experience, as anyone who has ever taught a class can likely tell you. This was my second time TAing (I had taught Bio 43 in the spring of 2012) but I can honestly say I learned as much, if not more, from TAing a second time. For those of you about to TA or any undergrads who happen to be reading this blog, I offer the following insights:

1)    TAs really want their students to do well. (I am sure this is even true of organic chemistry TAs.) We get really excited when people get full points on a question; it means the students learned something and (hopefully) we’re doing our jobs well.

2)    Lectures take WAY longer than you would think to prepare. To all of my professors who ever got the powerpoint slides up the night before the lecture, you are amazing. (For reference, after reading the chapter, looking up some supplementary material and deciding on a rough outline of my lecture, it still took me 10 hours to prepare the powerpoint… on a topic closely related to my dissertation research.)

3)    It is really hard to write good test questions. No matter how hard you try, someone will inevitably interpret your question in a completely different way than you ever thought they would. … And it will be hard to grade.

4)    People will learn more and be less bored if you give them an activity to do than if you lecture at them. Doing problems in section is more fun for everyone than a lecture redux.

  1. This doesn’t necessarily apply if the activity is “learn to code.” If you attempt this, allow for plenty of time and don’t be alarmed if you get panicked stares.

5)    Undergrads are awesome. There’s nothing like a bright-eyed, bushy-tailed student at office hours to make you remember why you decided to put up with experiment failure, grant writing and ambiguous work-life balance in the first place. Especially at a place like Stanford, the undergrads are really fascinating people with interesting hobbies and talents. (If you’re lucky enough to be on a three hour car drive with them you find out fun things like your 6’2” blonde male student does an amazingly faithful rendition of Nicki Minaj’s “Superbass.”)

6)    Did I mention the entire endeavor takes a lot of time? It does but it’s worth it.

I am very excited to TA again in the spring, this time for Paul Ehrlich. In the meantime, it’ll be great to have time to get some other stuff done. To all the TAs and professors out there, I salute you.

- Hannah Frank (@hannahkfrank)

Over the holiday break and before the Polar Vortex hit the east coast, I made it down to the Smithsonian National Museum of Natural History to take skin samples and photographs of solenodon museum specimens.

The collections at NMNH are wonderful because they have both Cuban and Hispaniolan individuals, and many of the specimens have great locality data. I had to share a few photos of the wonderfully weird Cuban solenodons I encountered while there…

I don’t know who could come up with the idea of mounting a solenodon head like a trophy….

A Hispaniolan solenodon can also be found on exhibit in the hall of mammals!

I can’t think of a better mammal to be featured next to the quote “As mammals adapted to a changing world, a wondrous diversity of shapes, sizes, and behaviors evolved.” Solenodons are wonderfully weird in their body size, amazingly flexible noses, venom production, and their mysterious ability to survive as witnesses to the collapse of their ecosystem through time. We need more solenodons on public display in US museums! And perhaps to also make reference to their more charismatic and memorable nickname —- “soli”!

- Alexis (@AlexisMychajliw)

‘Twas the night before winter break, when all through the lab

Not a creature was stirring, not even the pet crab*;

The pipettes were racked on the benches with care,

In hopes that the lab fairy would soon be there;

The grad students were nestled all snug in their beds

While visions of great data danced in their heads…

Late in the night, I went in to let samples thaw,

And then, in a twinkling, I heard a gnaw;

And the prancing and pawing of each little paw

As I drew in my head, and was turning around,

Down the flow hood the lab fairy came with a bound.

She was dressed in all canvas, from her head to her foot

And her clothes were all tarnished with field sand and soot;

A bundle of live-traps she had flung on her back,

And behind her trailed her lab rats, the mightiest of packs…

She spoke not a word, but went straight to her work,

And filled all the tip boxes; then turned with a jerk,

And laying her finger aside of her nose,

And giving a nod, up the flow hood she rose;

She sprang to her sleigh, to her team gave a whistle

And away the rats flew like the down of a thistle;

But I heard her exclaim, ere she drove out of sight,

“Happy lab work to all, and to all a goodnight!”

(Adapted from “The Night Before Christmas”)

*Technically he is a ghost shrimp, named Cooper

We celebrated the holidays before we all dispersed for break by having a combined party for the birthday of our fearless leader (Liz Hadly!) and a white elephant gift exchange (<$5 for a ridiculous but semi-functional gift). Here’s a photo of us all with our exciting presents!

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Ever since I took a course on vertebrate evolution my freshman year of college, I have been decorating my family’s Christmas tree as a —- phylogeny!!! Every year a different taxon gets the “top” of the tree. This year, to my mother’s dismay, the invertebrates took the top! It is surprisingly hard to find invertebrate ornaments, but I’ve managed to collect a jellyfish, snail, spider, and starfish. Next come the vertebrates, starting with fish, moving to amphibians, reptiles (turtles only so far), birds and dinosaurs (intermingled and loving it), and lastly, the mammals, with humans on the very bottom. Luckily I’ve loved animals ever since I was a little kid, so you could say my ornament collection was pre-adapted for phylogeny building…

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Happy holidays from all of us in the Hadly lab!

- Alexis (@AlexisMychajliw)

Members of the Hadly lab recently traveled to LA to participate in the annual meeting of the Society for Vertebrate Paleontology. Paleontologists from around the world gathered to share findings, results, and news!

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The Hadly lab was represented by Liz, a member of SVP’s executive committee, as well as by Melissa, Zixiang, and me. In addition, Ariel and Jessica, alumni of the lab, were also there to present their work!

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Melissa gave an excellent talk highlighting body size changes over time in Anolis lizards, and also helped showcase some work that she and Simon have done in our lab.image

All of us enjoyed the scientific discourse and the feedback we received on our work. However, it wasn’t all science! We took a field trip one day to the Natural History Museum of LA - the SVP meeting certainly wouldn’t be complete without a visit to see dinosaur bones and more!

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There was also a hilarious live auction, with proceeds benefiting the society. Here, the SVP auction committee gets into the Halloween mood:

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And of course, we had time to catch up with friends old and new! Below, members of the Hadly lab pose with friends from the Barnosky lab at Berkeley.

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— Jeremy

On Wednesday evening, we held the first Stanford Biology Thinks Big! symposium, where four Stanford faculty from across the biosciences each gave a short, ten-minute TED-like talk about a big idea in their research or their field.

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I first starting thinking about hosting such an event last year, as a way to showcase the amazing diversity of scientific research and viewpoints within the biosciences at Stanford, and to introduce people to science and research in an accessible, engaging format. To that end, I was thrilled with the four speakers we had, with John Boothroyd, Mary Teruel, Carlos Bustamante, and Susan McConnell each representing different departments here at Stanford. Even with such an amazing line-up of faculty, though, I have to admit that I was a bit nervous about turnout for the event - this is the first time anyone’s tried doing such an event here, and I had no idea what to expect.

The first indication that my nervousness was unwarranted, though, came when the first people starting arriving thirty minutes prior to the start time! More and more people filled in, and the response was overwhelming - not only was our room at maximum capacity (with the aisles filled with people sitting and standing), but our overflow room next door was also absolutely jam packed, with people still trying to peer in from outside the doors. image

It was clear that the audience was very enthusiastic and eager about this event. I took a moment to poll the audience at the beginning, and there was a good distribution of undergraduates, graduate students, post-docs, and general community members!

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Despite some of our A/V equipment not cooperating in our overflow room, the excitement of the audience was palpable. Dr. Boothroyd (Department of Microbiology and Immunology) began by talking about his work on a specific microbe, and Dr. Teruel (Department of Chemical and Systems Biology) highlighted the mechanisms behind the development of fat cells.

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Next, Dr. Bustamante (Department of Genetics) engaged the audience in a wide-ranging discussion on genetics, before Dr. McConnell (Department of Biology) wrapped up the symposium with an inspiring message on science and conservation, using her own photographs of nature and animals.

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It was a really great experience to hear four different perspectives on science, and to listen to such a diversity of ideas. Afterward, I was thrilled to see so many students come up to each of the speakers to ask more questions about their work, and many of the students even asked about advice regarding finding and joining a lab or the graduate school process!

Overall, it was clear that everyone was eager to hear the big ideas that Stanford researchers have, and I’m already looking forward to the next time we do this!

— Jeremy

I love biodiversity, so please allow me to occasionally direct your attention to organisms outside of our current research focuses. I thought about writing a blog on the adorable blobfish, but thanks to its recent publicity as the “ugliest endangered animal”, many people probably know this exotic deep sea creature more than the critters that share our backyards.  Speaking of under appreciated animals in our neighborhoods, American Kestrel (Falco sparverius) is a pigeon sized falcon whose range overlap with northern California. It is the smallest falcon in North America, as well as one of the most colorful raptors.  This fierce little predator has a beautiful rusty red back and slate blue wings, decorated with dark streaks (species account). It prefers open habitat, has about 5-6 young per brood, and often sings killy-killy-killy loudly. In case my description didn’t do this species justice, here is my watercolor painting of the majestic little bird, along with a little bit of life history and species identification information in the background. Enjoy!

lilycli's watercolor painting of AmericanKestrel

@ChengLilyLi

Upon becoming a student in the Hadly Lab, my first major tasks are to write scientific paper(s) and this blog. Growing up speaking a different language, writing was fun and easy … until I had to write in English.  It’s been years, my English is a lot better, but my relationship with writing has not improved much.  Here I am, sitting in front of the computer, pondering what to say, and I suddenly thought of an essay called “Writing is Easy”. It eases my mind when writers block strikes, and I think it’s worth sharing with others who suffer from a strained relationship with writing. For those who have read the article, here is a convenient link in case you want to revisit it. For those who never had any problem with writing, isn’t it great that writing is easy?

@ChengLilyLi