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At long last Danny and my paper on loss of phylogenetic diversity in neotropical agricultural systems is out in corporeal form! In cliff note form we find that while agriculture can support bird species from across the avian tree of life, it tends to favor younger, more recently diversified species, whereas the older, more evolutionarily distinct species have difficulty. Nevertheless, not all agriculture is created equal, and by increasing the amount of tree cover and vegetative complexity on farms you can support nearly double the number of species that can exist on more industrialized farms (thereby saving ~600 million years of evolutionary history that would have otherwise been locally lost).

Because this was published in a high profile journal, the media seem to care much more than they usually would, giving me a little bit more basking time in the (admittedly, none-too-bright) limelight than would normally come my way as a graduate student (e.g. here, here,and here). There’s been a great deal written about the often strained relationship between scientists and the media, especially as science desks at major newspapers dry up and crumble away like Claudia in a sun-tunnel (of ‘Interview with a Vampire’ fame). However, most of the interviews went quite well, and all the journalists I talked to did an admirable job distilling what could be a very
messy concept into a form that could be relatively intuitive to the general public. Yet there were some aspects of talking to the media that I found somewhat unexpected, and I think meditating on these topics briefly may be of some benefit—if for no other reason than to adjust my own expectations and plans for the next time.

1. Scheduling. Some reporters can be surprisingly flakey. Multiple reporters set up appointments to call for interviews and then missed them, only to attempt to reschedule a day later. As the media tries to rely on fewer reporters to cover more and more topics I suppose it’s not surprising that journalists end up with unexpected deadlines, and science stories (which tend not to be front and center breaking news) would naturally be put on the backburner. Fortunately it’s the summer so my schedule was pretty devoid of anything concrete, but I could easily see this being a source of annoyance during a busier, more regimented time of the school year.

2. Misquotes. This is a perennial problem, and a constant source of paranoia. A few of these cropped up in an article or two—nothing tremendously serious, just a few swapped words that somewhat obliterated the sense-making capacity of the sentence, and a little confusion about what particular random natural history fact pertained to which species. This however seemed especially problematic when dealing with words that rhyme over a phone connection jammed by 1-ft think walls originating from the 1960’s over-fondness for concrete (i.e. ‘extinct’ and ‘distinct’). I’ll remember to take interviews in line of sight of a cellphone tower, to enunciate very clearly, to cheerlead the demolition of the current Stanford biology building so it can be replaced by one that doesn’t inherently act as a cell jammer, to avoid using words that rhyme with other words, and to ask (probably with no hope of agreement given the way deadlines in journalism work) for reporters to send me copies of the quotes they’re going to use so I can spot check them for craziness.

3. Quotable moments. So I knew from listening to interviews of people on the radio and general exposure that you’re supposed to stick to the point, and not meander aimlessly down tangents. This is hard for me, as there are so many absolutely fascinating tangents in the world. I certainly got better at it over the course of the few interviews I did, and I suppose practice makes perfect. I also knew that having a few prepackaged sound bites to let the journalists use as quotes would help. Journalists took my sound bite ‘bait’ about 50% of the time (i.e. the overly used, but still useful biodiversity stock market metaphor, ‘not all agriculture is created equal’, etc). I got immense enjoyment reading the articles and seeing which quotes they decided to use. Sometimes, though, they choose the strangest damn things to quote. Not surprisingly, the prepackaged sound bites sounded
way more coherent to me when quoted than when they quoted me talking off the cuff regarding some subject that I didn’t anticipate. This tells me a) that I should probably learn to shut up when I feel like I’ve strayed too far off the point, and b) to have a larger supply of punchy one line statements about stuff connected to my work. Please send me any of the latter if you have any particularly clever additions. I’d love to add them to the repertoire.

4. Random moments of genius due to press-induced hysteria. So yeah, talking to reporters for essentially the first time was a little stressful. This media-stress led to both some terrible incoherent garbage, but also a few flashes of potentially useable material as the inner turmoil generated an upwelling of subconscious nutrients to the surficial layers of my brain. When asked “What are your policy recommendations?” I panicked (as this could actually be important) but thought of the large benefits in terms of total phylogenetic diversity preserved if farms possessed even minimal vegetative complexity. I blurted out the Portlandia-esque “If you have a plot of land, put a tree on it”. If there’s nothing else we’ve established in Costa Rica it’s that birds sure do love those trees. Still, I think “Put a tree on it” has lots of potential for the conservation zeitgeist. Do take note, oh manufacturers of ecofriendly apparel (but please cite the relevant studies on the back of the shirt).

5. Interviews versus no interviews. The final observation is that press articles that actually interview you do way better getting the research correct than the ones that go it alone and simply attempt to re-summarize a press release. Some of articles I found in this latter category simply approach the surreal and bizarre. So I suppose the final message is that talking to journalists really does help make science more accessible to the general public.

-Luke Frishkoff (@LOFrishkoff)

This past July, I ventured into the Sierra Nevadas for the first time to get some hands-on practice with camera trapping. Camera trapping, a technique used by both hunters and scientists alike, utilizes remote photography to capture an animal (usually a mammal) and its movements. Essentially, a camera sits in a weather-proof box in a habitat of interest and is triggered to take a photo or video when it senses infrared motion. Because of its remote nature, camera trapping can give us a glimpse into the lives, habits, and even population densities of the reclusive animals of the world without disturbing their regular activities.

When I first learned about camera trapping as a method to study wildlife, I immediately thought that it could be incorporated into graduate student Alexis’ solenodon studies. So little is known about solenodons and their social behaviors that any insights could help us better understand their conservation needs.

Thus, I found myself at San Francisco State’s Sierra Nevada Field Campus taking part in a one-week field course on camera trapping. I had the opportunity to work with two experts in the field, Chris Wemmer and Ken Hickman, and learn about everything from building my own camera traps from commercial point-and-shoot cameras to setting up good camera stations to data processing and organization. The most fun part, by far, was taking the cameras into the field to see what we could find.

Here are just a few of the shots that I got over the course of the week.


We found this little aplodontia (more commonly known as “mountain beaver” or “boomer”) in a grove of aspens. Experimenting with camera angles and mounting strategies eventually resulted in this photo.


Hidden in scree slopes live the American pika.


Golden mantled ground squirrels also live in the scree with the pika.


Deer mice found the camera trap late at night…


…and the usual suspect, the Douglas squirrel, visited during the day.

In addition to exploring the Sierra Nevadas and finding all of these amazing mammals, I got the chance to meet dozens of other like-minded individuals who loved wildlife, the outdoors, and conservation. On our final night of the field course, a huge rainstorm hit, flushing us all out of our tents and into the one large building on campus. We spent the evening singing, dancing, playing the ukulele, and watching really bad horror films about giant purple man-eating leeches.

All in all, it was a fantastic way to end a fantastic week.

- Lauren Gibson

Never underestimate the power of a good story.  From the whimsical world of J.K. Rowling’s Harry Potter series to the rich and complex tales of Gabriel García Márquez’s One Hundred Years of Solitude, stories captivate, thrill, inspire, sober, scare, and sadden.   They transport us to new and exciting places and simultaneously bring us back down to Earth to face the realities of the human condition.  No matter what form it takes, be it spoken word, text on a page, or an image, a story can change the world.

Humans are story-tellers by nature; we use drama, plot devices, and other narrative tools to convey important messages and ideas.  Just as organisms pass genetic information between generations, humans use stories to pass along culture, from lessons about morality to the history of a specific group of individuals.  Stories put humanity in context; they help us understand where we came from, what is happening in the world around us, and why we value certain things.

Though we often forget it, science, too, is a form of story-telling.  However, rather than looking to other humans for content, scientists look outward, to ecosystems, organisms, the planet, even the universe.  At its core, science combines the key elements and information the universe provides to convey a deeper meaning about how it all fits together and why it matters - the same as any good story.  Just as a story takes you on a journey, science is a process of discovery.  Science can be a saga, especially when methods prove challenging or fieldwork goes awry.

For many years, humanity has focused solely on the story of our success as a species, from technological advances to economic development, and has failed to listen to the stories of the planet itself.  Today, however, science is putting these stories together, and they all spell trouble: trouble for the land, trouble for the sea, trouble for the air, and most importantly, trouble for the organisms reliant on these systems to survive.  From climate disruption to mass extinction, our planet has a lot to say, and scientists are scrambling to find effective ways to share these stories with the rest our population so that we are all on the same page.

Home to some of the most groundbreaking environmental science in the country, Stanford University is now tackling the challenge of communicating these complicated but crucial realities in a meaningful and engaging way. Stanford faculty member Dr. Elizabeth Hadly and her graduate students Alexis Mychajliw and Melissa Kemp are leading the charge, along with a class of undergraduate students dedicated to inspiring environmental consciousness through the power of storytelling.

Teaming up with experts at Environmental Systems Research Institute (Esri), the global leader in geographic information systems (GIS), this class is building a Story Map, one of Esri’s newest and most accessible products, to track issues related to climate disruption, pollution, biodiversity loss, ecosystem degradation, the spread invasive species (and diseases), and population growth across the entire state of California.  This map will inform non-scientists and scientists alike and give policy-makers such as Governor Jerry Brown, a supporter of this effort, a tool for contextualizing the overwhelming amount of information.


Environmental disruption has been in the forefront of Dr. Hadly’s mind for her entire career, and she knows the importance of telling the stories of how these changes impact people. “Story-telling personalizes what happens to you,” Dr. Hadly says, “It’s a framework through which you engage all sorts of people no matter what their knowledge is.  When you hear the personal stories, it puts us all on common ground.”

A story map weaves together multimedia content - text, photos, video, and audio – and organizes it in the context of an interactive web map.  Dr. Hadly’s team uses this platform to collect articles that speak to the issues of environmental change and organizes them by location, so that readers can see where these stories are coming from.  Anyone who has used Google Maps already knows how to navigate a web map, making a story map the perfect tool for general audiences to explore the geographic setting of environmental stories. With the click of a mouse, one can learn about water theft in northern California or how sea level rise will affect residents of the Bay Area.

As an interactive tool, this map allows viewers to dive into local issues without spending hours on a search engine or wading through a report. This, Dr. Hadly feels, is the key to communication because “it allows people who are curious to probe the information as deeply as they want to go.”

“Curiosity, to me, is one of the most important things,” Hadly remarks, recalling how curiosity drove her to uncover the story of vanishing ponds and declining amphibians in Yellowstone.  “It is so valuable to be able to pursue your curiosity.”

Not only will this project cultivate environmental awareness statewide, it has already brought together members of the Stanford community, from undeclared freshmen to tenured professors, who share an enthusiasm for protecting the environment by encouraging others to value its existence.  Fueled by their passion for people, the planet, and vegetarian Chinese takeout, this team empowers students no matter what their scientific background may be and gives them the tools to tell the stories that will come to define the modern age.


This is a guest post by Simone Barley-Greenfield, a Stanford student who took our BIO 128 course and helped make the California Story Map.

Bats have an unusual relationship with people. They are simultaneously a symbol of our nightmares — blood sucking, malevolent creatures of the night — and the providers of services we rely on — pest control, pollination, seed dispersal, etc. — to ensure that ecosystems function and we are able to feed ourselves. With bats presumed to have a role in the recent Ebola epidemic, bats are back in the spotlight, this time for a much scarier and more tangible reason. It is true that bats have been recently identified as the reservoirs for a number of emerging zoonotic diseases, diseases that transmit from animals to humans. But many of these “spillover” events are likely due to humans encroaching onto bats’ habitats and disrupting relationships between bats and their diseases that have been worked out over thousands of years. We also only hear when something bad happens; most systems work just fine. 
With that in mind, Liz and I are excited to embark on a new project, in collaboration with Scott Boyd, a pathologist in the medical school, and John Openshaw, a postdoctoral fellow who works on bat-related disease in Bangladesh, to see if we can figure out what’s working in an agricultural landscape in Costa Rica and how things might change. We’ll be going down to Costa Rica and sampling bats, humans and domestic animals for pathogens that might be shared between species in this rural landscape to see if we can learn what about the bats, the humans and the livestock facilitate disease transmission in this landscape, as well as what pathogens are circulating in the system. To read more about it (and see a stunning example of mismatched gloves), click here: http://news.stanford.edu/news/2014/july/woods-evp-grants-070314.html

— Hannah Kim Frank (@hannahkfrank)

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













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!


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…




Happy holidays from all of us in the Hadly lab!

- Alexis (@AlexisMychajliw)