As far as my eye can see, perched on our house’s terrace here in Marie-Galante (French Lesser Antilles), it is dark. Absolutely black, not a glimmer of light from the sky or the road, save for the porch light at our house. At dusk there were fireflies rising from the nearby forest, but now they are gone. Now it is black. The clouds obstruct the constellations, which on a clear night pierce the darkness like a pinhole camera. The sea turtles are hatching on the nearby beach, and the local law mandates that the streetlights be turned off so as not to disturb the hatchlings as they journey to the sea. I haven’t seen skies this dark since I was a child, as light pollution renders the skies of Silicon Valley paler shades of blue, and in the worst places, bright pinks and reds.
I find dark skies particularly striking on small, isolated islands like this one. There are no cities on the horizon. My colleagues conversing in French over Ti Punch and the mating calls of Eleutherodactylus muddle the sound of the sea, yet despite all of this activity, I have retreated to my innermost thoughts to ponder this island I’ve just reached. My journey was long but rather easy: A flight from San Francisco to Miami and then onward to Pointe-a-Pitre, Guadeloupe, where I took a taxi to the port, and then a 45-minute ferry ride to Marie-Galante. The plants and animals that arrived before me did not have it as easy. It is fascinating to think about how they arrived here over thousands (if not millions) of years, and evolved endemic forms found nowhere else. Marie-Galante sits on its own island bank, meaning that it was never connected to other islands in the archipelago, so land bridges were not a viable method for colonization. Everything that arrived here likely came through wind or over-water dispersal. For such an island to have accumulated species is amazing.
I am conducting fieldwork with a group of French scientists who aim to understand the ancient biodiversity of Marie-Galante, which is preserved in some of the best archaeological and paleontological sites in the Caribbean. I am interested in comparing the lizard fauna of Marie-Galante to that of other Lesser Antillean islands in order to reconstruct patterns of extinction and diversification in this region. Marie-Galante is extremely special, because its caves host rich, Pleistocene-aged sediments that yield great temporal resolution for reconstructing paleocommunities.
[Grotte Blanchard during excavation]
The site of interest, Grotte Blanchard, is mystical itself. The cave has two large openings that look out onto the sea, drawing cool, fresh air into the entrance. Previous archaeological excavations have shown that this was an Amerindian burial site, so don’t be surprised if upon entering, you feel solemnity and awe. The view from the cave opening overlooking the oceans is breath taking, and it takes upon a spiritual air upon learning the history.
[View from inside Grotte Blanchard, looking out onto a pasture and the sea]
But please do not be fooled by the picture I’ve constructed of a far-flung, undeveloped wilderness perched in the middle of the Caribbean Sea. This island paradise is not untouched. As I alluded to when describing the Amerindian burials, it has been inhabited for centuries, long before the arrival of Europeans. Some of the so-called endemic fauna of the Lesser Antilles, such as the rice rats, are only found in association with pre-Columbian sites, raising the question as to whether they are actually endemic or human commensals like the European rat, which replaced them when Europeans arrived. And the sea turtles that the government is working hard to protect? Thus far, I’ve seen four sea turtles—-sea turtle skulls, that is. No one on our team has seen a live one, and the dead ones we’ve found are clearly discarded carcasses of hunted individuals. We’ve collected the carapaces and skulls of these turtles, and any other species we find, in order to create a museum reference collection.
Some other fauna disappeared after the arrival of Europeans, including the Iguana delicatissima that I last described during my visit to La Desirade in August. Conversion of forests to sugar cane plantations (some of the best rum in the Caribbean comes from Marie-Galante) and introduced predators like the mongoose are credited with extirpations and extinctions. Unfortunately, many species that disappeared recently were not described prior to their demise. My hope is to use ancient DNA to contextualize this biodiversity, and determine life history and environmental correlate to extinction in the Caribbean.
[A dead mongoose we found]
There is some hope though, a tiny light in the grim story I’ve painted of Marie-Galante’s endemic fauna. The endemic skink Capitellum mariagalante is thought to be extinct, but we are finding many individuals here.
[Capitellum mariagalante that we caught near the site]
Actually, we’ve seen more skinks than anoles, and I’ve personally looked high and low—literally—for anoles, suggesting that the skink population here is healthy. Of course, future work is necessary to understand the status of this species. I hope that our work here will catalyze future research on this lovely, agrarian island.
Melissa Kemp @melisabetta
It’s been a busy couple months. After quals, I have been serving as a teaching assistant again for Biology 43, part of the introductory biology course at Stanford. I enjoyed teaching the course immensely last year, and am fortunate enough to have the opportunity to teach again this year!
I also had a chance yesterday to attend the first symposium for the new Stanford Center for Computational, Evolutionary, and Human Genomics (CEHG). The formation of this new center was announced back in December, and all of us are tremendously excited about this; our lab is one of the many member labs that span a range of research interests across the Stanford campus. The new center will help to promote collaboration and facilitate discussions between the disparate labs here, as well as offer additional resources, workshops, and symposiums. Several of us from lab attended the symposium, which featured a host of speakers and also a discussion of the directions for CEHG.
Outside of lab, I’ve also been keeping busy, with orchestra rehearsals and two performances last weekend! I managed to snap this photo of the stage being set in preparation for our concert at Bing Concert Hall! We had two energetic performances of Beethoven’s 7th Symphony, as well as Beethoven’s First Piano Concerto and his Fidelio Overture, and now we’re gearing up for the season-ending performances of Beethoven’s 9th Symphony later this month, in collaboration with the Stanford Symphonic Chorus!
- Jeremy Hsu
I started volunteering with East Palo Alto Tennis and Tutoring (EPATT) during my first year at Stanford. EPATT is a non-profit after school program that brings K-12 students from the East Palo Alto neighborhood to Stanford Campus, where they receive academic tutoring and athletic instruction. My work with EPATT has been one of the most valuable experiences I’ve had at Stanford, as it allows me to engage with the broader community and impact local youths. For the past three years, I have been fortunate to work with the same student, a bright and determined young woman who was struggling with mathematics when I first met her. Together, we worked to improve her study skills, reading comprehension, and confidence. Today she is an independent, straight-A student who is able to articulate her thoughts, questions, and concerns to those around her. She is now applying to colleges and hopes to major in Environmental Science. I am extremely proud of her and all the students I’ve encountered at EPATT and I look forward to working with a new student next year when I continue working with the organization!
Contributed by Melissa Kemp
San Vito, Costa Rica, 29 March - Principal component analysis is a very special thing. It makes a great number of variables, smushes them together, and then tells you what’s important in differentiating your samples. As part of my current project investigating patterns of amphibian tolerance to deforestation I’ve had the pleasure of conducting a number of vegetation plot surveys along the transects that we’ll soon be using to sample frogs—measuring leaf litter depth, vegetation height and composition, slope, canopy cover, number of trees within 5m, just to name a few. I’ve spent the past few days sliding down precipitous slopes, getting tangled in lianas, wading through invasive chigger infested pastures, trying my very hardest to avoid poisonous snakes, and attempting to make up my mind as to whether vegetation plots are awesome and make me feel like a ‘real ecologist’, or something that I despise and can’t wait to be done with so I can go back to working with frogs. While I try to make up my mind, I thought I would summarize my past few days in Costa Rica in pictorial form:
Even though this represents only one out of my five study locations in Costa Rica, with the magic of statistics we can already quite clearly see that pastures have a markedly different vegetative structure than forests (who knew?). But what’s not entirely expected is the second axis really quite nicely pulls out your chances of rolling head over heels down an incredibly steep slope. I’m particularly happy that it tells you not only that some sites are insanely steep, but when sites are steep they’re also mostly bare earth/mud, and you don’t have any vegetation to hang onto. In retrospect I now know exactly where I should avoid. So thank you statistics.
One of the offending high PC2 pasture transects. Cows were thankfully absent from all the pasture sites—probably because they ended up at the bottom of the hill, and unlike crazy researchers decided that there was no point trudging up it again.
Luke
It’s been quite a busy few weeks for us. Katie, Hannah, and I have been diligently preparing for quals, which are next week for Katie and I and the week after for Hannah. We’re required to write a dissertation proposal and then give a presentation outlining what we want to do for the next three years or so. (Fortunately, there’s no general exam for us!) This has been a really edifying process, and I’m really looking forward to all the feedback and advice next week!
I also flew to Denver earlier this month to participate in a workshop on RAD tag sequencing, a next-generation sequencing technique which I am using for my tuco-tuco project. Hosted by the University of Colorado – Denver School of Medicine (which is technically in Aurora), I spent the week discussing technical issues regarding the technique, as well as the pipeline and analysis of sequencing data, with seven other graduate students and researchers. We were led by Ken Jones, a bioinformatics faculty at the school. It was a terrific chance to brainstorm together, discuss challenges we have all faced, compare protocols and strategies, and get feedback on ideas; I also gained a tremendous amount of information and learned a lot regarding the analysis of such data. It was also my first time in Denver (well, outside the airport) and while we didn’t have too much time to explore downtown, it seems like a really vibrant city!
Flying into snowy Denver
The workshop group
It hasn’t been all work, though, recently. I spent last Saturday volunteering at the California state MathCounts! competition. MathCounts! is a math competition for middle school students; the program is nationally recognized (the national competition is broadcast on ESPN and the winning team meets with the president each year!) and helps promote math and careers in science, technology, engineering, and math fields. I was a Mathlete (the term for a MathCounts! participant) for all three of my middle school years and went on to coach a MathCounts! team after my middle school years were over, and I still remember the excitement and thrills of the competition back then. It was thus so gratifying to be able to help out with this program again (I volunteered last year as well). It was similarly inspiring to see so many young students so passionate and eager about math; their enthusiasm was visible throughout the day. After the written individual tests and the team round, the top participants were invited to the Countdown round, which pits two Mathletes against each other in a series of questions to see who can solve the question correctly first. This was absolutely incredible – I had often barely even finished reading the question before the students would buzz in with the correct response, and there were several questions when I hadn’t even finished comprehending what the question was asking before they had gotten the question correct! The emotions were also visible for each of the kids – I could see the raw excitement and nervousness in their faces. While some kids were inevitably disappointed in the results, each of the competitors kept cheering each other on, and it was truly an inspiring scene.
I also took some time out of my preparations from quals to go cheer on the Stanford Cardinal women’s basketball team earlier this week. Stanford was lucky enough to host the first two rounds of March Madness for women’s basketball, the NCAA tournament. The Cardinal are ranked as a #1 seed in the tournament, and are looking for their fifth consecutive trip to the Final Four, and hopefully a championship this year too! I watched the Cardinal take on #8 Michigan at Maples Pavilion on Tuesday, and boy, was it a fun scene! The team plays with so much passion and energy, and their camaraderie is very evident. It was also a special night for the team, as this was their last home game of the season (with the next tournament games moving to the regional site in Spokane, Washington and the Final Four in New Orleans) and thus also the last home game for Joslyn Tinkle, the lone senior on the team, and she responded by hitting all five of her three-point shots in an emotional night. It was indeed raining threes all night, as Stanford raced out to an early lead and never looked back (it was 41-16 at halftime and the final score was 73-40). The near-capacity crowd at Maples responded with a standing ovation for her when she checked out of the game, and again rose to its feet to send off the entire team as they look to continue their journey in the tournament. Up next is #4 Georgia – go Stanford!
The scene from Maples on Tuesday
- Jeremy
As a little kid, I vacillated between wanting to be a paleontologist and a veterinarian. I think being an evolutionary biologist lets me do a little of both at times, but this week I did my younger self proud by bringing out my inner paleontologist through participating in a 3 day NSF sponsored workshop: “South American Megafauna Extinction: a test of synergistic effects of climate change and human population growth in magnifying extinction intensity”. It covered every science-inclined kid’s dream: Giant sloths? Check. Tar pits? Check. Sabertooth tigers? Check. Better than an Ice Age movie!
A team of about 30 scientists from all over the US and Latin America converged at Stanford’s Center for Latin American Studies — paleobiologists, archeologists, paleoclimatologists and radiocarbon dating experts— to develop a plan of attack for radiocarbon dating of over 100 megafaunal remains across a wide phylogenetic spread, with the ultimate goal of elucidating the Quaternary extinction chronology of South America in relation to anthropogenic and climatic perturbations.
Day 1: Wednesday began at 7am for Melissa and I as we picked up all the participants from their hotel and arrived at Bolivar house for the first time. The majority of the day consisted of participants introducing themselves and what role they will play in the project. Our very own Liz Hadly gave a talk on the genetic data describing the human colonization pathways of SA.
We had a very lively discussion on educational outreach strategies. One major point was that although in the US internet-based educational programs are highly effective, such as the Understanding Evolution website at UCMP, the internet is not the most effective medium for reaching students in SA. Instead, we floated ideas such as children’s books, making casts of local fossils, and TV and radio programs.
Day 2: Thursday was a long day filled with details and data. There was a discussion on good practices in radiocarbon dating protocols, and reports on new radiocarbon dates gleaned since the NSF proposal had been written. We were given an overview of currently existing databases, such as NEOTOMA, and how we could best make use of these structures to organize and publicize our data.
Rodolfo Dirzo of Stanford gave the research a very modern context by describing contemporary ecological effects of large mammal extirpation. The selective loss of large mammals, or “defaunation”, leads to an increased rodent abundance and a homogenization of vegetation. This could provide a testable hypothesis to examine the fossil record for similar ecosystem changes associated with the extinction of megafauna.
We also had a wonderful dinner at Liz and Tony’s house to further discuss our ideas over some homemade mole!
Day 3: Our final day was spent selecting taxa and sites to target. We outlined potential publications, chose a researcher or two to be in charge of a specific geographic region’s data, and even began discussing next year’s conference!
And of course, we took a group photo!
Hadly lab will contribute to this project by reviewing all available Caribbean radiocarbon dates, which is particularly useful for me as I study Caribbean mammals, extinct and extant. Understanding the patterns of extinction in SA, compared to what we know already in NA, will provide the most robust framework by far to really tease apart the details of extinctions in the Caribbean, particularly as they relate to “island” versus “mainland” patterns.
Throughout my undergraduate career, I often marveled at how papers in Science and Nature were able to tackle questions on a seemingly all-encompassing scale. Prior to this workshop, I had only done research involving myself advised by a professor- a very individualized approach to specific research questions. Now, I feel I understand how science gets done as a collaborative effort, with each researcher having his/her own expertise to contribute to the larger team. This is how big science gets done!
I am particularly excited to be a part of this project because I believe it comes at an important time when we seem to be recapitulating this loss of large-bodied mammal species all across the globe. Perhaps if we understand what we have already lost, what remains today will seem all the more precious to save.
- Alexis Mychajliw (@AlexisMychajliw)
Elizabeth A. Hadly (@LizHadly)
Paul S. & Billie Achilles Chair of Environmental Biology, Stanford University
Close encounters are wake-up calls. The recent near-miss of a 130,000-ton asteroid, hard on the heels of a 10,000-ton asteroid in Russia that caused injury to 1200 people, precipitated demands for international scientific and engineering solutions to avoid future calamity.
It’s easy for us to envision a comet-caused catastrophe because the fossil record tells us it has happened in the past, with disastrous results. But what about the slow-motion catastrophe that is global climate change? There is no doubt about this catastrophe’s impact either.
As a paleobiologist who studies survival and extinction in the fossil record, I have handled bones of animals long extinct and I’ve seen how animal communities change over millennia. What I study has shown me what is at stake. It has convinced me that we’ve created our own asteroid, and one that will not just fly by. Our climate is warming; our oceans are acidifying; our forests are disappearing; and our population is growing. Where is the public outcry? We must compel our scientists, our engineers, our businesses, our policy makers, our leaders—indeed, each other—to confront and plan for our future.
This is not a hypothetical disaster. This is real. The number of humans on Earth has more than doubled in my lifetime and it is projected to reach 10 billion by 2050. Temperatures then will be warmer than our species, Homo sapiens, has ever experienced. Sea-level rise endangers our beachfront properties and major ports; warmth-fostered beetle expansions have killed millions of acres of conifer forests; and drought strains our crops.
These changes are facts, witnessed every day. Our military is planning for them. Our insurance companies are dealing with them. And many of us are feeling the impacts of too many extreme events like this year’s fires and superstorms. Yet our policy makers have consistently failed to make environmental policy a priority. Of 932 bills now before the 113th Congress, only 11 even mention climate; only 5 mention fossil-fuel emissions—and of those, 3 bills oppose emissions regulation.
While climate change is an international problem, solutions begin at home. The US has an international commitment to cut greenhouse gases by 2020, but unless we enact legislation to cut power plant emissions, eliminate hydrofluorocarbons used in automobile air conditioners and elsewhere, and increase energy efficiency, we will not fulfill our promise.
For regulations and incentives to curb our energy use and dependence on fossil fuels, requirements need to become true political priorities, not just ideology. But this will only happen if everyday citizens and voters begin to adjust their own priorities—and the way they view the world. Compelling as the statistics may be, they pale in comparison to the power of individual attention.
In my own work and lifetime, I’ve seen changes due to climatic warming around the world. At the top of Africa, I walked to the edge of Kilimanjaro’s glaciers, now smaller than anytime in recorded history, and melting by the day along with the ice records of thousands of years. In Rwanda I sat among some of the last 700 remaining mountain gorillas, most bearing some scar documenting their encounter with humans—severed hands, runny noses, and fragmented families. In our own national backyard, I have watched drought evaporate our frog ponds. Beholding these changes with my own eyes has increased my sense of urgency and responsibility. I believe every one of us has a duty to take note of the world’s transformation. Indeed this is the only way to orchestrate political action.
The size of this metaphorical climate comet overwhelms us, but Americans have solved seemingly insurmountable problems before. We abolished slavery. We landed a man on the moon. Now we drill into Martian rock, see the edge of the universe, and calculate asteroid near-misses. We can conquer great obstacles and overcome enormous technical challenges—but not as bystanders.
Environmental events of the past year are our wake-up call. Drafting a blueprint to forestall and adapt to climatic change starts with a more careful, honest and widespread view of our changing planet. Lend your voice to our leaders’. Ask policy makers and your neighbors to make limiting emissions a priority. And just as important, bear witness yourself. As we pay attention to the small, incremental things around us—not just the violent cataclysm of an asteroid collision—we may find the keys to living with our own dramatic impact on the planet.
Seven more sites to go and things are going swimmingly (er, flyingly?) with the bats. On Sunday alone we caught 100 bats, including several individuals of one of my favorite species, Platyrrhinus vittatus. On Saturday we caught two individuals of Pteronotus parnellii, each of which had over 20 bat flies!
Some of you might be wondering what sampling in the field looks like. Below is a photo of our processing station, set up outside of a forest fragment (which is not visible in the photo).
More dispatches to come but in the mean time, @Luke, this *Anolis* biporcatus is standing just fine.
-Hannah (@hannahkfrank)
Regardless of your feelings towards the long-standing lab debate as to whether Norops exists or not (http://en.wikipedia.org/wiki/Norops), you have to appreciate this intrepid Norops (=Anolis) polylepis. He just keeps on trucking, maintaining haughty disdain for those so-called ‘necessary’ body parts like tails and legs. This individual was captured in one of our agricultural sites in Coto Brus, Costa Rica in July 2011, and seemed to be in relatively good health despite the predator-induced (?) missing appendages.
Luke (@lofrishkoff)
(For the record, this particular lizard, during a long heart felt conversation, unequivocally defended the genus level status of Norops.)
Greetings from Costa Rica! Two nights of sampling and 56 bats in, I’m off to a great, if slightly overwhelming start to my field season. I am catching bats in this region to determine how land use and host ecology affect parasite and infection prevalence in Neotropical bats. Most of the bats we catch belong to the ecologically diverse family Phyllostomidae. Included in this family are (1) nectarivorous bats, like the orange bat, Lonchophylla robusta, (2) frugivorous bats, like the fig specialist, Artibeus jamaicensis, (3) carnivorous bats, like the very large Phyllostomus hastatus, (4) insectivorous bats, like the adorably big eared Micronycteris hirsuta, and even (5) the infamous vampire bat, Desmodus rotundus. This presents an excellent study system in which to examine the effect of ecological differences on disease dynamics and immunogenetic evolution. In particular I’m excited because we have caught 5 Micronycteris, more than all of last field season!
More stories and photos to come, but for now, I prove that there’s no reason jungle style and lab style can’t mix.
Saludos!
Hannah
(@hannahkfrank)
