Sunday, December 27, 2015

big data, big ideas and a big gorilla

Not a raindrop, or a mushroom, or a dark-eyed junco, just a “ >” and a “#” and a “/”. 

I have been thinking a lot about the paradigm shift in biology towards the computational analysis of big datasets. The most important skill-set for modern biologists is no longer getting crazy dirty, sweaty and blissed-out studying wild populations in the field -- but understanding how to analyze big datasets, at your computer, sitting on your butt, in your half-office. 

Now, you can be a biologist and study gigabytes of information about the natural world (DNA sequences, gene expression data, geographic distributions etc.) without ever being close to a bit of anything natural. Or you can be a biologist who studies the natural world, but does not really know the modern methods of study, just browsing the forest with a keen eye, an old-fashioned big idea (and a little secret). Are either of these biologists compromised, or can they both add valuable knowledge to our understanding of the world? Who wins: the indoorsy computer nerd, or the wild energetic explorer? Blessed are the unicorns who are both, but let’s imagine one isn’t. 

These seemingly disparate activities are unified by thoughtfully designed research questions, and the traits of curiosity, critical thinking and grit. Wake up again and walk into the cool morning forest to find species x, even though you would rather rest more in your crappy tent. Wake up again and work on the script that won’t work, even though you would rather rest more on your pillow-top mattress. Nothing is working, so think of a new approach. Didn’t get the grant you applied for? rewrite and resubmit. Paper got rejected? resubmit to another journal. Whatever it is, forest or FASTA, poison or polytomy, keep going, keep looking and keep thinking critically and creatively. 

So, what can we teach students who are interested in natural history and genetics
 that now need to know Python and R? Do we start by teaching the mechanics of Python, and save the actual pythons for later? And what if you like catching snakes, but you aren’t good at, or drawn to, coding? Is there a place for you as a biologist in this new computational jungle? 

E.O. Wilson said that you don’t have to be great at math to be a biologist, some people freaked out about this. But what he said echoes into the practice of bioinformatics too. Can you be a computer dud, but still do science today? And will this new computational paradigm favor computer wizards who may not know, or care, about complex biological processes like species formation or migrations? And how do you learn to care about these abstract processes if not by seeing and knowing the breathtaking bird, or the scales of the snake, or the big gorilla itself? 

Sunday, August 16, 2015

Darkness at the edge of wonder

The starling’s beaks are darkening into a marbleized browny black for late summer. They are no longer the cheery yellow of the breeding season.

As an educator working with high school students in an informal scientific learning environment, our great goal is to inspire students about the wonders of the natural world. We regale them with tales of discovery, dazzle them with biodiversity, and let them experience the highs of self-directed inquiry. This requires an enthusiastic, optimistic, and sometimes histrionic teaching approach.

But, the reality of doing science is not all awe-inspiring. Most times it is the opposite. Most times it is a thankless slog, indistinguishable at the daily level from other detail-oriented, challenging jobs. Most times things don’t work as planned, and there is no discovery, just confusion followed by more confusion, stress, and then disappointment.

It is a life of the lab, of the accidentally dropped 96 samples; a life of the forest, drenched in sweat and not having seen a single species-you-came-for all day. It is a life of the desert, hunched over hunting for fossils and finding nothing. It is a life of awkwardness, bad advice, insecurity, and mountains of other people’s arrogance. It is a life of having to prove yourself, right after having just proved yourself. But it is also, a life of the mind, which is the big yellow hope that guides us through the darkness. Asking a question with an answer that is millions of years old, making a new connection, illuminating a pattern, or uncovering unknown diversity. It is all gloriously bigger than us. And no wasted day in the lab or the field can take away the intellectual euphoria that accompanies this imperfect journey. 

But what can we tell our students, that will speak to the darkness, but not turn them away? And maybe some of them should be turned away. It is not for everyone. It is not for most people. It makes no sense, and yet perfect sense. 

Most times you find nothing, but keep looking darlings. Their beaks will be yellow again in spring.

Tuesday, June 2, 2015

I saw your heart

Last week we prepared starling specimens as if they were bound for a research collection. We skinned them, gutted them, stuffed them, and sewed them back together again into a once-and-beautiful-bird. We sat in almost-silence learning how all the pieces fit together, by slowly ripping them apart. 

I once posed a question on my blog asking biologists to tell me why they work with the species—or group of species—that they do. Is it because they are a model for understanding humans? or because of their interesting behavior, morphology, or adaptations? or maybe, you are just flat-out inexplicably drawn to them? Unscientifically adoring of your fascinating and sweet species. You watch them move in the wild, you know their tendencies, and how to tell individuals of the same species apart. You get a rush when you see something rare. You think about them all the time. We cannot deny that we are moved by the animal kingdom, yet I have been told in so many ways that it’s not typical or acceptable to bring these feelings to scientific inquiry. But I truly think it is artificial to pretend otherwise. Give me a break. I know what science is, and what it isn’t. I trust my measurements are not inaccurate because my eyes are blurry with tears. I can quantify something cute. And isn't knowing about something, wholly and deeply, the most comprehensive kind of love? 

First, we blew gently on the ventral side of the tiny body so the feathers naturally parted. We slowly sliced into the starling flesh. We started in the middle of the chest. And worked our way towards the head. We stripped the flesh away from the skin on the inside of the breast and then wings and legs. We removed the guts. Then, we did something unthinkably weird. We inverted the head so that the skull was inside the body cavity, and the skin that was previously over the head was a headless floppy feathery costume. We cut the back of the skull open, and removed the brain tissue. We popped each eye out. Then, the brainless, eyeless, skull went back inside its original skin. We made small cotton stand-ins for where the eyes had been, and pushed them through the bloody neck back into the orbits. The wing bones were tied together on the inside of the skin. The leg bones were wrapped in cotton, which looked like some kind of last ditch effort at wound care of a badly bedraggled bird-thing. We stuffed the inside of the chest cavity with cotton, reestablishing the original plumpness of the living bird, and we sewed it up with a needle and thread. My colleague spent time lovingly straightening the feathers. We crossed the legs, and tied them together with a string, which felt like we were finally laying this little life to rest. 

Sentimentality has no place in science, so I will stop by saying thank you specimen #8, you helped me learn about bird anatomy, and how to prepare a study specimen, and through that process, I can say I saw your heart. 

Wednesday, May 13, 2015

spring starlings

It was a long winter. All winters are long. Spring is undoubtedly here. First the white flowering pear trees, then daffodils, pink cherry blossoms, outdoor cafes and seasonal allergies. It’s all here. And —as always—it’s warm and hopeful and glorious.

We spent the fall and winter collecting genetic data from our modern (airport) specimens. Now we can spend time this spring watching the starlings behave. In early April, I started noticing more starlings on the museum lawn. Now, they are everywhere. Their beaks are yellow, their plumage is getting shinier, and they are pecking furiously at the grass. Grackles, pigeons, sparrows, and robins are out there too. But starlings are unmistakable, even from a distance, with their long legs and distinct gait. They look more comfortable walking on the ground than some other birds. They are at my bus stop in the morning, and again when I arrive at the museum. Sometimes they fly alongside the moving bus. They sport triangular wings while in flight and, needless to say, move much faster than the bus.

Their plumage changes with the seasons. It is not a color change though, it is a shedding of the little light colored bits on the ends of their winter feathers. Then, for the breeding season, they are ready to strut around in their more flashy iridescent feathers. Their beaks turn from brown in fall to yellow in spring. I always cherish the onset of spring, but it is my first year really noticing the starling’s seasonal transition, which —just like the warmth and the blossoms—is predictable and comforting and totally marvelous.

*I need a new starling picture for my blog header, send me your pics of spring starlings!*   

                                                                     image from

Sunday, April 12, 2015

Adventure is for the birds

Six o’clock was approaching in inconceivable leaps. You label the tubes, I’ll label the package. We send our DNA out for sequencing, which means we ship little tubes of clear liquid in an envelope to New Jersey. In a few days, we receive a computer file with strings of A’s, C’s, G’s and T’s that we carefully analyze for key differences. The last package pickup is at 6:00pm. We were running late.

I took the envelope and ran through the grand halls of my work place; past the 145 year old canoe, through the 1950’s forest, past protists and dodos and horeshoe crabs. It was a natural history themed This is your Life episode. I felt fleet-footed and brave.

This project is not a traditional adventure. No traveling to far off places to collect rare specimens, no field clothes, no tent sleeping. No plane ticket, no goodbyes. All the work occurs less than 2 miles from my apartment. Specimens are sent directly to me. Even my “time travel” to collect historical specimens involved going in some very nearby doors I had never entered. Maybe I am missing out, or maybe I am incredibly lucky.

Out of breath from my run, I reached the desk. “Did I miss package pickup?”, “No”. My mind sailed away to temporary confident places, I did it! imagine what other impossible things I am capable of? I think about these birds constantly. I regularly wonder what the complete data will show. I am dying to know. I am an over-thinker, but I am also an immovable beast, I don’t love going places like everyone around me seems to. I recently diagnosed myself as an indoor dreamer. But even though I haven’t crossed rapids, or hiked for hours, the intellectual journey is an adventure to me, one that I would gladly run through the halls to achieve.

After my focus returned, the man took my package and smiled, “the last pickup is 8:00pm”. Ashamed, exalted, I told him about my gloriously unnecessary run, and how great it felt. He told me to run back. So I did.

Thursday, March 12, 2015

Bird heaven

Thousands of specimens sit in silence, waiting for a scientific research question to give them life. Birds from different decades sit together in one drawer. Birds that lived thousands of miles apart might share a cabinet. It is a time capsule, and a pile of places — it is a collapsed little world.

I have been dreaming of this starling project for months. What motivates me is not their striking beauty, or their precious handwritten specimen tags, it is looking for patterns and tracing the biological legacy of their dramatic story. I sat at my desk and stared out the sliver of almost-window, I read, and researched, and emailed about it. But what I didn’t realize is that the historical specimens that would allow me to understand how the species changed through time were sitting —without much exaggeration—on the other side of my office wall. Behind my office wall there is a bathroom, and then not far beyond that, it is bird heaven.

Tuesday, January 27, 2015

old little toes

Are New Yorker starlings different than Californian? I would bet yes, but how so? some do yoga, others drink too much coffee and double park? Maybe. 

We are studying starling populations throughout North America to detect genetic and phenotypic differences across the country. But, aside from detecting geographic variation, we also want to chronicle how the species has changed over time. For this, we will look inside hidden museum collections. Museum research collections are important scientific repositories for data that are otherwise inaccessible to researchers. Some specimens may represent species, or populations, that are now rare or extinct. It is critically important for the advancement of science to maintain and make available the specimens within research collections. Thousands upon thousands of specimens of birds, mammals, reptiles and fish have been collected, prepared, stored, and made available for research purposes like this project. 

We will be soon receiving 33 samples of starlings from The Field Museum. We will not receive whole birds in a bag, or a box, as we have before. The samples will consist of small pieces of old little toe pads cut from bird specimens. Some from England, others from the East Coast of the US—all old, some over 100 years. From these pieces, we will extract ancient DNA. This will bring a new dimension to our starlings study. I am thrilled.

We can answer questions like: Have North American starlings lost genetic diversity over their 100 year time here? Have some genetic groups gone extinct? Do starlings in North America have less genetic variation than those in England from the time of their original arrival in 1890? 

And I keep thinking of the hilarious Big Lebowski toe storyline: I can get you a toe by 3 O'clock

Sunday, January 18, 2015

strange familiar birds

Their beaks are brown for winter, their plumage blurry with stars. They convene on the sidewalk for a brief bird-minute, and I stare at them as if I will be able to see urban evolution in action. I haven’t seen it yet, but I know that it is there; in their genes, in their bones, and in that walk - that rises and falls with a graceless bounding pride. What can we learn from these strange familiar birds?

The concept for this project grew out of a basic evolutionary question I had about how populations evolve. We know that a dramatic and prolonged decrease in population size results in lower genetic diversity, and stronger genetic drift 
for succeeding generations. But what happens to morphology under these conditions? I don’t think there is one answer for all taxa. Variation differs from species to species, and from trait to trait. Because of the stunning history of starlings in our country, I am deeply curious about the diversity of their skeletons, feathers and beaks. By bringing a cage full of lively birds from England to the US and releasing them in Central Park, an accidental evolutionary experiment began in the winter of 1890 - one that we are following up on today.

The data are coming in. Our sturnus vulgaris mitochondrial DNA sequences look clean and strong. One goal of our project is to better understand the genetic diversity of North American (NA) starlings, and compare that to other sturnus vulgaris populations around the globe. The expectation is that genetic diversity will be low in NA starlings because of the small size of their founding population (60 individuals in 1890), and their rapid expansion (to 200,000,000 in just 125 years). It is too early to tell how much, or how little variation, we have yet. I am highly hopeful that we will get solid results this year. We are lucky to have the great help of wildlife authorities throughout the country for suppling birds. And I am working together with two conscientious students who are doing careful lab work. We have started a database for recording information about each specimen. It is exciting to see it grow. Data accumulation is one of the great thrills of doing science, it’s work made visible.