Tuesday, October 27, 2015

Post #42 - My newest addiction...eBird!

I am sure that many of you are familiar with eBird, the crowd-sourced database where individual bird sightings go to become meaningful scientific data. As can be imagined, accurately assessing bird distributions is very difficult. Birds move around with seasonal periodicity, and they often inhabit or visit widespread areas. It is virtually impossible for one birder or researcher to generate a completely accurate, representative picture of how a species is distributed at any given time. However, if we pooled the observations of ten of thousands of observers, a more dynamic, more representative picture is going to emerge. This is the invaluable, curatorial function that eBird was conceived to perform. This is an article from the New York Times that uses a few more words to convey the same message.

Here is an idea of the sort of distribution information we can glean from eBird. The following 4 images are sightings of Magnolia Warbler, filtered by month for March to June of 2015. The purple boxes represent Magnolia Warbler sightings, with darker colors corresponding to increased frequency. We can literally see the birds moving north from their wintering grounds to their breeding grounds! How cool is that?!?! Bird migration in near real time! There are dozens of similar applications for an trends in the collected data. It is all archived and readily accessible and will be so in perpetuity (hopefully!)




Now, I will confess that I was a bit late to the eBird party; I only started eBirding in December of last year. Why did I wait so long to get on the eBird bandwagon? Much of it had to do with my career as a scientist where my entire professional existence revolved around counting various things: numbers of embryos, numbers of synapses etc. At that time, birding was my escape from data, and, as a result, I could not face additional data collection and entry on my personal time. Also, as I began to take a more-photography-centric view of birds, I didn't think my input would really prove that valuable since I wasn't really looking for birds beyond my photographic radius.

During my bicycle Big Year, I relied very heavily on eBird to help formulate bird finding strategies. One thing that became painfully clear to me was that I was taking infinitely more from the database than I was contributing to it. As my year started to wind down and birding settled down a bit, I decided that I should make a conscious effort to contribute. This was done as much out of feeling of obligation as anything else. I am a relatively competent observer, and I bird very frequently (or at least I did before I moved to LA!); I am exactly the sort of person who should be contributing to eBird.

Anyway, what I quickly discovered is that eBird is TONS of fun, so much so that I am now totally addicted to it. As someone who is obsessed with data, record keeping, and trends, it really cool to see not only the amount of data collected in eBird, but also how the site manages my personal data. I now have a list for everything (hemisphere, state, county, etc) - and they're all in one place! My data, beyond its obvious scientific utility, now functions as a personal birding history, a chronicle of what I saw when and where. I only wish eBird had been around from the instant I started birding. This is sadly not the case, and, as I cannot go back in time, I will make what efforts I can to ensure than my birding history moving forward is complete. It is fantastic that my data serves both a communal, scientific function and a personal, historical purpose. 

"I didn't eBird Broad-billed Sandpiper from Jamaica Bay in 1998!"

As I am headed to Texas next week for the Rio Grande Valley Birding Festival, I have been using eBird to keep daily tabs on 2 particularly interesting species: Northern Jacana and Collared Plover, both of which would be life birds for me. It's really a lot of fun to log in and see if the birds are still being seen. Fingers crossed that both stay put!

Lastly, I also want to send a shout out to the eBird curators and reviewers. I am sure that this job is usually thankless, but without proper administration and quality-control the long-term utility of the data would certainly be compromised. I am sure its a lot of work, so thank you.

Lastly (again), please also check out iNaturalist. This is a similar crowd-sourced data collection platform that includes (beyond birds) insects, plants, fish, mammals, whatever. It is also a very valuable resource!

Ooooo  Ooooo Ooooo. Before I finally go, here's an actual bird photo for you! I took this at Malibu Lagoon a few weeks back. Photography has been painfully slow recently, but I'm hoping to make it out for at least some shooting this weekend. Please stay tuned!

Spotted Sandpiper - Arctitus macularius
Canon 500mm f/4 IS on EOS 7D2
1/3200 at f/5.6, ISO 800
Manual mode, handheld 

Monday, October 19, 2015

Post #41 - The Curious and Controversial case of the Moustached Kingfisher

Moustached Kingfisher is an apparently rare bird that is found on - and only on - the Island of Guadalcanal (of WWII fame) in the Solomon Islands in the South Pacific. I say 'apparently rare' as it has not been the focus of significant study and there seems to be at least some disagreement as to how many of the birds might currently exist. Miraculously, one individual wandered all the way across the Pacific and was sighted in Los Angeles this weekend! Just joking! Seriously though, this species has recently been in the news, and I wanted to take a few minutes to discuss the controversy surrounding it. 

Moustached Kingfisher

Guadalcanal is marked by the red pin

I am sure that many of you have already read at least something about the great Kingfisher Controversy of 2015. The basic idea is that a team of scientists recently caught, in a mist net, a male Moustached Kingfisher while on a research expedition to Guadalcanal. This species is rare enough that no western scientist had ever laid eyes on a male before that individual was captured. What little was known about the species was gleaned from 3 female specimens that dated to the first half of the 20th century. As no formal, systematic study of the species had ever been performed, they decided to sacrifice the captured bird and preserve it as a specimen to be taken back to the Museum of Natural History in New York City. There it would be further studied and archived in the museum's collection. Their decision to do this has sparked at least some amount of outrage, most of which stems from the fact that we do not have a concrete idea what the loss of this individual bird means for the sustainability of the kingfisher's population moving forward.

The truth of the matter is that we know very little about the population of this apparently rare bird. This is why research expeditions are initiated, to fill in the gaps in our current understanding or knowledge. Speaking with locals who know more about the species than they or any westerners did, the scientists decided the population could tolerate the loss of this single individual. The locals apparently concurred as the outrage has come mainly from elsewhere. 

I understand the uproar, but I fully support the decision to collect the bird. It is awful that this one bird had to pay die to further our understanding of the species? Yes, certainly. However, the potential upside for the species in my mind outweighs the cost of that one individual. Given the information they were presented by locals, their decision seems reasonable. While there is debate as to the precise population size and status, the chance that the removal of this exact individual will ultimately lead to extinction is small. However, that we will learn at least something beyond that that was known prior to the collection is difficult to debate. Many might say that DNA analysis, for example, could have been performed from feathers taken from the bird prior to release. This is certainly true, but this would not permit us to have an intact reference specimen, or "type-specimen" against which future comparisons could be made. It is as important that we have a reference specimen for each species as we do for weight and distance measurements, for example. As the definition of a species has become increasingly malleable in recent years, it is important that we have a reference point from which to start any taxonomic classification scheme or discussion. The specimen in question will serve as the reference point for all future discussions and analysis of Moustached Kingfishers. 

I am sure the scientists took no joy in taking the life of the bird, but I think that the cost of their decision to do just that will be paid by the longer term attention that will be focused on the species moving forward. Hopefully what I penned here makes at least some sense to some of you. If none one disagreed, there wouldn't be much point of putting my opinion out there, would there?

Lastly, and considering the subject matter of my last post, I thought this was too funny and appropriate. It's worth watching, I promise!

One more shot I found from Monterey a few weeks back
Pacific Golden-plover
Canon 500mm f/4 IS on EOS 7D2
1/2000 at f/5.6, ISO 800
Manual mode, Handheld (while in knee deep surf).

Tuesday, October 13, 2015

Post #40 - Some thoughts on our connections to the natural world

I am a biologist, not in the casual sense, but professionally. In the past 20 years, I have spent time designing and performing experiments to further our understanding of neuronal differentiation, molecular embryology, cell polarity, tissue morphogenesis, synaptic plasticity, small RNA biogenesis, and a host of other fancy-sounding fields that neither of my parents understand. The goal of my collective work, in the end, is to understand how our bodies and those of the other living things around us function at the cellular level. This basic biological knowledge, when applied by others to disease states, has the power to alleviate human suffering in many capacities. When reductionist work such as mine is coupled with the top-down approach employed by organismal and evolutionary biologists, a still more complete biological picture emerges. Beyond an understanding of our own intrinsic biology, we realize that we are actually just a single, though incredibly important and often destructive, player in a carefully coordinated biological dance that has been occurring at the planetary level for hundreds of millions of years.

A particular protein I study fused with a red
fluorescent protein in the C. elegans germline.
The protein localizes to the nucleus of the cell. 

I use this as a backdrop to explain and to explore an experience and series of thoughts I had today. Today is Tuesday, and like most, I find myself in my lab at USC. This morning I was analyzing some DNA sequence data. As per usual, I put some music on my headphones so as to block out any other distraction while I focused on the task at hand. Staring at the biological code as depicted in my sequence data, the seemingly endless quaternary code of nucleic acid bases that defines and dictates much of our biological existence, I caught my own reflection in the screen. Hands extended towards the computer keyboard, headphones upon my head, digital music formed by little more than 1's and 0's playing in my ears, I suddenly felt incredibly detached from biology, the same biology that I have dedicated my life to understanding. For a split second, I felt more a part of the machines to which I was connected than to my own biology, to my own being.

Lesser Goldfinch on Primrose
Apropos of more organismal approaches to biology
Canon 500mm f/4 IS on EOS 7D2
1/4000 AT F/5.6, ISO 800

Beyond a terrifying but altogether temporary experience, I think this sort of moment reinforces precisely why it is important that we maintain some form of connection to the natural world around us. Time with nature and the natural world's constituent organisms - both macro- and microscopic - reinforces the connection that we have to them, a connection that is sadly being lost as the sphere of human influence expands to previously undisturbed regions of the globe. In the digital age, not much of what we touch, see, hear, or generally experience has escaped the heavy hand of human design or manipulation. I am reminded that the time when I am the absolute happiest is when I am in some natural place simply looking at birds. Beyond photographic subjects and ticks on life lists, birds provide one of the most common reminders of the natural world that exists beyond the confines of our usually human-centric horizons. I know that when things in my own life seem their most tumultuous, I recenter myself by retreating into decidedly more natural spaces to sort myself out. Maybe today's brief episode is a reminder that I owe it to myself to do just this every once in a while. Biology is everywhere - inside AND outside the lab.

Monday, October 5, 2015

Post #39 - Interesting snowy egret behavior w/ PHOTOS! Plus herons doing cool stuff!

Two weeks ago I visited one of my "local" spots, Malibu Lagoon. I say "local" since there is zero true local birding where I live (see below). Anyway, on that particular visit, I spent quite a bit of time photographing Snowy Egrets. Beautiful, but sometime overlooked by birders seeking for rarer species, they are incredibly skilled fisherman. They generally hunt by stalking prey in shallow water, relying mainly on patience and lightning fast reflexes to catch prey that swims past them. All birders are familiar with a motionless Snowy Egret, a seemingly spring loaded-neck ready to extend the moment a fish approaches. It's basically industry standard for most waders.

I live at the red dot, smack in the middle of endless sprawl. 
Malibu is the small peninsula at upper left, 41 miles from home
The sprawl goes upwards of 50 miles in some directions.

On my last visit to the lagoon (Sept 20), I witnessed a foraging behavior that I had not before seen. On that day there seemed to be an ever-shifting throng of small fishes at water's surface. However, these fish consistently stayed well-clear of the shore and the half dozen hungry Snowies that lined it. Growing impatient, the birds took to the air to pursue the prey. Flying as slowly as possible, the egrets hovered above the water while they did their best to snatch fish from water's surface. The weren't truly hovering, more like awkwardly flapping as they tried to find a balance between directed forward flight and stalling completely. After a while I realized there was a periodicity to the behavior, and I set up shop to try to photograph it. Though not up to my normal technical standards, here is a series of shots of one bird that shows the behavior really well!

Target acquired

The plunge



Meal time

The shots above were taken once the sun was higher than ideal. I also managed a number of nice single shots from earlier the morning when the light was a bit better.

Snowy Egret fishing "on the wing"
Canon 500mm f/4 IS on EOS 7D2
1/6400 at f/7.1, ISO 400

Snowy Egret slowly cruising over water's surface in search of fish
Canon 500mm f/4 IS on EOS 7D2
1/6400 at f/7.1, ISO 400

Sprinting after prey in the shallows
Canon 500mm f/4 IS on EOS 7D2
1/6400 at f/7.1, ISO 400

Lastly, here is probably the most unique shot I got all morning. How this bird didn't end up in the drink I have no idea. Light was rough as it was late, but its still a keeper.

Here are two particular videos that showcase other clever foraging behaviors. Both are pretty amazing, so take the few minuets to check them out. You won't be disappointed!

Here a Green Heron used bread as bait to attract fish......

and a Black Egret creates shade to attract fish.

Hopefully you have a new appreciated for how clever waders can be. See if you can find a common bird doing something different next time you are in the field!