Anna Coogan Sings the Blues

For those of you out there with the Sunday blues. Anna Coogan is a friend and fellow fish biologist at the UW, and she has a talent for writing some of those songs that can just wreck you.

Anna is moving soon from Seattle to Ithaca, New York. Google Analytics tells me I have at least a few loyal readers upstate. So let me make a recommendation to you folks—keep your eyes peeled for upcoming performances, and when you see them, run, don’t walk, to the door. For those in Seattle, she’ll be at the Northwest Folklife Festival May 28.

I’ll be traveling the next couple of weeks, first to Iceland (!) for a meeting of the ICES fisheries acoustics working group, and then home to the East Coast for my little bro’s college graduation, so posting may be sparse. I’ll sign off with a question: if I’m offered hákarl in Iceland…do I eat it?

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“Now I am become death, destroyer of worlds.”

Yesterday, The Atlantic ran a series of photos of atmospheric nuclear tests, including one taken 25 milliseconds after the detonation of the first atomic bomb on the morning of July 16, 1945 near Alamogordo, New Mexico.

The Trinity Test, the first explosion of an atomic bomb. Click through to the photo essay at The Atlantic.

J. Robert Oppenheimer, the American physicist who directed the Manhattan Project, said that he remembered a line that morning from the 11th chapter of the Bhagavad Gita, when Krishna reveals his true universal form, brilliant and terrible: Now I am become death, destroyer of worlds.

As it happens, I’m working my way through “American Prometheus” by Kai Bird and Martin J. Sherwin, their voluminous biography of Oppenheimer. It’s an absolutely fascinating read, both for the chance to see physics going through a scientific revolution and getting caught at the crossroads of history, and to get to know Oppenheimer himself.

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A Very Short Introduction to Time Series

Last week, I gave a presentation on the basics of time series statistics to an informal group of students in biology, forestry, and fisheries who meet every week to share tips and talk over problems involving statistics and R. A time series is just a sequence of observations recorded at regular intervals, one after another. The basic motivation behind time series statistical techniques is the fact that the observations making up a time series usually violate the assumption of independence that underlies most of traditional statistics. Instead of being uncorrelated, they are related to each other, or autocorrelated: what has happened before affects what will happen in the future. Time series models are intended to incorporate this autocorrelation, making it possible to understand the process underlying a time series, and to forecast its future values.

I got a good response to the talk, so I’ve decided to post my slides here, along with an R script including a series of short examples that dovetail with the presentation. I have used a number of these techniques in my own research, and mostly had to teach myself; this presentation is essentially an overview of everything I wish I’d known before I started reading seriously about time series. I’ll emphasize that this is a very cursory overview of an immense field of statistical research and techniques. There’s only so much ground you can cover in a one-hour seminar. The last slide has a list of the books I’ve been working out of for further reading.

Slides [PDF]

R script with examples

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What Does A Migration Look Like?

Every afternoon at about three, my officemate puts on her coat, picks up her binoculars, and walks down to Sakuma Viewpoint, a little patch of park across the street from our building on Portage Bay, to do a five-minute survey of all the birds in sight. She is what you might call a bird nerd—her research is on seabirds, and when she needs a break from her research, she goes outside and counts them for fun. Every so often, I join her, to get a breath of fresh air and remind myself how little I actually know about birds.

These short surveys are part of a larger project, run by the Audubon Society and the Cornell Lab of Ornithology, called eBird. Birdwatchers from all over the country do their own short surveys and send in their sightings electronically. What good are a motley assortment of observations, neither fully random nor systematic in design, made by a bunch of amateurs? Turns out, when done on a continental scale and stitched together with some geostatistical wizardry, a whole lot. Sightings made by eBird’s network of citizen scientists, coupled with geographical and climatological knowledge, allow the scientists at Cornell to produce truly spectacular maps of bird migrations across the United States.

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DIY Scale Dependence

What’s the big deal about “scale?” It’s a word that I’ve written about before here, and one that certain types of ecologists can’t seem to stop talking about. But it can be an infuratingly vague word to pin down, given that it can have more than one meaning, even in technical usage. And the fact that scale-dependent thinking is applicable to such a staggeringly wide range of phenomena, while a testament to its relevance, hardly helps in nailing down what it means. As a grad-student friend of mine, no slouch when it comes to quantitative reasoning, asked me recently, “What’s the deal with ‘scale?’ It all just seems kinda theoretical to me.”

Let’s take a concrete example. Say you’re interested in how seabirds forage for small fish, and so you put small GPS recorders on some birds which record their position every second. Examining the tracks, one of them looks like this:
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Beaked Whales and Naval Sonar: What’s Going On?

ResearchBlogging.org
There have been huge fights in the past decade over Naval sub-hunting sonar and its effects on certain species of whales. In several cases, mass strandings of marine mammals have occurred shortly after naval exercises where mid-frequency active (MFA) sonar was used. There is particularly strong evidence that several strandings of beaked whales—a family of small whales that look a bit like oversized dolphins—were associated with naval exercises involving mid-frequency sonar.

Baird's beaked whales in the Bahamas.

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Shades of Grey

I’m halfway through my second winter here in the Pacific Northwest, and, strange as it sounds, I’m starting to love the weather. It’s true that it’s all grey and damp. But there are so many different shades and textures of grey in the sky and water, and some of them are truly beautiful. I was trying to explain this to my cousin Allie, who was visiting last weekend from Boston. I’m not sure she bought it.

On Friday, after sandwiches at Paseo in Ballard, we went to Discovery Park, overlooking Puget Sound at the west end of the city. The day was shifting from clouds to rain, and in the two hours we spent there, the sky went through several transformations that seemed subtle only if you weren’t paying attention to them.

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Happy St. Patrick’s Day, Biologically Speaking

Another fantastic video from my friend cadamole. Old Irish folk song. I’ve been humming it all day. If you haven’t seen this yet, you owe it to yourself…

I wish I could be enjoying the products of some Sacharomyces cerevisiae right now. Instead, I’m writing a class paper. Oh well.

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House Committee Votes Climate Change Out of Existence

I kid, of course.  Mostly.  The Energy and Commerce Committee today knocked down three symbolic amendments to legislation that would prevent the EPA from regulating CO2 under the Clean Air Act. These amendments, each put forward by a Democrat, would have acknowledged that a) the Earth is warming, b) it’s because of our emissions, and c) that climate change threatens public health. That last was put forward by Jay Inslee, from Washington’s first district, just a few miles north of where I sit in Seattle.

But in three party-line votes, the Republican members of the committee unanimously opposed them. To be clear, these amendments had no teeth whatsoever. No regulatory anything. Still, the comittee’s Republicans felt obliged to vote them down.

Of late, allusions to Soviet Russia have become quite popular in certain quarters.  While I suppose that progressive taxation and organized labor might look like Stalinism if  you squint really hard, it’s also worth noting that Stalin was incredibly multifaceted when it came to repression.  Not to go all Glenn Beck on you here—but are there other kinds of commie sleeper agents, besides the liberal ones we already know about? I submit that these comparisons can cut both ways.

For instance, did you know that during Stalin’s tenure, the law of large numbers and the idea of random deviations were declared “false theories?” If you haven’t heard of them, they are two of the bedrock mathematical principles that underlie all of statistics.  Or that Stalin embraced a biological fraud who denied the genetic theory of inheritance, and imprisoned or killed geneticists who disagreed?  There are many more examples of the Party “changing” science where it conflicted with the official ideology.

One guess which side won that conflict in the long run.

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Carnival of the Blue XLVI

Welcome to the 45th Carnival of the Blue! In the nick of time, the submissions arrived, and I didn’t have to follow through on my threat to replace this month’s Carnival of the Blue with Carnival of the Bieber.  So here, without further ado, is the best online ocean writing of the past month.

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