Monday, May 28, 2012

Vacation: San Juan Islands

I used a few more vacation days to explore the San Juan islands with Simiao since she's still in town.  We rented a room in Anacortes with AirBNB and used it as our home base while hiking and kayaking around the various state parks.  Sadly, my camera did not have a good time, as it was totally submerged in salt water for about a second while we were sea kayaking.  This camera has been through countless adventures, exploring urban ruins in Pittsburgh, scaling walls, braving the stinging desert sands of Arizona, taking pictures in the pouring rain without a cover, and even belly-crawling through mostly-flooded passages in a cave in Costa Rica.  I'm going to try to thoroughly clean it with an isopropyl electronics cleaner, but I fear that it is now doomed to lose the battle versus corrosion.  If I can't fix it, I will rest easily knowing that the Digital Rebel XT died as it lived:  bravely documenting the extreme places in our world.  I've learned quite a bit about photography from it, and am looking forward to buying a new camera with some features I've come to envy in my friends' cameras:  vibration reduction, a larger preview screen, automatic HDR bracketing, active autofocus, and I've been dying to get a 18-200 or maybe even a 17-270 lens.

I've always wanted to try tilt-shift photography, too, and I'm a long exposure fanatic and still haven't gotten around to building my dream remote nor a pinhole camera.  Someday, I will make these dreams a reality.  For now, you can enjoy some of my favorite shots from this trip!

Pacific sideband snail

Double rainbow at sunset from Perego's Lake

Disappearing gun at Fort Casey

Broadleaf stonecrop on Rosario Head.
This lovely picture is my new desktop background!

Hooded nudibranch,  a very graceful swimmer!

Tuesday, May 22, 2012

White House Open Science Petition

If you watched Lessig's talk that I wrote about in April, you learned that closed access journals are hampering scientific innovation by making it difficult for citizens and even scientists at institutions with limited funds to access papers that by all rights everyone should have access to.

The vast majority of scientific research at academic institutions and elsewhere is in some sense taxpayer-funded, whether directly through grants, through access to state-subsidized labs, or even as part of the curriculum of students who are using federally-subsidized student loans.  Shouldn't the taxpayer have access to what they paid for?  The publishing industry thinks not, and recently lobbied for the Research Works Act which would have prohibited the NIH among other agencies from mandating that the work they fund be open-access.

Until June 19, there is an open petition at that you may digitally sign to ask the Obama administration to ensure that, to the contrary, all taxpayer-funded work be free for everyone to access on the internet.  At the time of writing, the petition already has over 10,000 signatures.  Signing it is a small thing that you can do to promote open science.

Tuesday, May 15, 2012

Vacation: Breitenbush Hot Springs

A harmless fly that mimics a bee.
I took a few days off to spend a relaxing vacation hiking the trails and enjoying the natural hot springs in Breitenbush, Oregon with Simiao.  If you loved summer camp as a kid, you will love Breitenbush Hot Springs!  We hiked up the "Cliff trail" and were rewarded with an amazing view of the valley, enjoyed delicious vegetarian cuisine (this is coming from an unapologetic carnivore), and of course spent plenty of time soaking in the hot springs.  I appreciated the chance to see some of the native Northwest wildlife, something I'd been wanting to do since I first moved to Seattle.  We found a cute little whipsnake that I wish I'd been fast enough to get a picture of, but he slipped away into the undergrowth before I could get his portrait.  Anyhow the pictures I did get turned out well, and I think you'll like them too!

A long exposure of Simiao on a creek fed by melting snow on the mountains.
Calypso bulbosa, an orchid native to the Pacific Northwest.
A long exposure of the night sky over the Breitenbush river.

A darkling beetle and an olive.

Thursday, May 10, 2012

How Often are Aurora Borealis Visible in Seattle?

A friend and I were sitting on my balcony the other night, enjoying a wonderful 10-year old Lowland malt and talking about whatever came to mind, when we started talking about aurora borealis.

This is the highest latitude I've ever lived at, and I wondered:  how frequently could I expect to see the aurora borealis in Seattle?  I've only seen it once before, while driving a high school girlfriend home in the dark countryside near Boiling Springs, PA, and I'm overdue for seeing this wonder of the night sky again.

First, I learned an interesting (and disappointing) fact while perusing the NOAA website:  Seattle is actually at nearly the same magnetic latitude as Pittsburgh, so I'm only slightly more likely to see aurorae in Seattle as I was in Pittsburgh!  A map of magnetic latitude can be found on the NOAA website, reproduced here since the US government is not allowed to hold copyright.

Magnetic latitude lines corresponding to areas likely to see aurorae at certain geomagnetic storm strengths.
Image reproduced from NOAA.

So, both Seattle and Pittsburgh may see aurorae during a geomagnetic storm with a K-index of 7.  How often does this happen?  I downloaded 11 years of K-index data (one solar cycle) from the NOAA website, and produced a histogram of frequencies of K-indices.  The K-indices are averaged over three hour periods, for eight readings per day.  My data spanned from May 13, 2001 to May 10, 2012.  A simple bit of R code, then, produced the distribution of K-indices over these 11 years:

data <- read.table("~/Desktop/spidr_1336629415966_0.txt")

graph <- hist(as.numeric(data[data[,3] > -1,3]), 
              main="Histogram of K-indices")

Frequency of three-hour periods with various K-indices from May 13, 2001 to May 10, 2012

The histogram above shows that the K index is 0 through 3 during about 90% of 3-hour periods, and periods of strong solar activity where aurorae might be seen in the continential US become increasingly rare.  To answer my question, only 1 in 245 3-hour periods had a K-index of 7 or higher, corresponding to approximately one per month.  Since this has to occur in a six-hour window around midnight for me to be able to see the aurorae, then assuming each event is independent of the last then if it were clear out then the northern lights could appear at night in Seattle about once every four months.  The assumption of independence is obviously wrong, since if the last three hours were calm I certainly expect it to remain that way, but I really just wanted an estimate.  A more sophisticated choice would be to model K-indices over time as a Markov process, or even to model solar flares themselves as self-organized critical behavior.   
If you happen to live near the red line, with Kp = 9, then frequency of events that strong at night is about once every 3 years.   Hope it's not overcast!  For those of you even further South: ice cores indicate that an event as strong as the Carrington Event, when aurorae were reportedly visible at the Carribean, occurs about once every 500 years!  

Incidentally, I found a page on the NOAA's website where you can see predictions for upcoming days, so if the NOAA is predicting a strong geomagnetic storm I can plan ahead to be away from city lights and improve my chances of seeing the northern lights again.  

Wednesday, May 9, 2012

A Day Off: Gas Works Park

Today I took a personal day so that Simiao and I could explore the city together.  We visited the Fremont Troll, the Theo chocolate factory, and had amazing Cuban sandwiches at Paseo.  Gas Works park had an urban-exploration feel to it, with a number of industrial relics there for you to touch and explore.

Fun fact:  The name of the "Theo" chocolate company is actually short for "Theobroma", from the genus of the cocoa tree.  When the tour guide asked if anyone knew where the name of the chocolate company came from, I jokingly guessed "theobromine," assuming that nobody was actually so nerdy as to name their company after the principal alkaloid present in chocolate.  It turns out that they actually were, in the sense that the genus and alkaloid obviously share the same origin!

Simiao sees him trollin', but she's not hatin'.

Friday, May 4, 2012

USMLEworld Client on Ubuntu 12.04

[UPDATE 14 Sep 2013:  In order to use this method, you must download the version of USMLEworld for OS X 10.6 or earlier, which is still a .jnlp file.]  

I was setting up a laptop for a friend to use while she visits me and studies for her Step 2 exams, and decided to set her up with Ubuntu 12.04 and KDE Plasma, which are both excellent, free and open source products.  Though I still don't like Unity and prefer Gnome or KDE, I was so impressed with Ubuntu 12.04 overall that I converted over all of my systems without incident.

Other than a word processor and web browser, the only thing she needed was to run the USMLEworld software.  While the USMLEworld website proclaims that it is Windows, Mac, iPhone/iPad and Android only, I assured her that it would work.  It's a Java app, and perhaps the biggest selling point of Java is that it runs basically anywhere.  I downloaded the app using the instructions for Macintosh, and ran the command

javaws qbankclient.jnlp

It happily loaded up a number of files, then popped up a window that said, "Windows and Mac Only" and quit.  Really?  A simple multiple choice question program won't run under Linux?  I found that hard to believe. I wondered what would happen if I spoofed the operating system.

javaws -property qbankclient.jnlp

Note that if you're using Ubuntu with Gnome instead of KDE, you may also have to remove gnome-screensaver as apparently they are able to detect it and disallow you from taking any tests.

sudo apt-get remove gnome-screensaver

At any rate, it works just fine!  USMLEworld, shame on you for crippling your software just to exclude open operating systems, and double shame for being so bad at it.  By the way, should you require the services of an internationally recognized programmer with three bachelor's degrees and a PhD in Physics, as well as over 10 years of industry experience, a link to my CV is to the right, and I am available for contract work!

Technical details:  I am using openjdk-6-jre and icedtea-plugin.