Archive for the ‘Uncategorized’ Category

Notes on Web Tunneling While Traveling

October 13, 2012

I’m currently traveling in Germany, and I need to use the internet.  I’m able to find internet hotspots almost everywhere, but I’m not interested in paying 3-5 euro to access each hotspot.  The curious thing is that many of these hotspots are setup such that port 80 is closed (i.e. HTTP traffic) for non-paying customers, but all other ports are open.  This means that without paying, I’m able to get an IP address with DHCP, SSH into my remote server (on port 22), and send email (on ports 25 and 587, depending on the mail server).  So, that’s useful, but what about viewing web pages on port 80?  The solution to this problem is to use SSH tunneling.  It’s rather simple.  I found these instructions to be useful:

Basically, I setup SSH tunneling and then modified my Safari SOCKS proxy to use the tunnel.  The instructions in the URL (above) are accurate, except for one point that needs clarification: the “ssh” command to setup the tunnel requires sudo, like this:

sudo ssh -ND 8888 username@host

After launching ssh, I modified my SOCKS proxy:

Preferences > Network > Proxies > click box next to SOCKS proxy, then list “localhost” and “8888” for the SOCKS proxy server.

. . . and now I’m online!


Tea Time in the Palisades

June 25, 2012

The sun was blazing, the snow was melted, and the trail was mostly missing on our six-day circumnavigation around the Palisades Range in the California Sierra Nevada.  Before leaving the city, we took a detour into Chinatown and bought special tea for our trip.  We made a video about the heady brew of mountaineering and tea:

Our route started at Big Pine (BP) Creek, west of Big Pine, California.  From the BP trailhead, we followed the south fork creek and camped at Elinore Lake.  On the second day, we crossed Scimitar Pass (which is not marked on all maps), took a tea break in Palisade Basin, and then crossed Cirque Pass and camped on a shelf below Palisade Lakes.  On the third day, we followed the Pacific Crest Trail (PCT) to Grouse Meadows in LeConte Canyon, where we enjoyed more tea took a zero day on the day 4.  On the fifth day, we climbed from Grouse Meadows into Dusy Basin and over Bishop Pass.  In the burning afternoon, we climbed Jigsaw Pass and camped near the outlet creek to the fifth Big Pine Lake on the north fork.  On the sixth day, we cruised downhill and visited the fourth, third, second, and first Big Pine Lakes, and then finally returned to the BP trailhead.

Scimitar Pass and Jigsaw Pass are both class 2-3 passes, and it was difficult to find comprehensive information about their conditions.  Some general information about cross-country Sierra passes has been collected here:

For Scimitar Pass, I wrote a detailed description on High Sierra Topix bulletin board: link here.

Most of my research about Scimitar came from Bob Burd’s website.  His reports and images were accurate:

Bob traced a blue line on the map linked below.  This blue line generally follows a use trail across and around Willow Lake.  Once crossing to the north side of the creek (past Willow Lake), the use trail disappears.  At this point, boulder-hop along the creek; you may see cairns.

On the approach to Scimitar Pass, Bob’s route goes up the right-hand slot (shown below).  However, I climbed the scree to the center-left.  I avoided the slot because I couldn’t determine it’s difficulty.

For Jigsaw Pass, I found good pictures at this Webshots collection:

. . .and I also found good data at Bob Burd’s website:

In general, when I climbed Jigsaw west-to-east, I chose the right side chute (indicated in this photo).  The scree looks crazy from below, but I stuck to the cliff wall and found plenty of hand holds to pull myself up the scree slide.  When I reached the thick white mineral band descending from Aperature Peak, the scree ended and the route continued on solid class 2+ rock (like a steep staircase).  About halfway up the chute, there are remnants of a rock switchback (once upon a time, there was a trail over Jigsaw Pass).  Basically, the top half of Jigsaw’s west side climb is straightforward and safe, although it looks crazy from below.  After reaching the pass, the descent down the east side is not difficult, per se, but it does involve seemingly endless boulder-hopping.  The best route is to follow the creek — sometimes boulder-hopping above the creek — all the way to the fifth Big Pine Lake.  There are cairns along the way, but they’re not really necessary.

New paper in Nature 2012.

January 11, 2012

I recently finished a lovely collaboration with Greg Finnigan, Tom Stevens, and Joe Thornton.  Our work shows how a molecular machine — in this case, a proton pump — increased in structural complexity over evolutionary time.  On a personal note, our project demonstrates the type of interdisciplinary work that can emerge when computational skills are combined with “wet” bench work.

Also, W. Ford Doolittle wrote a companion essay about our paper.


“Evolution of increased complexity in a molecular machine” — Finnigan, Hanson-Smith, et al. Nature 2012.

“Evolutionary biology: a ratchet for protein complexity” — Doolittle. Nature 2012.

A Mix for Tarantula – October 27, 2011

October 27, 2011

lehua for 34 points

October 26, 2011

In 1778, British explorer James Cook landed on Hawaii, which later attracted international trade — and international diseases — to the Hawaiian islands, which ultimately led Queen Liliʻuokalani of the Hawaiian Kingdom to be overthrown in the year 1883, which ultimately allowed U.S. President Dwight D. Eisenhower to admit Hawaii as the 50th U.S. state in March 1959. Because of these things, I was able to play the word “lehua” as valid word in a Scrabble-like game for 34 points.


Notes on Benson Lake, and 2011 snow conditions in Oregon

July 16, 2011

North and Middle Sister, moonrise

I just returned from a quick overnight hike to Benson Lake in the Mount Washington wilderness (see hike #46).  As of July 15 2011, the snowline is at about ~5000 feet, but the melt is very uneven.  Many south-facing slopes are snowfree, especially above tree line.  The bald southern face of Scott Mountain (6100′) is entirely melted.  Black Crater (7251′) and Belknap Crater (6872′) appear to have snowfree hiking routes above treeline, but I suspect their approach hikes are snowbound.  North facing slopes and deeply shaded forest areas have four-foot drifts all the way down to Highway 242 (at about 5000′).

The Benson Lake trailhead (-5000′) remains unreachable by car.  Instead, I parked about 1/2 mile down Scott Road.  I found the trail to Benson Lake (5200′) about 80% snowbound, but I was able to follow good boot prints from early-season day-hikers.  Benson lake basin was mostly snow-free; I found a dry campspot with a view and built a fire.  Silent lightning flashed for hours in the southern sky , and later, rain clouds consumed me, Benson Lake, and the entire wilderness.

fire (2 of 3)

Check-out more photos on Flickr.

Notes on trekking from Squaw Dome to Iva Bell Hot Springs, June 2011

June 26, 2011

Balloon Dome

Summary: Here is a novel route to access Iva Bell Hot Springs in the John Muir Wilderness of the Sierra National Forest.  Most people reach Iva Bell from the north (via Red’s Meadow), or from the east (via the PCT).  However, in heavy snow years—such as this year, 2011—the north and east trailheads may be unaccessible early in the season. The route I describe here provides early-season access to the hot springs from the west, starting at the McCreary trailhead in the Ansel Adams Wilderness.  CAUTION: This route uses trails that are poorly maintained.  Navigation skills are required, especially to traverse the section from Heitz Meadow, around Pincushion Peak, and down the Silver Creek drainage.

Trip Statistics: Approximately 25 miles one way.  About 6000′ total gain one way.  McCreary trailhead is located at 6774′. Cassidy Bridge is the lowest point at 4400′.  The saddle north of Pincushion Peak is the highest point at 8622′.  Iva Bell hot springs are located at about 6450′.

Conditions in June 2011: Small snow patches lingered on the Minarets Road, but we were able to drive a sedan within one mile of McCreary trailhead.  We parked our car alongside the road, left a note in the window (and crossed our fingers).  The trail from McCreary to Cassidy Bridge was completely snow-free and easy to follow.  Further down, we encountered a dozen poison oak patches at the bottom of the San Joaquin river canyon.  The poison oak was difficult to avoid; pants and a long-sleeve shirt are highly recommended for this short section.  Past the poison oak, there are several excellent campsites on the canyon floor near Cassidy Bridge.

The switchbacks east of Cassidy Bridge were in great condition, and we easily found Rattlesnake Lake — which is mostly a marsh these days.  The ascent to Rattlesnake Lake offered several good places to pause and enjoy views of Balloon Dome.  Although Rattlesnake Lake lacks the majesty of high-elevation Sierra tarns, it nonetheless felt extremely wild and lost; it seemed like no human had visited this area in a very long time.  Beyond Rattlesnake Lake, we sometimes struggled to follow the trail to Heitz Meadow.  The cross-country walking was easy, fortunately, so we followed what clues we could find: sawed logs and occasional water bars.  We found Heitz Meadow with its collapsed cabin, destroyed outhouse, and broken horse corral.  It was apparent that no human has lived here in decades.

East of Heitz Meadow, the trail disappeared under fallen trees and forest litter.  Views were minimal, so we took a compass bearing and tried our best to stay on course.  The cross-country walking wasn’t bad, but there were endless downed trees to negotiate. We found hints of the trail several times, so that was reassuring.  We eventually lost sunlight, so we camped near a creek at snowline (~7500 feet).

The next day, we hiked on solid snow over the saddle north of Pincushion Peak, past String Meadows, and into the Silver Creek drainage.  We used the compass to hike directly to the saddle, but — if you get lost — you could just as well follow the counters around Pincushion Peak and find the saddle.  A map is 100% required for this section. We dropped to Silver Creek, and then checked our GPS; surprisingly, we were only 100 feet away from the trail.  This early in the season, Silver Creek was an unfordable white stallion, but we found a wide log spanning the creek nearby.  This log seems to be a permanent fixture, and it should be easy to find for anyone hiking through this area.  (Hint: the log sits in alder bushes on both shores).  From Silver Creek, the switchbacks down to Fox Meadow were easy to follow, but they were overgrown with manzanita and huckleberry oak; this is another section where long pants are recommended to protect your legs from sharp branches.  At Fox Meadow, we rejoined the well-maintained trail that connects Reds Meadow to Iva Bell, and we cruised to the hot springs in luxury.

Iva Bell hot springs are scattered across a grassy hillside; we found at least seven pools, but there may be others.  I strongly suspect we were the first people to soak in the springs this season.  The meadow pools were covered in algae, but we easily scooped away the mess and enjoyed soaking in clean hot water.  The pool in the open meadow by the boulder is probably the hottest and cleanest, but the pool under the trees by the campsite has seats and shirt hooks and other nice features.  The highest pools are perched on a shelf (about 200′) above the meadow, but unfortunately they were filled with hundreds of tiny leeches; I think these pools are unsoakable until the leech problem is solved.

We camped near the meadow pools for two nights; it was heavenly.  A duo of hikers briefly passed through — apparently they entered over Mammoth Pass — but they seemed rushed and quickly departed.  The shuttle to Red’s Meadow was not yet running during our trip, so I’m not surprised that Iva Bell was basically empty.  Over the next three days, we returned to McCreary trailhead using our original route.

A note about navigation: We carried topographic maps, a compass, and an iPhone with GPS.  We relied on the map and compass to navigate the cross-country northeast of Heitz Meadow, but we also used the iPhone a few times to validate our decisions.  The iPhone GPS, surprisingly, worked very well in the wilderness.

Map: view the route in Google Maps:

Video Postcards from the trip: 

William Sullivan slideshow

April 16, 2011

Jefferson Park, September 2009

Today I saw a captivating slideshow by William Sullivan, based on his book “Oregon Favorites”.  (Sullivan is best known for his “100 Hikes” series of trail guides, which are really excellent.)  Sullivan has a busy year-round lecture schedule.  Today’s slideshow featured one favorite place in Oregon for each month of the year, with an emphasis on places that are rarely visited.  Here is the list. . .

MarchThe Mulino Flour Mill is not a wilderness hike, but the water-powered flour mill still functions and is interesting the visit.

April – The Badlands loop, in the Oregon Badlands Wilderness near Bend, OR

May –  Cape Horn in the Columbia River Gorge

June – The Scout Camp Trail, near Crooked River Ranch, OR

July – Visit the Wallowa Mountains, near Joseph, OR.  Avoid the crowded trails, and visit McCully Basin.

August – Pinnacle Ridge on the NE side of Mount Hood.

September – Jefferson Park

October – Sisters Rocks, on the Oregon coast between Port Orford and Gold Beach

November – Eight Dollar Mountain along the Illinois River.

December – rent a fire lookout tower.  Sullivan recommends Warner Mountain.

January – visit Fort Hoskins Historic Park

February – ski around Broken Top, using the pass/notch near Iceberg Lake

Random Gaussian distribution in libGSL

March 17, 2011

I think the gsl_ran_gaussian function is broken in the GNU Scientific Library.

This function is supposed to return a random value from the Gaussian distribution with a mean = 0.0 and a user-specified standard deviation.  However, consider the C code (below), in which the user-specified standard deviation value seems to have no effect on the random value.


#include "gsl/gsl_rng.h"
int main( int argc, const char* argv[] )
printf( "\nHello World\n\n" );
gsl_rng *rng;
int random_seed = (int)time(NULL);
rng = gsl_rng_alloc(gsl_rng_mt19937);
gsl_rng_set(rng, random_seed);

double rand_gauss;

int reps = 5;
int i = 0;
for (i = 0; i < reps; i++)
rand_gauss = gsl_ran_gaussian(rng, 0.001);
printf("sigma = 0.001, random value = %f\n", rand_gauss);
rand_gauss = gsl_ran_gaussian(rng, 0.01);
printf("sigma = 0.01, random value = %f\n", rand_gauss);
rand_gauss = gsl_ran_gaussian(rng, 0.1);
printf("sigma = 0.1, random value = %f\n", rand_gauss);
rand_gauss = gsl_ran_gaussian(rng, 1.0);
printf("sigma = 1.0, random value = %f\n", rand_gauss);


Hello World

sigma = 0.001, random value = 6304.000000
sigma = 0.01, random value = 3104.000000
sigma = 0.1, random value = 1952.000000
sigma = 1.0, random value = 1536.000000
sigma = 0.001, random value = 3712.000000
sigma = 0.01, random value = 1312.000000
sigma = 0.1, random value = 3424.000000
sigma = 1.0, random value = 6752.000000
sigma = 0.001, random value = 6016.000000
sigma = 0.01, random value = 8000.000000
sigma = 0.1, random value = 6752.000000
sigma = 1.0, random value = 7200.000000
sigma = 0.001, random value = 5408.000000
sigma = 0.01, random value = 7136.000000
sigma = 0.1, random value = 1056.000000
sigma = 1.0, random value = 4160.000000
sigma = 0.001, random value = 7744.000000
sigma = 0.01, random value = 5376.000000
sigma = 0.1, random value = 3072.000000
sigma = 1.0, random value = 4896.000000


New Music, “Snow Day”

November 23, 2010

Enjoy this new electronic music composition.   I recommend listening with good bass headphones.
snow texture
“Snow Day” (3:39, MP3, 8.4 MB)