At first glance, it may seem clear that scientists do science, much like an engineer engineers things, a referee referees things, and a janitor—well, forget that last one. Unfortunately, there seems to be a rather severe disconnect between what scientists tell their family versus what they actually do. The goal of this feature is to try to break that barrier down.

A few times each month, I will post an explanatory version of what I’ve done in lab that day. Most of these will be biological procedures because I am a biologist, and most of them will be explained in layman’s terms, hopefully with hyperlinks to more explanatory information if desired. The goal is to give nonbiologists a window into what “I work on cancer” truly entails and how a person can spend their entire career on those four words.

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A beginner’s guide to neurotoxic jelly and high voltage

Well, I suppose it’s time to kick this feature off with a… well, hopefully not with a bang because “bang” isn’t a good sound to hear in a laboratory. Today I began what’s known as a Western blot. It’s a procedure designed to separate proteins by size, which presumably will allow you to identify them. Usually, some manipulation is done to the proteins beforehand, but we’ll save that for another post.

The technique basically exploits high school geometry.  First, the proteins move through the gel in one direction, let’s call it “vertical.”  This separates them by size.  Unfortunately, gels aren’t permanent, so we need a way to store this vertical sorting.  We do that by shifting the proteins horizontally onto paper (but it’s very fancy).  Their vertical position stays the same so we can still see their size, but they move from a fragile gel to a (relatively) rugged paper.

So, first I have to make a gelatin that will separate these proteins. The “gel” is only a few millimeters thick and is mostly made of neurotoxin, bubble bath, and water.  It remains liquid almost indefinitely until I add a catalyst, as which point it becomes almost the consistency of Jello Jigglers.  Delicious, especially since the neurotoxin’s neutralized in the process.

Then we put our protein samples on top of the gel and run an electrical current through the whole mess.  The nature of the gel means all our proteins get pulled toward a positive charge, but this gelatin is kind of like a maze of sewer tunnels.  Slim Eddie is going to have a lot easier time running through the maze than Jimmy the Behemoth (apologies to anyone who actually bears those names). 3-4 hours later, Eddie’s near the end while Jimmy is still mired in the middle, searching for tunnels he can fit through.  In other words, our intrepid aqueductal adventurers have been sorted based upon size, just like our proteins.  Then comes more electricity!

To “transfer” the proteins from the gel to the “fancy” paper, we lay the gel on top of this explosive paper (told you in was fancy!) and apply another electrical current in a different direction (horizontally).  Besides launching projectiles, it turns out that this paper is really good at sticking to proteins too.  So all of the protein stays where it was in the gel vertically, but after an hour, it moves horizontally from gel to paper.

Finally for the day, I “blocked” my paper (commonly called a “blot,” hence Western blot).  This is done by adding milk or something else filled with protein to the blot and it basically coats all of the unoccupied areas.  I like to think of it as sprinkling glitter on my 1st grade art project that was drowning in glue.  Remember kids, sticky things are bad in your backpack.  So, to carry the analogy further, my “blot” is a piece of construction paper that’s covered in glue.  My “proteins of interest” are macaroni, and the milk is a fine layer of glitter.  So really, today I got to be a very sophisticated 8-year-old for a grand total of about 6 hours.

Next time, I’ll explain how we tell the difference between the elbow macaroni and the wagon wheels because this is critical when you study cancer.

–Zach Bohannan

Last week I was honored to receive the award for Best Publication of the Year from the Associated Students of UC Berkeley.  First, I would like to give special acknowledgement to Meredith Carpenter and Jackie Chretien, the Editor-in-Chief and Artistic Director, for the Spring 2008 issue, and Kate Kolstad and Tim DeChant for Fall 2008, as well as all the editors, authors, and layout artists who made the magazine happen.  At the BSR we strive to make science accessible and engaging for all of our readers, whether they come from a scientific background or not, and winning this award confirms that we are on the right path to achieving this aim.  It’s easy to feel like an underdog when it comes to convincing people that science is interesting, constantly justifying why science deserves attention.  Hopefully the BSR is doing its small part to overcome this barrier and capturing the public’s attention and imagination with the incredible scientific research happening not only here on the UC Berkeley campus, but also across the entire scientific community.

Our new issue comes out this week.  I think it follows well in the footsteps of our award-winning issues, and I hope you all enjoy it!

- Rachel Bernstein

Astronomers have been in the news recently thanks to the exciting launch on Friday of the Kepler space telescope, which will search for Earth-like planets within our Galaxy. But you’re likely to see astronomy in the news throughout the year, since 2009 has been designated as the International Year of Astronomy by the United Nations.

Why 2009? Because it’s the four hundredth anniversary of Galileo’s first observations of the heavens with a telescope. (In that same year, 1609, Johannes Kepler also published his famous Astronomia nova.) With this key instrumental breakthrough, the field of modern astronomy was born. Four hundred years later, astronomy is one of the branches of science that’s most in the public eye, and we’re celebrating its discoveries and impact.

The International Year of Astronomy isn’t just for astronomers — an important goal of the IYA celebrations is to reach out to the general public and boost their interest in astronomy and science in general. There are a number of events happening throughout the year, many of which will be right here in the Bay Area:

• In conjunction with the Lawrence Hall of Science and Space Sciences Lab, the Berkeley Astronomy Department is presenting a series of monthly astronomy lectures for the general public. The next one will be given on March 21 by Dan Werthimer, the inventor of SETI@Home. More information about his talk and the schedule for the rest of the year can be found on the Berkeley IYA homepage.
• From April 2 to April 5, live images from observatories around the world will be broadcast nonstop as part of the 100 Hours of Astronomy event. The featured observatories will span the EM spectrum from radio to gamma rays and will include Cal-affiliated sites like the famous Keck Observatory. The climax of the event, however, will be a 24-hour global “star party” on April 4, when telescopes will be set up for public viewing all over the world (including Berkeley!).
• If you want to get even more hands-on, a team of astronomers and engineers has put together a low-cost, high-quality telescope kit called the Galileoscope. For $15, you can get an easy-to-assemble telescope with up to 50x magnification, which is enough to see Saturn’s rings, the phases of Venus, and the topography of the moon.
• Of course, these events are being blogged. The Cosmic Diary website hosts an international group of astronomers blogging about their work, their field, and the occasional fun stuff.

If you want to learn more about the International Year of Astronomy, visit the global website or the Berkeley IYA homepage, or email the Berkeley IYA organizer, Steve Croft.

Between Gary Larson’s Far Side images of nerdy-looking men and women in lab coats, and the well-manicured technicians of CSI:  Las Vegas, the public perception of scientists and their workplaces is more than a tad suspect.

With the goal of correcting some of these misconceptions, a group of researchers and teachers based at UC Berkeley recently released a website called Understanding Science.  This site is designed to explain both the methods of science and its role in our world.  Topics range from the common goals and approaches that scientists take in their research, to the relevance of science in society.  With an enthusiastic and kid-friendly approach (check out the revision to the usual way the scientific method is taught), they have created a site that is both informative and engaging to browse.

Understanding Science also provides tools for teachers, to help them develop lesson plans and bring their students to the site to learn on their own.  This is a great resource, allowing the teachers to integrate these lessons into their own classes without having to start from scratch.  It’s exciting to imagine a generation of children who have been trained not in just the rock-solid facts of biology, chemistry and physics, but in concentrating on the ways in which these facts were obtained.

Related link:
Drawings by 7th-graders before and after a visit to Fermilab show how their perceptions of scientists changed after the visit:  http://ed.fnal.gov/projects/scientists/index.html

Today in a press conference, three UCB astronomers announced the first image of an extrasolar planet. And it’s around Fomalhaut, a star we profiled in this week’s featured article by Danae Schulz, From Dust to Dawn: How Solar Systems Arise. (Well, the Berkeley astronomers tied for first. Another group today announced an image of three stars around HR 8799 in Pegasus.)

This is big news! We know of over 200 extrasolar planets (planets orbiting stars other than our Sun) already, but so far we’ve only detected them indirectly, either by the gravitational tug of the planet on its host star, or by the faint dimming of the host star as the planet crosses between us and it. These are the very first images of planets themselves. They might just look like dots, but they’re EXCITING dots.

The UC Berkeley astronomers who made the announcement are Paul Kalas, James Graham, and Eugene Chiang. They’ve been imaging Fomalhaut (pronounced FOO-mal-oh or FO-mal-hout, depending who you talk to) with the Hubble Space Telescope for a few years now, and the star is known to have a dusty debris disk around it. The inner edge of the ring is very abrupt, a phenomenon astronomers suspected could indicate the presence of a planet. Detecting a planet, however, required overcoming two challenges: how to see the planet in the glare of the central star, and how to tell a dot of light is actually a planet and not a background star.

Astronomers overcome the first obstacle by obscuring the central star with a coronagraph, a small disk that blocks out the star’s light and allows observers to take longer exposures that reveal the star’s surroundings.

The key to the second obstacle, differentiating between planets and background stars, is time. Stars have some velocity in space and move relative to one another. Their motion is slow enough that most stars appear to be fixed in the sky, but nearby stars like Fomalhaut (which is only 25 light years away) will move relative to the more distant background stars. Anything that is in orbit around Fomalhaut will move along with Fomalhaut—anything that isn’t, won’t.

The Berkeley team took an image of Fomalhaut’s dust ring in 2004 and again in 2006, both times with a coronagraph on the Hubble Space Telescope. As expected, most of the dots of light didn’t move in the same direction as Fomalhaut (indicating they’re background objects), but one little dot did. And it even progressed along a circular path centered on the star, just as astronomers would expect an orbiting planet to do. The UCB team thinks that the planet is orbiting at 25 astronomical units from Fomalhaut, and that it’s probably about three times the mass of Jupiter.

There will likely be plenty more direct observations of planets in the future, but this is the first, and it has astronomers pretty excited. Every time observers detect a planet by a new method, they take a great leap in learning about worlds other than our own. And to think, the extrasolar planets field didn’t even exist twenty years ago. It’s a brave new world out here.

Read more:
The UC Berkeley Press Release
The NASA Press Release
The New York Times (good graphic of the planet’s progress over time, and HR 8799)
From Dust to Dawn: How Solar Systems Arise

Last year, the New York Times reported that UPS managed to save 3 million gallons of gas in 2006 by altering the routes of delivery trucks to avoid left turns. According to the article, the company uses software called “package flow” to map out daily routes for drivers. Clearly, the algorithm or method this software employs to design efficient routes has sizeable economic (and greenhouse gas) consequences. And, not only is it far from perfect, but the general routing problem is so difficult that, well, if in the course of reading this article you happen upon an efficient solution, you will become immediately famous, at least among computer scientists.

The problem the UPS driver faces, generally speaking, is that of the “traveling salesman”, in which our hero seeks the shortest possible round trip route given a list of required stops. Arising in road trip planning, school bus pickups, parking meter coin collection, power cable layout, and microchip design, it is not a new problem. The famous 19^th century Irish mathematician Sir William Rowan Hamilton, who at age 12 once defeated the notorious American “calculating boy” Zerah Colburn in an arithmetic-off, invented the “Icosian game”, in which players attempt to find round-trip routes through a twelve-sided figure such that each vertex is visited exactly once and no edge is visited twice (Regarding the spin-off “Traveler’s Dodecahedron”, the puzzle museum website states, “the rules have been simplified and made much more attractive than the original”. The puzzle museum also notes that the Icosian game is more of a puzzle than a game.) Inspired by Hamilton’s early work and puzzle-making prowess, mathematicians in Vienna and Cambridge began studying the general form of the traveling salesman problem (TSP) in the 1930s.

In 1972, UC Berkeley Professor Richard Karp published perhaps the most famous paper written to date in computer science, called “Reducibility Among Combinatorial Problems”. The point, broadly speaking, is that most problems that appear difficult to solve exactly most likely are. Rather than proving that all kinds of problems have no easy solution, Karp gave a clever method for showing that many different sorts of problems are equivalent in a certain sense: if you provide a magic fast solver for hard problem A, Karp uses it to build a fast solver for hard problem B. As a result, researchers are amassing an impressive set of hard problems, all reducible to each other, so that if anyone ever found a magic solver for just one of them, well, things would get pretty crazy. A variant of the TSP, that of undirected Hamiltonian Circuits (same Hamilton), was in Karp’s original list of 21 problems.

To understand what this means for the salesman, consider: A TSP with 5 cities has 12 possible routes; with 10 cities there are 181,440 possibilities; with 61 cities there are more possible paths than there are atoms in the universe. Seriously. In computer science terms, the solution space is exponential – adding one city roughly doubles the number of possible paths. Karp’s result suggests that in general, determining the optimal path for the salesman is a matter of checking all those possibilities – though shortcuts may exist, none are likely to lift the exponential burden. And though computers are growing more powerful, even IBM’s supercomputer, Blue Gene, which can perform a ridiculous 500 thousand billion computations per second, would have little hope of solving a 30-city TSP by the brute-force approach.

Instead, computer scientists spend much time devising heuristics – approximate methods for dealing with intractable situations. Here’s a simple heuristic for the traveling salesman: when trying to decide which stop to visit next on the tour, pick the closest remaining one. While in many cases, this rule yields a route much less efficient than the optimal one, it works reasonably well on average. Many papers have been written about more complex heuristics for the TSP. For example, in 1997 Marco Dirigo used a simulated ant colony to explore the space of solutions, iteratively refining paths left by virtual ants (virtual pheromones were also involved).

The TSP variant that UPS would like to solve is no Icosian puzzle game. There are 95,000 trucks delivering packages every day, and each one needs a route assignment. These routes are not independent: removing a stop from one means adding it to another. The resulting problem is staggeringly difficult to solve exactly, and good heuristics are necessary. The no-left-turn innovation is a heuristic that helps realize the difference between driving time and driving distance. Or, as Jim Winestock, a UPS vice president in Atlanta, explains, “I know it drives my wife crazy, but I’ve been known to pass up drug stores, three or four on the left-hand side of the road, just to get to the one on the right.”

–Dan Gillick

Brace yourselves, everybody. The BSR just got a blog.