Archive for the ‘Science’ Category

Stanford goes to Court….

Monday, November 1st, 2010

Future site of the IP smackdown

…and not just any court.  The Supreme Court.

Just this morning, the U.S. Supreme Court agreed to review an intellectual property case between Stanford University and Roche, a company that focuses on diagnostics and drugs for infectious diseases.

The case, entitled “Board of Trustees of the Leland Stanford Junior University v. Roche Molecular Systems, Inc.,” will profoundly influence the way America assesses patent rights with regard to university and government funding.

Holodniy's work on PCR for HIV testing are the root of the controversy

The controversy stems from developments in HIV testing using polymerase chain reaction (PCR) technology conducted by Stanford fellow Mark Holodniy in the late 1980s.  Holodniy’s team relied substantially upon generous research grants provided by Stanford University and the National Institutes of Health, a federal agency.  When Holodniy joined Stanford as a Research Fellow in the Department of Infectious Disease in 1988, he signed a “Copyright and Patent Agreement” (“CPA”) that obligated him to assign his inventions to the university.  The next year, Holodniy began collaborations with local biotech company Cetus Corp.


The Search Virus: What Your Online Activity May Say About Your Viral Load

Tuesday, October 26th, 2010

Solve this riddle: Student A sits in Humbio 151: Introduction to Epidemiology (i.e. the study of disease outbreaks), listening to a representative from the Center for Disease Control (CDC) discuss how his organization conducts epidemic surveillance.  Student A’s eyes are drooping slightly due to sleep deprivation, a consequence of her participation in the hallowed “Full Moon on the Quad” celebrations the night before.  Between bleary-eyed blinks, Student A decides to Google “flu shots” and “become effective.”

The question: does this student have the flu?

Okay, let’s be real.  If I didn’t already lose you back at Intro to Epidemiology, you are probably thinking “WTF? That makes no sense” right about now.  You probably think you don’t have enough information to answer that question.  And that’s where Google comes in.

That’s right, it’s the G-word.  The giant Mecca of search engine has the answers again.

Let’s break it down.  Here’s what we sans Google know: Last night at Full Moon, Student A was likely exposed to massive quantities of bacteria, viruses, and a variety of scarring mental images.  Her Google search terms suggest that she only recently received a flu shot (I’ll give you a hint: it was yesterday) and she wants to find out if she is successfully vaccinated yet.  For those of you who might care to know, the flu vaccine takes approximately 2 weeks to kick in (it isn’t lookin’ good for Student A).

But here’s the missing link that the average blog reader doesn’t know but Google does: what is everybody ELSE searching online?

Allow me to introduce you to Google Flu Trends (also known as the hypochondriac’s newest enabler).  The brainchild of Google Insights (which tracks how the volume of specific search terms is distributed geographically, seasonally, etc), Google Flu Trends tracks certain flu-related search terms to estimate when and where flu outbreaks are likely to occur.  So, to solve our riddle, all you need to do is pull up Flu Trends in your browser, zoom in on California, then on San Jose (sorry Palo Alto, you don’t qualify with your puny population) and look at the predicted flu levels based on search terms.

BAM.  The reult?  LOW.  Seeing this, Student A does a victory dance in her chair, much to the displeasure of the CDC representative who is still talking to the class about lime disease outbreaks.

Blissfully ignoring her professor’s warning about applying statistical generalities to the individual, Student A breathes a sigh of relief.  Her poor planning and free-spirited promiscuity are unlikely to result in the flu any time soon (I’m aware all you statistics peeps are groaning in agony as this flawed logic, but roll with me here).


Inventions for Stanford Students

Tuesday, October 19th, 2010

Bike safety:

Because God forbid anyone just wore a helmet to protect all that knowledge up there. In case of an accident, a helmet might protect what you remember from that foreign language you took in high school:

“Un sac à dos intelligent et signalant par des LED les directions prises par le cycliste : gauche ou droite. Conçu par Lee Myung Su Design Lab et intitulé “Seil Bag”, ce projet a remporté le prix du Design Concept au Red Dot Awards 2010. Explications et vidéo dans la suite de l’article.”

Earthquake safety:

This one is a bit ridiculous. It might calm the nerves of some, knowing they could rush to any doorway during an earthquake.

“In anticipation of a 7.6 magnitude earthquake possibly hitting the city of Istanbul by 2030, an MA design student named Younghwa Lee from Kingston’s University has designed a special kind of door that protects residents from falling quake debris. Designed to ensure safety and reduce injury or death, the door folds horizontally in the middle, while the bottom part remains braced against the floor for support. This allows the door to sit in an angle when the earthquake strikes while the person takes shelter under the fold.”


What is CCARE???

Thursday, October 14th, 2010

CCAREI was also among the crowd that gathered at Maples Pavilion this morning to hear the Dalai Lama speak about “The Centrality of Compassion and Human Life in Society”. It was mentioned that His Holiness had previously donated to Stanford’s “Center for Compassion and Altruism Research and Education” (CCARE) . His generous donation ($150,000 generated from book sales) was one of the largest he’s ever made to a non-Tibetan cause. Dr. James Doty, director of CCARE, comically told the audience that his first thought at the time was “Who am I to take the Dalai Lama’s money?”.

Not knowing anything about CCARE, I was curious about that same thing. (more…)

New SEQ Changes the Face of Stanford Engineering

Thursday, October 7th, 2010

Artist's rendition of the final SEQ design

Stanford has always been the West Coast’s tech Mecca.  Finally, with the advent of new Science & Engineering Quad (SEQ), we’re actually starting to look like it, too.  A decade in the making, the SEQ has blessed Stanford’s techiest with an appropriately grand tribute to Stanford’s world-renowned School of Engineering as well as the amazing facilities needed to maintain and enhance that reputation.

Why the new SEQ?  According to Dean Plummer (SoE) and representatives from the Stanford Challenge, the massive new facilities will enable engineers to work alongside researchers from a variety of fields to solve “large-scale, systems-oriented problems,” focusing on those in medicine, energy and the environment, and national security.  With four new buildings and impressive underground laboratories, the SEQ has the space and the state-of-the-art resources to make Stanford’s vast interdisciplinary goals a reality.

Here’s a layman’s guide to all that is awesome about the new SEQ!

Huang Engineering Center:

Stanford's new center for all things tech

Weighing in at a whopping 130,000 square feet, Huang Engineering is the centerpiece of the impressive new techie stomping grounds.  Huang is the new home to the SoE administration, the MS&E Department , and the Institute for Computational and Mathematical Engineering, and its high-tech, 300-seat NIVIDIA Auditorium already hosts some of the more popular CS and MS&E lectures on campus.  Huang is physically attached to Y2E2 via a second floor corridor and is also connected to all the other SEQ buildings via various underground labs and tunnels!  Did someone say University-condoned steam-tunneling?!  That’s right, my fellow engineers, we don’t even have to go outside anymore!  Not that I’d personally recommend a subterranean lifestyle, as Huang boasts a series of majestic terraces and trellises with impressive views of the Main Quad. (more…)

Terence Tao Talks About Things That I Can Understand

Wednesday, October 6th, 2010
Terence Tao

You're not a mathematician without a blackboard, apparently

Earlier this evening, Terence Tao, math professor at UCLA, gave a talk about “The Cosmic Distance Ladder” as a public lecture on-campus. Although you might think that basically all lectures are “public” since no one is seriously going to kick you out of “Signal Processing and Linear Systems I.” What “public lecture” actually means is that a very famous, very smart, very cool person is giving a lecture on something far below his or her capability to make preppy and only vaguely informed people (like me) think they’re learning and interacting in academic discourse. Before getting too much further, a few details on Terence Tao to show how awesome he is:

  • He got a PhD from Princeton by age 20
  • He won the Fields Medal in 2006 (The Fields Medal is the Nobel Prize for math, sort of)
  • If you’re not convinced by the above, believe me when I say that he is one of the smartest people alive today
  • He’s a blogger!

If I understood the real work that he does, I would go to one of his other two lectures, but being the layperson I am, I instead sat in on about an hour long lecture on the history of astrometrics, or how we figured out how far away things in space are without actually going there. He described the series of “rungs” of progress, beginning with Hipparchus estimating the size of the Earth over 2000 years ago to WMAP estimating the size of the universe today. Using no more than simple geometry and the fuzzy version of physics, he described the series of really good ideas that got us to where we are.

It was satisfying, if very “public lecture-y.” In my mind, I just saw a good hour-long PBS special on astrometrics and can now spout more trivia. The really good trivia, that is, that makes you feel smarter. Did I really want him to talk about his math instead? Probably not as it would’ve gone over my head. Neither did I really need the lecture he gave. Call me a nerd, but I think it was basically just a celebrity sighting for me.

Einstein’s Relativity Manuscript

Monday, March 8th, 2010


Photo courtesy of

This is probably the closest we’ll ever get to seeing how Einstein derived special relativity. His original manuscripts which explain the role of light and relative velocities in the universe are, for the first time, going on display in their entirety in Jerusalem. Sure, that’s cool and all, but what I really like is how much his papers look like a problem set. Good luck to everyone on their last problem sets for the quarter; who knows, maybe they’ll end up in a museum some day.

Photo courtesy of

The above paper is actually from his manuscript on general relativity, but all of Einstein’s work can be found online here.

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Stanford Study: Great White Sharks More Endangered Than Tigers

Monday, February 22nd, 2010

Great-White-Shark.jpgOne of the ocean’s most fearsome predators may be in dire straits. According to a research team led by Barbara Block, Professor in Marine Sciences at Stanford’s Hopkins Marine Station, there are fewer than 3,500 great white sharks remaining in the wild, making them rarer than tigers.

Scientists had previously believed great whites were rare but not endangered because they were spotted in a variety of distant locations. However, according to the team’s unpublished study, people have been seeing the same sharks.

To gather data, Professor Block and her team used satellite and acoustic tracking devices to monitor over 150 great whites in southern California and Hawaii. They found that great whites are remarkable long distance swimmers, capable of travelling 12,000 miles in nine months. In addition, the researchers discovered that sharks spotted in Hawaii were the same individuals observed off the coast of California just six months later.

Professor Block is a recipient of the Presidential Young Investigator Award from the National Science Foundation and the MacArthur Foundation Fellowship.

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Monday, October 5th, 2009

We have a disposable society. We love using things once or twice and then throwing them into pits in the ground. Cups, plates, gloves, hats…you name it. Perhaps this tendency towards the disposable is a reflection of our transient, liminal, earthly nature. Everything dies – everything, even our species, will be eventually “disposed of.” But more likely our love of the single serving is a sign of our inability to grasp the scale of our disposable lifestyle.
We are producing sterile, unusable trash outputs faster than we are receiving inputs from our planet. The scales are off. Units are wrong. We’re headed for trouble.
Luckily, a few simple changes in lifestyle can change our trajectory.
Try the next time you need something for your dorm room. Welcome to the craigslist of Stanford! Bulletin boards, desks, chairs and refrigerators abound. A sweet resource. And let’s face it, used stuff is super trendy right now.
Furthermore, if you’re feeling really saucy consider This Stanford-produced idea is simple: refuse to use disposables. Bring your own plate/containers/silverware to those wonderful info session lunches. I know I go to them for the free food and am always dismayed by the predominance of flimsy disposable plates/forks/knives that are bound straight for the landfill with my saliva still on them. Join me in refusing disposables and bring your own! Feel nerdy or awkward bringing your own supplies? GET OVER YOURSELF. You are on the cutting edge of a snowballing trend. Be a role model and suck it up.

Academic Lessons from P. Z. Myers and Expelled?

Friday, April 25th, 2008

The fact that the creationist “documentary” Expelled used more than questionable interview tactics to try to interview Eugenie Scott, P. Z. Myers, Michael Shermer, Hector Avalos, and Richard Dawkin has been circulating around the internet for a couple of months.
By representing themselves as another movie production company (Rampant Film) which was producing a documentary called Crossroads: The Intersection of Science and Religion, Expelled producers (Premise) were able to obtain a couple of interviews with scientists like P.Z. Myers.
Expelled was able to use the interviews because the scientists had signed a release which states the footage can be used for “the feature length documentary tentatively entitled Crossroads (the ‘Documentary’) and/or any other production.”
The questionable interview tactics of Expelled, reflect those used in Borat andthe Ali G Show. These tactics seem to be a more and more prevalent tactic for either groups interviewing someone they think are controversial, or “spoof interviews” a la the Daily Show.
As a grad student who hopes to go on to research and teach in a university, this has made me think about what I want to do if I’m ever asked to be interviewed, to help members of the press, to go on a show (radio, tv, or otherwise), or to participate in a documentary. While the odds of appearing in a film are pretty low, it might be easy get suckered into participating in a podcast, interview for a newspaper, journal, etc. with a group you object to or know will misrepresent your work. This is particularly difficult to avoid if they use the tactic that the Premise production team did, and set up shell identities (including fake webpages).
While academics want their viewpoints disseminated and are often willing to participate in documentaries, be interviewed for articles and news stories, and help journalists, maybe, they also need to start thinking about how to protect themselves from this kind of exploitation.
For starters, scholars need to closely look at the release forms they sign and decide if the standard “any other production” is ok with them. Maybe a modification, in which they need to give permission for each new use of their interview is something some scholars should start considering adding to the release forms. Maybe even crossing out the phrase (and initialing and dating it) is as far as they want to go (also making a photocopy of the document).
Another tool that universities could develop is a contract that faculty members can use which production companies will need to sign if they want to interview the faculty member.
The contract could contain provisions (translated into legalese) which state:
– the production company is not misrepresenting itself to the scholar
– the production company is not misrepresenting the film to the scholar
– if the scholar is participating without being paid, that the film is not a for profit enterprise (aka Borat)
– the production company will pay some sort of compensation if it has misrepresented itself or the film to the scholar
– the production company will pay for the legal fees of the scholar to enforce this contract
Not being interview is a chance that scholars will take, if they adopt this kind of tactic, but given the fact that “spoof interviews” and misrepresentations are occurring, maybe not being interviewed by someone sketchy is a good thing. Each scholar needs to gauge their own preferences. On the other hand, your area of study can dictate the types of interviews you get asked to do.
If a production company refuses to change the “any other production” language or sign the interview contract, scholars need to make sure they know who they are dealing with, particularly famous and/or controversial scholars.
As for myself, I’m only a grad student, but I’ve already been volunteered once by the university institute to talk to, and help, a member of the press under the mistaken assumption that I did research in a particular area. The poor researcher got a, “I study a completely unrelated area, and I’m not sure who studies this, but I think X does…” from me.
The experience got me thinking about this whole thing in the first place, particularly as I had just read about P.Z. Myer’s expulsion from Expelled.

That’s so…. Cute?

Monday, May 21st, 2007

The New York Times today ran a short article on a fabulous new book released a couple of months ago by the University of Chicago Press. It features 220 color photographs of deep ocean species, some found as far as four and a half miles under water. They will blow your mind.
Check out photos from The Deep on the book’s website, or click on the image below.
Freaky as hell.

Science at Stanford

Thursday, May 17th, 2007

Since I’m a scientist, I figured I should at least post a little about some of the science that goes on at Stanford. Today’s inaugural installment is about Folding at Home. I’m a little biased because the faculty member is part of my PhD program and one of my best friends was a graduate student in his lab. But the concept is really cool and simple: use distributed computing to perform biological computations to study protein folding that were previously inaccessible.
If you’re not a biologist you might be wondering why we should care about protein folding. There is some fundamental biological principles that we can learn, but there are important clinical implications. Each gene has information that encodes a specific protein. In order for proteins to perform their proper function, they adopt a very specific three dimensional structure. That is, they “fold” to a specific shape that allows them to carry out their job. When proteins “misfold”, they can’t carry out their function and this can lead to serious problems. By understanding what goes wrong, we can begin to figure out how to go about fixing problems.
You can find out more at the Folding at Home website. You can help out the effort by downloading the software which runs in the background while you’re sleeping or out having a drink.
Update: If you want to contribute to my F@H team, I’m number 72156. I just started it a few days ago so I’m way behind.