Sunday, January 31, 2010

It’s a Small World, After All

Just finished my grading for ‘Concepts and Ideas in Biology,’ a ‘new’ (two-year old) course for Freshmen Life Sci majors at PKU. My Dean RY and Prof LMY came up with the concept for an overview course a while back. The idea was to give entering undergraduates a “big picture” view of modern life science, through a series of lectures each introducing a topic in biology. In Fall ’08 this class was established as a 2 credit hour class on Thursdays during the 3rd and 4th period (10:10-11:00 and 11:10-12 noon, respectively). Last year ten professors gave 14 lectures. Seemed fairly well received by the students.

This year eleven professors gave 14 lectures. Topics included lectures on biodiversity, photosynthesis, stem cells, molecular genetics, the genetic code, evolution, developmental biology, bioinformatics, and biophysics. I gave my lecture on Mathematical Modeling and “Systems Biology.”

My first slide is black and white with only a few huge block Chinese words on it: Learn More Physics and Math! I flashed it quickly and started to talk about the difference between descriptive and mechanistic mathematical models. I  told the students my wish of developing more mechanistic models that are based on physics, chemistry, anatomy and physiology, … that would bridge different levels of description. (For instance, the Hodgkin-Huxley neuronal model connects ionic channel properties with the dynamics of the membrane potential of the neuron to model action potentials.)

I turned next to examples of networks, talked about Stanley Milgram’s famous sociology experiment (mailing letters from Omaha to Boston) that led to the phrase “six degrees of separation,” and discussed the Small World model (of Watts and Strogatz) and scale-free networks. A few examples of networks, scale-free or not. A personal tale of the August ’03 blackout of the US Northeast (the power grid is a “scale-free” network), and we’re at 11 AM, the start of the 10 minute break between the 3rd and 4th class periods at PKU.

In the second half of the lecture, I discussed some systems neuroscience concepts (neurons and networks, action potentials, information processing  and coding) and ended up spending the last 20+ minutes on a possible ‘roadmap’ for studying model animal behavior. The idea is to use model animals transgenic for certain types of calcium indicators in combination with modern optical imaging techniques and well-designed mathematical (data) analysis to examine the correlation (and perhaps even a causal relationship) between neuronal activity and possible behaviors.

The zebrafish imaging movie that Andrew and I made led to some ooohs and ahhhs from the first two rows, mostly girls, in the front. (Note to Andrew: the movie is a bit dim. Plus the resolution is fine for the laptop, but doesn’t quite project as impressively.) I concluded with summary of math used in the lecture (highlighting simple concepts from dynamical systems and linear algebra). My tagline: With 19th century math, 20th century physics, one can work in 21st century life sciences. As I finished wishing the students well, the 12 noon bell rang. Most students shuffled off, eager to get some lunch before their afternoon lectures, but a group of 10-15 students stayed around and asked questions.

My lecture was in mid December. Term ended the very last week of December, with Reading and Finals period from 1/04-1/17. (The duration of the Fall Semester at Chinese universities is typically dictated by the date of the Chinese New Year, which is Feb 14th this year.)

The final grade is based on a 4-7 page essay, in either Chinese (number 5 Song font) or English (12 pt Arial), 1 ½ line spaced. Each professor assigns either one (or more) classic (or not) paper and/or a review on the subject of their lecture. The essay itself should include a short intro, an explanation of the relevance or importance of the choice of topics, the student's personal viewpoint which may or may not be in agreement with the paper or review and a defense of the viewpoint. For the term paper, I assigned Steven Strogatz’s Nature ’01 review on ‘Exploring Complex Networks,’ which I had suggested as reading material supplemental to my lecture.

On January 6th, the TA e-mailed the final essays to each professor. I downloaded and unzipped a collection of 7 essays. Six were in Chinese and one was in English. The next day, I looked briefly at a couple of the Chinese essays before I decided to read the one written in English first.

The abstract read fine. ( I didn’t think small world and scale-free networks quite deserve the “big breakthrough” tag, but they are usually considered “front-edge research.” Quotations taken from the essay.)

First paragraph read very well, “the slightest bit of rewiring transforms the network into a ‘small world’, with short paths between any two nodes, just as in the giant component of a random graph. Yet the network is much more highly clustered than a random graph.[1]” The words “slightest bit” sounded too colloquial to my ear.

Next paragraph. “Barabási, Albert and Jeong have dubbed these networks ‘scale-free’, by analogy with fractals (we will talk about this later), phase transitions and other situations where power laws arise and no single characteristic scale can be defined.” Hmm… Didn’t think a Chinese kid would know to use “dubbed” this way. With a nagging suspicion, I looked at the Strogatz’s Nature review. And there it was, word for word, on page 274. Sure, the student added his/her own parenthetical on fractals, “we will talk about this later.”

Went back to the first paragraph and checked Strogatz’s review again. Yep, sentence containing “slightest bit” was taken verbatim directly from Strogatz. There was a reference number 1 attached, but no quotation marks around the sentence.

At this point, I started to look for more definitive signs of plagiarism. First paragraph of the second section, “In 1997, West, Brown and Enquist announced their controversial theory that fractals hold the key to the mysterious relationship between mass and energy use in animals.[4] Now, they are putting their theory to a bold new test: an experiment to help determine if the fractal structure of a single tree can predict how an entire rain forest works.” Reference 4 was to the ’97 Science paper by West, Brown and Enquist on “A General Model for the Origin of Allometric Scaling Laws in Biology.” But the phrase “a bold new test” was a bit too rich for me. So I decide to google it.

And there it was. Search result number 3,

28 Oct 2008 ... Now, they are putting their theory to a bold new test, an experiment to help determine if the fractal structure of a single tree can predict ...

A NOVA program on fractals.

A careful reading of the NOVA transcript revealed that the student had in fact used quite a bit of the program transcript, using indiscriminately quotes from the narrator and from G. West, J. Brown, and B. Enquist and other scientists.

And so I spent the rest of my Thursday evening marking up the essay, going carefully through it a few times. Found that the paragraph on chaos, attributed to Wikipedia, was, in fact, taken word for word from Wikipedia, sans quotation marks. Then I printed the NOVA transcript and attached to an e-mail to the course coordinator alerting her this case of plagiarism. Various phone calls were exchanged. And the next morning, the course coordinator LP called me at home.

I wasn’t so sure how to deal with this. The initial idea was to give this student a chance, explain what was wrong with the essay and ask for a new essay. LP’s idea was better. There were possibly others who “copied.” We should use this opportunity to teach the kids about plagiarism. So we agreed to announce to the class the following

·        some lecturers found instances of “剽窃(plagiarism)
·        PKU’s rules on students found plagiarizing and the consequences
·        since this is a class of Freshman students who are writing “正式论文” (babelfish’s translation: “official paper”) for the first time, we are giving everyone a chance to resubmit
·        some links on plagiarism (definitions and examples)
·        a new due date of January 17th

(There were more things announced, but those were the more important points.)

I remember that two years ago, a Yale professor, Stephen Stearns, while teaching at PKU in Life Sci found a few cases of plagiarism. Stearns wrote an e-mail to PKU students that was posted on PKU's BBS.

Friday, January 22, 2010

A Stroll through Sha Ping Park

For me, the indelible moment in MacFarquhar’s Cult. Rev. lectures came when he asked the entire class to clutch their notepads, as if it was the Little Red Book, and chant with him, “Mao Zhu Xi Wan Sui” (“毛主席万岁”, i.e., “Long Live Chairman Mao”). The entire Mem Hall rocked in unison, “Mao Zhu Xi Wan Sui, Mao Zhu Xi Wan Sui, …” I was sitting next to Bill and Viv then, and I still remember to this day how shaken I was. Partly it was being caught up in a mob, and realizing that this collective had a will of its own, that was beyond individual logic or rationalities. Partly because of the questions it and its memories kept bringing up: What would I do in Cult-Rev China? How would I behave had I been in some of the circumstances?

(And “No,” it’s not the reason I married a neo-Red Guard and moved to Beijing, but that’s for an entirely different blog.)

I made my first, and thus far, only visit to Chongqing in January 2008, just before my move. My wife was visiting XiNan DaXue (Southwest University) and I was the accompanying spouse. The campus of XiNan DaXue was far from city center and so we did not get to visit Chongqing city itself until the afternoon before our flight back to Beijing. Our hosts insisted that we get taken by a university car to see the night lights and skyline of Chongqing by the river; however, my wife first wanted to see Sha Ping Park in Sha Ping Ba (沙坪坝), a park that housed one of the largest cemetery commemorating the Cultural Revolution. Chongqinq was one of the most intense and bloody "battlegrounds" (supposedly due to the proximity of major arsenals).

It is also with some sense of urgency that my wife wanted to see Sha Ping Park. She felt that with the way real estate development was going (especially in megapolises such as Chongqing), it may be only a matter of time before the real estate developments get to these cultural relics (witness the ever diminishing number of Hutongs in Beijing). And for a while, there were some clamoring over the eventual fate of Sha Ping Park. But on December 15th, the cemetery was made into an official Chongqing city preservation site (as a cultural relic; 文物保护单位)

Here are a few photos of the tombs in Sha Ping Park. The photo aren’t very good, mostly because I’m not a very good photographer, but also because it was already very close to dusk on a cloudy day. And Chongqing is inclined to be cloudy and foggy. The perpetual cloud cover was one of the primary reasons the Nationalists picked it to be the war time capital during the War Against Japan, after the fall of Nanjing. That and the mountainous surrounds made it very hard for the Japanese to bomb Chongqing.

The cemetery is just off a lake and next to the southwestern corner of the park. You can see some taller buildings from outside in the first photo. It's a very typical cemetry. But, at the time of our visit, it was not very well attended to. You could see quite a bit of wild growth everywhere.

In the photo to the left, you will see engraved the names of 3 men, ages 58, 27 and 24. The tomb was erected in 1968 by the self-proclaimed Chongqing's 815 8-1 “Army” of Red Guards. (815 presumably means that the “Army” was established on August 15th.)

The inscriptions in the photo on the right read 可挨打、可挨斗,誓死不低革 [命头]. “(We) Can be beaten, (we) can be struggled against, (but we) pledge to the death not to bow (our) revolutionary heads.” The last two Chinese characters, in my square brackets, have already faded away.
It seemed very quiet when we left the cemetery. Almost dusk, the lanterns in the park were coming on. On our way out, we saw some people who just got off work join retirees in a couple of mahjong games in a well-lit pavilion next to the lake.

Sha Ping Park was on my mind again this week, after I read Roger Cohen’s column, “Chinese Openings,” in the NYT / IHT.

And here’s my wife’s letter to the IHT regarding “Chinese Openings”:

Talking about ‘honest’ history, I have to say a few words here:

Quote 1: ‘the frenzied attempt of Mao Zedong in the decade before his death to revitalize his rule by spreading terror.’

What terror?  Who were terrified?

What I observed on Mao's birthday (December 26th) last year was that many ordinary people in different places spontaneously organized commemorations of ‘Chairman Mao’.  These people are in their 50s to 80s who had lived through the ‘dark times’ of Cultural Revolution.  Why do they remember Mao on his birthday if they used to be terrorized by Mao?

In fact, some government officials were not happy with people commemorating Mao and they tried to disrupt many such events.  Why?  Because they did not want people to be reminded of the greatest supporter of the oppressed!  Who were terrorized in the Cultural Revolution?  The oppressing bureaucrats!

Quote 2: ‘a cemetery containing the remains of 573 people slaughtered during the Cultural revolution’

Slaughtered?  By whom?

These tombs were built during Cultural Revolution by the friends and relatives of the victims who were killed in the factional fights.

If Mr. Cohen does not know the history well enough, can he please at least not spread rumors?

in Beijing

Sunday, January 10, 2010

Name That Cartoon

While I wait around for  "The Simpsons 20th Anniversary Special", here's an imagining of Mo’s reaction to my blog on running:
 Mo: Interesting. No, wait, the other thing. Tedious.
Me: Let’s go check it out. You can see how I lived before I met you.
Mo: You lived before you met me?
Me: Sure, lots of people did.
Mo: Really?

(Can somebody tape 'The Simpsons' for me tonight? Thanks!!!)

(Answer: the 'Jurassic Bark' episode of Futurama)

Blogs Titles

Here's a list of titles of possible blogs, some of which I may eventually get around to write and post:
  • ‘Clueless’ on the CCTV Premiere Movie Channel
  • The US$10K Mistake or a 7 hr Flight Delay: How We Hi-jacked an Air China Plane
  • What We Talk About When We Talk to Taxi Drivers
  • The Heart is a Lonely Hunter: A Stroll Down Nan Luo Gu Lane
  • How I Became a ‘Foreign Expert’ at PKU
  • Anatomy of an Intersection
  • A Tale of ‘Two’ Parks
  • What I Saw at the ‘Reform and Opening’
  • Grant Applications and Presentations, Misc
  • Snapshots from the Qing-Zang Plateau (or On Our Way to Lhasa)

Dragon in the Park

For those of you who were curious about the crescent shape of the ponds in the Olympic Park, here's a full view of the Olympic Park and the Olympic Forest Park (directly to the north of park proper). As you can see in the google maps satellite image, the 4 ponds I run next to form the belly of a Dragon.

Saturday, January 2, 2010

Running in the Olympic Park

First things first! A Happy (Gregorian) New Year to Everyone! Finally mustered up enough energy to blog (and find a proxy so that I can post and see my own blogs from China).

So I have started to run semi-seriously again, ever since getting back to Beijing in November. I actually started an Excel spreadsheet to detail the time and length of each run (and which pair of shoes, which route, time of day, …). I did pick up a new pair of New Balance (NB 1224, size 8D) while I was in the States and wanted to track the mileage I put on the new shoes.

Luckily the weather (and, even more importantly, the pollution/smog) in Beijing has been unusually cooperative, and I have been able to run 15 times in the last month and a half. (And I could have put in a few more runs had I not come down with a cold the second week in December.) It has been much colder than last year but overall the pollution levels are noticeably lower than last winter. I presume it is due to a greater portion of heat in Beijing being generated by natural gas instead of coal, but I cannot be sure.

In any case, when I’m at PKU during the week, I usually run around Weiming Pond (Weiming Hu, 未名湖, i.e., the pond whose name is 'Nameless Lake') or on the track of the May 4th Athletic Field. Once around Weiming Hu is about 950 meters, so I usually run 5-8 laps. Weiming Hu is very scenic, especially in the Fall and in the Spring. Unfortunately, I usually run in the afternoon and most times I have to compete with automobiles on the north side of the shore, as west bound car traffic is permitted on that side.

That’s why I prefer to run on the days when I’m working in my wife’s office/lab at the Datun campus of the Chinese Academy of Sciences (CAS). The 4 year old campus is a block west of the Olympic Park, which is the site of the Olympic Stadium (aka the ‘Bird’s Nest’ and the silver doughnut in the satellite image below) and the National Swimming Center (aka the ‘Water Cube’ and the pinkish square to the west of the Bird's Nest). The park is organized around a broad, tree-lined, pedestrian-only boulevard that runs north-south through the length of the park. A series of man-made ponds run mostly parallel to this pedestrian walkway from the Bird’s Nest to the even newer Olympic Forest Park (not shown in the image below). I have mapped out my basic running route, which is a loop around the 4 easily accessible ponds. (I mark the route in dashed white lines on the Google satellite map posted below. The dashed cyan line marks partly our commute to the CAS from home and will be the subject of a future blog.)

From the CAS campus, I run due east along North Datun Road to the closest pond, turn left and head up north. The series of Olympic Park ponds end at one of the side entrances to the Olympic Forest Park. There I turn right and run back south along the eastern edge of these ponds until North National Stadium Road. Some time in the summer I have run south one more pond to get to the foot of the Bird’s Nest, but lately that area is fenced off, with entrances on the east and the west of the stadium and an exit-only gate on North National Stadium Road. So here I turn up north again and run up along the western shore of the ponds up to North Datun Road. Here I have two choices. I can either run back to the CAS Datun campus, making it a 5 km run, or loop again around the 2 northern ponds and making it a 6 ½ km run. (A couple of times last summer, I have run 2 full laps around the 4 ponds. But, so far this winter, I have not tried, partly because I have not quite worked myself back to it, after various trips and the weeklong bout with a cold. But mostly it is because it has been so windy in the last 2 weeks. On Christmas, I ran the usual 6 ½ km route but with the last 800 meters straight into a 20 kph wind from the west.)

During my runs in the Olympic Park, which is extremely scenic (especially at sunset), I mostly enjoy looking at the people visiting. I see families out walking with their kid, with or without strollers. I see old couples walking hand-in-hand, some times walking their dogs. I see young couples seated on benches (and usually in each other’s arms). I see old men flying kites. I see park workers sweeping at the end of the day, keeping the park extremely clean. And some times I even see other runners, although in the last, bitterly cold, month, basically I have been the only runner out there. Some times I nod to people I run past, but usually they do not respond. When they do look at me, fully decked out in running shirt and running tights, it is as if I am from another planet. Even my fellow runners don’t seem to acknowledge other runners.

This afternoon, I went for the first run of the year in the Olympic Park. It snowed a little bit last night, and so there’s a thin layer of snow on top of the solidly frozen ponds. (But not enough snow to stay on the paths or the walkways.) There were noticeably more people than on the regular, weekday, afternoons. Many people were trying to skate on the frozen ponds. One person even came out with an office chair with wheels and was using a tree branch as a pole.

There were also new winter fair-like events in the tents next to the stadium and the stadium proper made into a snow theme park (filled by snow machines). (The latter I did not get to see first hand but has been in the news on CCTV recently.) But what was eerily missing this afternoon was the music blaring from speakers along the pedestrian walkways and along the ponds. Usually the park speakers play three songs in a loop: ‘Beijing Welcomes You,’ (the claustrophobic-at-least-to-me) ‘One World / One Dream,’ and ‘You and Me’ (as performed by Liu Huan and Sarah Brightman during the 2008 Olympic Opening Ceremonies). I prefer running to the rhythm of ‘Beijing Welcomes You,’ especially after I have warmed up. For me, the other two songs are a tad too slow to run to. The three songs are in an endless loop broken only by the park information announcement (in both Chinese and English) between ‘You and Me’ and ‘Beijing Welcomes You’, with the lady’s voice reminding everyone to shop only at ‘official’ Olympic Park shops and that there are 3 zones (she pronounces the English word ‘zones’ to rhyme with ‘ruins’), each with their own information centers and services.

Remind me to ask my British friends how they pronounce ‘zones.’

Anyway, my New Year's resolution: a 10-k run under 50 mins.