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.

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