oh, you mean wheelbarrow!

January 30, 2007 at 9:01 am | | crazy figure contest, literature, stupid technology

Ok, another contender in the worst-figure contest:


In case you didn’t know what a wheelbarrow was. No really, this is a real figure in the paper. (Hat-tip to MetaDatta. And Sujit thought that Tetrahedron Letters is a funny journal title, too. Back in undergrad, I thought it was a joke journal. Now I am a co-author on a paper in Tetrahedron, so don’t I look the fool.)

P.S. My favorite part of the figure is the triple equal mark.

Who’s on First?

January 29, 2007 at 9:27 am | | grad life, teaching

A modern day “Who’s on first,” that most lab teachers have experienced…. attributed to “Unknown” on the internet.

    TA: What went on in this lab?
    Student: What do you mean?
    TA: What did you do in this lab?
    Student: Lab 3.
    TA: And what did you do in lab 3?
    Student: We measured the result.
    TA: Assume I’ve never seen this lab before, and you’re going to explain it to me. What would you say?
    Student: (pause) Well, it was all about getting the slope.
    TA: The slope of what?
    Student: The slope of the plot.
    TA: I know that, but you have to assume I’ve never heard of this lab, ok? How would you explain what you did?
    Student: We got the wires and measured at each point.
    TA: Measured what?
    Student: What the meter said.
    TA: (pause) Look. Your report tells me nothing; this could be an experiment about baking cakes. What’s this number here?
    Student: 5.
    TA: Yes I KNOW it’s 5. What did it measure?
    Student: The slope. Of the line.
    TA: What line?
    Student: The line. On the plot. We measured the points and plotted them.
    TA: Why?
    Student: (knowing smile) Because that’s what the lab said.
    TA: If I was a total stranger, how would you explain this to me?
    Student: You just connect it up–
    TA: Connect WHAT up?
    Student: The circuit.
    TA: Why?
    Student: I’m sorry, I don’t know what you’re asking.
    TA: I’m asking: what is this lab all about?
    Student: Well, we put in the wires and got 5.
    TA: 5 what?
    Student: The slope.
    TA: WHAT was it’s slope?
    Student: 5.
    TA: I KNOW that, but what was it a measurement of?
    Student: The meter.
    TA: (sigh) One more time — consider me a total stranger. How would you explain this to me?
    Student: You just put on the wires and vary the dial until you get the readings.
    TA: What dial?
    Student: On the power supply.
    TA: Why was there a power supply?
    Student: Well, for the circuit.
    TA: And what readings are you talking about?
    Student: The readings in the plot.
    TA: They gave you a plot in the lab manual?
    Student: I’m sorry, I don’t know what you’re asking.
    TA: Where did the plot come from?
    Student: We drew it.
    TA: From what?
    Student: From the experiment.
    TA: The experiment about what?
    Student: About lab 3.

the internets make you live longer

January 25, 2007 at 10:15 am | | crazy figure contest, science and the public, software, stupid technology, wild web

Proven: Using the internet makes you live longer. And, as a nice side effect, the internet reduces child mortality. Don’t believe me? See for yourself (click on the chart below):


(To manipulate the chart or see a map or make your own chart, click here.) Cool Google stuff.

seminar: bianxiao cui

January 23, 2007 at 9:30 pm | | seminars, single molecules

Bianxiao Cui, a postdoc in Steve Chu‘s lab here at Stanford, gave a job talk in the Chemistry Department last week. The title was approximately “Single-Molecule Analysis of NGF in Live Neurons (Using Quantum Dots).” Anyway, that gets the point of the talk. It was pretty cool. Here are my notes:

cui_seminar_1.jpg     cui_seminar_2.jpg     cui_seminar_3.jpg

Summary: Nerve-growth factor (NGF) is transported down the axon from the distal end near a target to the nerve cell body, and this tells the axon to grow. To image this transport in live cells, they labeled NGF with quantum dots (QDs) using a biotin/streptavidin linkage and tracked the labeled molecules using “pseudo TIRF”—somewhere between TIR illumination and columnated epi so that the excitation extended a little more into the sample than TIR, but kept background low. They used special compartmented sample containers (and later, microfluidic cells) in order to separate the cell body from the axon (because the labeled NGF nonspecifically labels the entire cell body and makes it too difficult to image).

Cui showed some beautiful (false-color) movies of individual QD-NGF-endosome complexes being actively transported down microtubules toward the cell body. Also found were instances where endosomes moved backward (toward distal axon) and endosomes allegedly passed over each other (although it was unclear to me how they proved that the two endosomes were on the same microtubule and if they actually passed over, because each diffraction-limited spot is indistinguishable). She made some claims about only one NGF per endosome (i.e. the endosome does not wait for more passengers), but that part was a little fuzzy to me (although it was probably the point of the talk). Also, they found that labeled NGF co-localized with signaling molecules in the cell body. Cool.

By fitting the point-spread function of the QDs, they were able to localize each endosome to individual microtubules (imaging below the diffraction limit). This was very cool, and Cui showed tracks of endosomes switching microtubules and then changing speed or direction. Finally, she even did a mouse study, but this seemed tacked on. The real results were the imaging and single-particle tracking.

scientific article filtering

January 19, 2007 at 8:27 am | | everyday science, news, science community, software, wild web

The wave of social bookmarking is finally reaching scientific journal articles. What YouTube, de.licio.us, and digg are to stupid videos and strange websites, now biowizard, CiteULike, and BioInfoBank are to scientific articles. (See also my previous post about CiteULike.) I suspect Connotea, with some social features already existing, is on its way to more filtering of scientific articles, too.

I welcome this progress. I find it pretty tedious reading journal tables of contents every day/week, which is necessary to keep up with new ideas that you hadn’t thought of (and thus are hard to search for in a database). Also, with journals such as PLoS One (which publishes anything—whether it’s interesting or not), filtering of journal articles will become more and more useful to pinpoint only articles you’re interested in reading.

The ranking mechanism of these science social bookmarking sites is far from perfect. But it’s a good start. Go check them out and make it easier for me to find papers I want to read!

[Note: My favorite site is still CiteULike. Connotea is nice and probably less buggy, but it seems to progress at a much slower rate, probably because CUL programming is open-source and collaborative. I can’t imagine biowizard really being that helpful in the long run, because it doesn’t have any of the functionality of CUL or Connotea and only applies to biology. I’m going to stick with CUL until someone else wins unequivocally (then I’ll export my library). I’ll update you as things change.]

new Ar laser installation

January 16, 2007 at 11:41 am | | everyday science, hardware

My lab bought an Argon-ion laser to replace an older one that wasn’t working anymore. That’s good news. Then we had to physically replace the old one. That’s the bad news. (We’re chemists, not weight-lifters….) But it ended up being really fun. I missed the worst part—moving the heavy laser down the stairs into the basement—because of a well timed vacation. But after the winter break, we moved it into the lab.

First, out with the old laser:


That wasn’t too bad, but the new laser was heavier and longer. But we did it:


The old power supply was fascinating: Read more of this post…

laser cowboys

January 10, 2007 at 2:28 pm | | everyday science, grad life, hardware, lab safety, nerd

The 23rd century cowboy…



Hey, is there a “sexy men of the spectroscopy laboratory” calendar out there? Here are January and August for you!

news update: photonics, publishing, and elephants

January 8, 2007 at 8:43 pm | | literature, news, science and the public, science community, stupid technology, wild web

Just a few (sciency) news updates today…


This month, NPG launches its new (sub)journal Nature Photonics. It might have some cool articles in the future. Also PLoS One launched at the end of 2006 and will be an open-access journal that publishes any submissions that pass very limited scientific criteria (i.e. not including the impact or “coolness” of the paper). Who know? It might even work. If there were a good way of filtering the papers after they’re published, this open-access fad might be the new paradigm.

Invisible Cloak (not)

OK, everyone’s calling it an invisible cloak, but the “metamaterials” technology isn’t really even close. But it just got closer, with Opt. Lett. 2006, 32, 53–55. The authors report a metamaterial with a negative refractive index for visible (780-nm) light. And it’s really cool because … hey wait … where’d you go??

Stupid Elephant Picture

Many newspapers etc. have been publishing a picture of an elephant fetus in the womb (allegedly).


Cool eh? But it’s bogus! (Yeah, I was fooled, too. I saw it in Nature, where they claimed it was “enhanced with computer graphics.” Riiiiight. That should have tipped me off.) Actually, it is a silicon model of this ultrasound image:


I guess that’s cool.

offset your entropy footprint

January 2, 2007 at 10:31 am | | news, science and the public, science@home, stupid technology, wild web

You’ve probably heard of websites like CarbonCounter.com, where you can offset your personal carbon footprint to help prevent global warming. Well, I’ve created a site that will let you calculate and offset your entropy footprint in order to help prevent a more dangerous inevitability: the heat death of the universe!

Please help before it’s too late.

Powered by WordPress, Theme Based on "Pool" by Borja Fernandez
Entries and comments feeds. Valid XHTML and CSS.