Everyday Scientist

chemicals ad campaign

Paul has a good first draft of a chemicals ad campaign. But I was more inspired by Klaas Wynne‘s “We love … eat … live chemicals” poster:

The reason I like it is that it points out that “chemical-free” is a stupid label, and that not all chemicals are bad (at the right doses). This type of poster could be also applied to “chemical-free” shampoos, by listing what’s in natural coconut and mint oils. I also think it would be cool to draw all those chemicals (make the size of the structure correspond to the relative amount in the apple), and repeat for several “natural” and man-made products.

I think that the “We love chemicals” posters could be combined with a set of “Natural isn’t aways safe” posters. For instance, Andrea writes about an example of dangerous natural foodstuffs. And there’s always Jim Collman’s book Naturally Dangerous.

Here are my quick drafts:

I’m moderately satisfied with them.

UPDATE: MRW posted his really cool posters:

Very cool. I like them, MRW!

heineken solvent

(hat tip to efdm and brsmblog.com.)

3d FtsZ

My friend Julie just published these beautiful 3D images of the FtsZ ring closing off two tiny dividing Caulobacter cells:

The scale bar is only 400 nm. Love it! (Video link here.)

self-plagiarism and JACS

Hi all! I’m back! Well, not exactly: I won’t be posting nearly as much as I did a few years ago, but I do hope to start posting more than once a year. Sorry for my absence. There’s no real excuse except my laziness, a new postdoc position, commuting, and a new baby. I suppose those are good excuses, really. Also, I’m sorry to say, that I’ve been cheating on you, posting on another blog. We love each other, and I won’t stop, but I want to keep you Everyday Scientist readers in my live, too. I’m just not going to pay as much attention to you as I used to. You’re cool with that, right?

Anyway, I thought I’d comment on the recent blogstorm regarding Ronald Breslow’s apparently self-plagiarized JACS paper. Read the full stories here (1, 2, 3, etc.).

I feel bad for Breslow, because I like him and I respect his work and I think his paper in JACS is valuable. However, I think he should retract his paper. Sorry, but if some no-name had been caught completely copying and pasting his or her previously published paper(s) and submitting that to JACS as an ostensibly novel manuscript, that paper would be retracted when found out. If he had just copied the intro paragraph, I’d be more forgiving, but the entire document is copied (except, that is, the name of the journal)!

That said, it might be possible to save the JACS paper, but the editors would have to label the article as an Editorial or Perspective or something, and explicitly state that the article is reprinted from previous sources. I know that might not be fair, to give Breslow special treatment, but life isn’t fair. Famous scientists might get away with more than peons. And, honestly, Breslow’s paper remaining in JACS might be good for future humanity, because JACS archive will probably be more accessible than other sources. That way, we’ll be able to look up what to do when space dinosaurs visit us!

more lytro pics of lasers

An optical parametric oscillator and related optics:

Enjoy.

refocusable images of microscope and laser table

I bought a Lytro camera, which captures the entire depth of field and allows you to refocus a picture after you take it. It accomplishes this by having a microlens array in front of the sensor, which captures information about light rays and angles in the entire field, then the image can be reconstructed in post-processing.

Here are some shots of microscopes and laser tables. Click around on the images to refocus.

More to come…

P.S. Sorry I’ve been so absent. Postdoc+baby = no time for blog. :)

SPRAIPAINT

Great paper from my previous lab. And with a ridiculously hilarious acronym (a play on Hochstrasser’s PAINT): superresolution by power-dependent active intermittency and points accumulation for imaging in nanoscale topography (SPRAIPAINT). This acronym fails almost all my ”GINAP” rules for initialisms, but I still love it because it joins the plethora of acronyms in the super-resolution microscopy field: PALM, FPALM, STORM, dSTORM, STED, GSDIM, PAINT, RESOLFT, SMACM, FIONA, SHREC, SHRIMP, SIM, SOFI, NALMS, … and I’m sure I’m forgetting some. This acronym shitstorm certainly deserves more. In all honesty, I think we should drop all the acronyms and just call it “pointillist super-resolution microscopy.”

The images in this paper are just beautiful! The bacteria they image are very small, basically at the diffraction limit of a conventional microscope. But they are able to image three-dimensional helices of protein filaments inside these tiny guys!

The movies are awesome:

(Click here for Movie 2)

Cool. Keep up the good work, Moerner lab.

sam’s three most important safety rules

Top three safety rules, especially for new students:

1. If you’re unsure about any safety issue, ask someone!
2. Wear safety glasses when freezing things.
3. Wear a face shield when piranha etching.

An addendum rule is to not work sloppily in general. Or when you’re very tired.

Of course, there are many other important rules. But these are my favs.

2011 nobel predictions

Wow, it’s already Nobel season! ChemBark and the Curious Wavefunction already have predictions. My 2010 Nobel predictions are here (and, of course, the Simpsons had their own last year). I don’t have too much to add to my 2010 predictions; instead, I’m going to put my chips all in and give just one prediction for each category.

Physics: Moerner, for single-molecule spectroscopy

Chemistry: Matyjaszewski, for polymer synthesis

Medicine: Djerassi, for The Pill

Peace: Twitter, for liberating Egypt

Literature: Twitter, for making literature shorter

playstation joystick control on electron microscope

Fancy electron microscope…

…uses a game controller to manipulate the internal robots. Ha!

405 nm laser fun

I bought a 10 mW (30 mW, actually, according to our lab’s power meter) 405 nm laser from Amazon. No this pointer isn’t for presentations, for reasons I have already stated. This pointer is for fun.

For instance, I’ve enjoyed shooting the beam through tonic water and seeing the fluorescence from quinine. Here’s some total internal reflection:

Any other ideas for cool “experiments”?

(Note, please be careful with this or any laser pointer. Although the purple light emanating from this pointer doesn’t look bright, it can damage your eye or skin. Even if your eyes aren’t sensitive to 405 nm, that doesn’t mean they can’t be damaged by 405 nm. This pointer is dangerous to be viewed even in diffuse reflections.)

(P.S. The sorta shitty photo credited to E.Y.L.)

UPDATE: It turns out that urine is also fluorescent:

Especially after taking a multivitamin.

extraordinarily repeatable data

UPDATE: My friend on Facebook pointed out that Figure S5c in the supporting info is even more fishy (click on the image below to see a zoomed-in version). Clearly, some portions of the image were pasted on top of other parts. On the right, it is obvious that the top part of the image is from a different frame as the bottom part. On the left, it looks like there’s another image hidden behind (see the strip showing through on the left top part of the image). I’ve added red arrows to aid the eye.

This could possibly be mistakes by someone who doesn’t know how to use Photoshop layers, but I’m thinking there might have been some intentional manipulation of the data. Either way, this type of slicing and stitching and Photoshopping of scientific data is totally unacceptable. I think Nature editors and referees should be more than ashamed to have let this slide.

Nature editors announced that they are investigating.

(Original post below.)

This paper in Nature contains some serious errors: some of the images that are purportedly from different samples (different mice, even) appear to be identical! Note the triangle of spots in the two images below:

Many commenters have noticed the weirdnesses in the figures. This is my favorite comment so far:

2011-04-22 09:31 AM aston panda said:
This is an excellent article shows extraordinary .. skills and amazingly repeatable data. for example
Fig.1a, 2 middle vs 3 bottom left
Fig.1c, 2 right side vs 3 left side
Fig.S4, 1 left side vs 2 right side
Fig.S5, c4 middle right vs e4 middle left
GOOD JOB

I suspect that some sloppy organizing by the authors led to them mixing up some files on their computer. That’s my optimistic view. If they were trying to fabricate data, they wouldn’t use the same region of the same image of the same sample! It must have been sloppy bookkeeping. I hope their results stand up after they correct these errors.

It just goes to show that real science can’t get accepted into Nature and Science. ;)

UPDATE 2: RetractionWatch is surprised that this paper eventually was published with only a correction!

why is the left bike pedal left-hand threaded?

Any cyclist knows that the left bike pedal is left-hand (i.e. reverse) threaded. This is so the pedal doesn’t unscrew itself while you’re pedaling. But go grab a bike and spin the pedal and crank around and you might be a little confused. Last time I did this, I thought, Wait why isn’t the right pedal reverse threaded? When you spin the pedal and crank forward, as if you’re actually powering the bike, the effective spinning of the pedal around its axle (AKA the spindle) should actually unscrew both pedals: lefty-loosey on the right pedal and righty-loosey on the left. Did every bike manufacturer get this wrong?!?

Of course not, and the real answer blew my mind. (Probably because I’m not a mechanical engineer.)

It is not, not mind you, because of the effective unscrewing force from the non-zero friction of the ball bearings. Instead, it is an effect that works in the opposite direction (in this case): mechanical precession:

“Precession is the process of a round part in a round hole rotating with respect to that hole because of clearance between them and a radial force on the part that changes direction. The direction of rotation of the inner part is opposite to the direction of rotation of the radial force.”

The source of the unscrewing force is thus radial on the spindle—the downward force you put on the pedal—instead of the twisting force from the ball bearing friction. This radial force translates into an unscrewing force because there is a small amount of clearance between the spindle and the threaded hole in the crank. I picture it like a pencil in a toilet-paper tube: crank the end of the pencil around, and there is a force that wants it to rotate on its long axis (from friction with the wall of the tube).

The unscrewing force from precession is much stronger than the unscrewing force from friction of ball bearings, so bike manufacturers ignore the latter.

I wish I could find an animated gif of mechanical precession, but I haven’t found one. Anyone have a book on “advanced thread theory” and want to make an animation?

UPDATE: Here’s a nice figure. Not an animation, but it might be helpful:

wtf?! acs fall meeting deadline is already passed?

Before the Spring meeting has even started? This is not cool.

It’s almost impossible to actually find out, but the deadline for submitting an abstract to the ACS Fall meeting in Denver has already passed. This is how I tried to find out:

First, I went to the ACS website, and clicked on the “Meetings” tab. The Fall 2011 meeting isn’t even listed there (see screenshot on the left). OK, that’s silly.

Next, I searched “deadline” from the ACS homepage and clicked on the top link, “Events & Deadlines.” That brings me to the Events & Deadlines page. Where the Denver meeting doesn’t even have a link. The Anaheim meeting’s link is live, but you can’t click on the Denver meeting. OK, maybe that means the deadline is so far away that you don’t need to worry about it. Wrong. Apparently, the Events & Deadlines page is only for past deadlines. Why have a deadlines page only for past deadlines?!? Wouldn’t future deadlines be a bit more helpful? I guess, the “Events & Deadlines” page is more a shrine to the deadlines you’ve already missed, not intended to help you meet future deadlines.

OK, let’s try going directly to the Denver meeting homepage. Not a lot of info there. But it turns out that, if you click on the symposia link, you’ll find that many of the deadlines have already passed!!! And the Spring meeting hasn’t even started yet! (There’s also this strange PDF I found somewhere on the ACS website; it list different deadlines.)

That really, really sucks. I feel like, with all the stupid emails I get from ACS every day, I’d have seen this deadline coming. I suppose it’s all my own fault: I should have been paying attention. But I figured that the deadline for the next meeting wouldn’t be before the current meeting starts. And I do blame the ACS website: I’ve been looking at the “meetings” tab for info on Denver, but it isn’t even there yet.

My suggestion: Why doesn’t ACS have one deadline for all the divisions, have it after the current meeting is finished, and actually announce that deadline on their webpage?

I am annoyed.

great escape

Fun paper:

Harvey, A.; Zukoff, S. Wind-Powered Wheel Locomotion, Initiated by Leaping Somersaults, in Larvae of the Southeastern Beach Tiger Beetle (Cicindela dorsalis media). PLoS ONE 2011, 6(3), e17746. http://dx.doi.org/10.1371/journal.pone.0017746

Escape mechanisms in the animal kingdom can be pretty cool. Or just downright entertaining. This little guy does a somersault, grabs his tail, and rolls away in the wind (see Video 1). Check out Video 4 for a slo-mo version.