2014 nobel predictions

September 12, 2014 at 10:07 am | | news, nobel, science and the public

Time for 2014 Nobel Prize predictions. Actually, it’s a little early, but with Lasker Prize announcements, I just couldn’t wait. Here’s my track record:

So here are my 2014 predictions:


ChemistryNanotechnology: Alivisatos, Whitesides, Lieber

MedicineDNA/blottingSouthern, Jefferys, Burnette

PhysicsCloaking/nonlinear optics: Pendry, Harris

Peace: Ebola: Médecins Sans Frontières


Other and past predictions:

Biomolecular motors: Vale, Sheetz, Spudich, Brady

Unfolded protein response: Walter, Mori

Soft lithography and microfluidics: Whitesides, Quake

Chaperonins: Horwich, Hartl, Lindquist, Ellis

Polymers: Frechet, Matyjaszewski, Wang, Willson

Electrochemistry/bioinorganic: Bard, Gray, Lippard

Single-molecule spectroscopy: Moerner, Orrit, Xie (as predicted by The Simpsons)

Solar: Grätzel, Nocera

DNA synthesis: Caruthers

Next-gen sequencing: Webb, Craighead, Klenerman, Church …

Super-resolution optical microscopy: Betzig, Hell, Zhuang, Hess

NMR and membranes: McConnell

Electron Transfer in DNA/Electrochemical DNA Damage Sensors: Barton, Giese, Schuster

Pd-catalyzed Alkyne/Alkene Coupling and Atom-Economy: Trost

Nuclear hormone receptors: Chambon, Evans, Jensen, O’Malley

Two-photon microscopy: Webb, Denk, Strickler

DNA microarrays: Brown

AIDS: Hütter

The Pill: Djerassi

T-cell receptor: Allison, Reinherz, Kappler, Marrack

Quantum dots: Brus

comparing Nikon immersion oils

August 27, 2014 at 2:53 pm | | everyday science, review

I typically use Nikon type NF immersion oil. But I hate the dropper that it comes in, and I’ve recently been having trouble with the oil crystallizing, especially if I aliquot it to smaller dropper vials. So I decided to compare the different oil types available, namely A, B, 37, and NF. (Type 37 is sometimes called type B 37.) Note that types B and 37 are actually Cargille part numbers 16484 and 16237, respectively.

A B 37 NF montage

See full slide deck here.

My conclusion: Use type A for routine imaging (the dropper is much easier to use and it’s less stinky than NF). For samples at 37 C or single-molecule imaging, use type NF.

stop…

August 20, 2014 at 12:31 pm | | nerd

hammer time

Coherent Obis Galaxy review

August 1, 2014 at 10:50 am | | hardware, review

We recently purchased new lasers for our TIRF scope. I wanted the flexibility and low cost of a home-built laser combiner, but also I wanted the ease and stability of a turn-key laser box. I stumbled upon Coherent’s Obis Galaxy combiner, which uses up to 8 fiber pigtailed lasers and combines the emission into one output fiber. What I really love about the idea is that you can add lasers in the future as your experimental needs grow. (Or your budget does.)

The other aspect I love is that it’s just plug and play! If I were on vacation when a new laser arrived, anyone in lab should be able to add it to this system.

2014-07-03 15.22.03

We also purchased the LaserBox, which supplies power, cooling, and separate digital/analog control to 5 lasers.

2014-07-03 15.07.33

The new system just sits on the shelf. It’s tiny:

2014-07-03 15.45.57

Here it is in action. The lasers were being triggered and sequenced by the camera and an ESio board, so they were running so fast I had to jiggle my iPhone in order to see the different colors.

One problem that I have faced is that the throughput is lower than spec (should be 60%+, and it’s down at 40%). Coherent is going to repair or replace the unit. And fortunately, we’re only running the lasers at 10% or less for most experiments currently, so there’s no rush to get the throughput higher!

If you’re ever in Genentech Hall UCSF and want a quick demo, drop me a line!

Pro:

  • Flexibility to add laser lines or upgrade lasers in the future at no additional cost (besides the pigtailed laser itself) and no downtime
  • Super easy installation
  • Cheaper than many of the other turn-key boxes
  • No aligning or maintenance needed
  • Each laser can be separately triggered and modulated (digital and/or analog)
  • Replaceable output fiber if it gets damaged (although it might not be as high-throughput as the original fiber)
  • Small and light, so it’s easy to find a place for it in any lab

Con:

  • No dual-fiber output option
  • Two boxes and some fibers going between the two makes it a little less portable than some of the other small boxes
  • No space to add optics (e.g. polarizers) in launch
  • Fans for LaserBox are not silent
  • Power and emission LEDs are too bright

Bottom line: I’d definitely recommend the Galaxy if you’re primary goals are color flexibility and simplicity. If you want more turn-key (and probably stability, but I can’t speak to that yet), there are other boxes to consider: Spectral ILE, Vortran Versa-Lase, Toptica MLE, and so on. Also, if you needed two (or more) fiber output, the Galaxy doesn’t have that option.

home-made plasma cleaner

July 23, 2014 at 12:52 pm | | everyday science, hardware, science@home, stupid technology

I really want a plasma cleaner, for cleaning coverslips and activating glass for PDMS bonding, but they cost thousands of dollars. I thought that was a lot of money for a glorified microwave. So I made my own.

Drill a few holes in glass:

2014-03-10 11.16.58

 

Make a PDMS seal (thanks Kate):

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Glue the chamber:

2014-03-10 12.29.04

We’re ready to go!

2014-07-17 13.19.41

Fill the chamber with argon, evacuate it, turn on the microwave oven, and … voila! … a plasma:

2014-07-17 12.54.18

2014-07-17 12.56.04

Below are slides before and after (right) plasma treatment. You can see the contact angle of water is dramatically reduced.

2014-07-17 13.14.40

It works!

Well, not really. I found that the plasma really only stays lit with argon. When I flow air in, it extinguishes, but also burns some of the rubber hoses. That adds more dirt to my slides than I want.

Conclusion: don’t do this at home. :)

(Well, that might be a little harsh. It does work well to bond PDMS to glass. And I’ll try a longer etch sometime to see if it will ever clean the coverslips.)

checklist of unusual phenomena

July 22, 2014 at 1:40 pm | | nerd, stupid technology

AKA “troubleshooting.”

image

eyepiece laser safety filter and 3D printing

July 8, 2014 at 3:57 pm | | hardware, lab safety

With TIRF and lasers on many fluorescence microscopes these days, there’s a huge risk of seriously damaging your vision. Not so much from a stray beam (which is probably diffuse or your blink reflex will be faster than the damage threshold), but more from looking in the eyepiece without the proper filters in place. A reflected laser beam focused with the eyepiece lenses right onto your retinas can be vary damaging.

(That happened a Berkeley a few years ago, and EH&S asked everyone to take the eyepieces off their TIRF scopes. I removed one, so that you’d only lose one eye.)

Interlocks between your scope port setting and your laser is one option. But that means you can’t ever look at your sample with your eyes (at least the fluorescence). The elegant solution it to put a multi-band emission filter in your eyepiece tube to block any laser light:

eyepiece laser safety

I got this idea from Kurt, who even designed a filter holder that you can 3D print. I modified that part for one that would fit in our Nikon TE2000.

2014-05-13 19.28.12

I also printed some other parts for our TE2000. After we upgraded our epi illumination source from a Hg lamp to a Lumencor Spectra-X LED, we no longer needed the ND filter sliders on the illuminator tube, because the LED intensity is easily controlled by software. I’ve always hated those sliders, because they are easy to accidentally knock into the wrong position. That, and they aren’t encoded into the image metadata, so you have no idea what slider settings you had when you look at an image 3 months later!

2014-07-07 15.27.14

So I removed the ND sliders and replaced them with a nice plug to block the light.

I have my 3D designs on the NIH 3D Print Exchange.

thorlabs lab snacks boxes for arduino enclosure

July 3, 2014 at 7:38 pm | | everyday science, hardware

On the topic of hardware syncing, I figured I should boast about my very fancy Arduino enclosure. I used a Thorlabs Lab Snacks box (one of the Great Boxes of Science):

2014-06-11 18.17.49 2014-06-11 18.17.33

2014-06-11 18.17.26

Of course, Nico makes beautiful laser-cut boxes for his Arduino, and Kurt has a nice 3D-printed box. But I think I’ll stick to this reduce/reuse/recycle approach. :)

UPDATE: I guess I’m not the only one. Labrigger posted a similar pic!

UPDATE 2: I made a bigger one to fit two Arduinos:

2014-08-07 14.07.19 2014-08-07 14.10.30

on the importance of hardware syncing

June 10, 2014 at 9:42 pm | | hardware, software

Before hardware syncing:

After:

For more details: https://micro-manager.org/wiki/Hardware-based_synchronization

EDIT: And now incorporating a Sutter TLED transmitted light:

electronics company

June 9, 2014 at 4:12 pm | | hardware, stupid technology

assmann

speck of dust

April 18, 2014 at 10:43 am | | crazy figure contest, history, literature

The scope room dustiness post reminded me of the hilarious story of the first report of second harmonic generation of a laser. The authors presented a photographic plate that showed the exposure the main laser beam, as well as a “small but dense” spot from the doubled beam,

shg dust

See the spot? You won’t. Because the editor removed the spot, thinking it was a speck of dust on the plate. Ha!

When I first heard this story, I didn’t believe it. I assumed it was a contrast issue when the paper was scanned into a PDF. So I went to the library and found the original print version. No spot their, either!

That really made my day.

reduce scope room dustiness

April 15, 2014 at 11:17 am | | hardware

I installed this simple dust filter over the air input register in our microscope room to (hopefully) reduce some of the excess dust. It also has the benefit of directing the air flow away from the microscopes, so I hope it will also reduce sample drift.

dust cover

I’ll update you in a few months if it seems to be working.

am i finished using Papers?

April 4, 2014 at 1:39 pm | | literature, software

I’ve been using Papers for years. When Papers2 came out, I was quick (too quick) to jump in and start using it. It’s worst bugs got ironed out within a couple months, and I used it happily for a while. Papers2 would let you sync PDFs to your iPad for offline reading, but it was slow and a little clunky. Papers3 library syncing is not for offline reading and it is VERY slow and VERY clunky. And it relies on Dropbox for storage. The plus of this is that storage is free (as long as you have space in Dropbox); the downside is that they syncing isn’t clean and often fails.

Mendeley has proven itself the best at syncing your library and actual PDFs to the cloud (you have to pre-download individual files for offline reading you can sync all PDFs in iOS in settings). Papers PDF viewer is still better, but it’s not worth the hassle: Mendeley syncs cleanly and the reader is fine. Not only that, but Mendeley has sharing options that make managing citations possible when writing a manuscript with co-authors (as long as they’ll use Mendeley).

Mendeley is also better than Papers at automatically finding the metadata for the paper (authors, title, abstract, etc.). The program simply works (most of the time), so I’ve given up and finally started using it. Almost exclusively.

PubChase syncs with Mendeley and recommends related papers weekly. (Update: the recommendations update daily, and they send out a weekly email with updates from that week.) They also have some pretty nice features, like a beautiful viewer for some journals and alerts when papers in your library are retracted.

Readcube still has the best recommendations. And they update daily, unlike PubChase’s weekly. And you can tell which recommendations you’ve marked as read, so it’s very quick to scan the list. But that’s really where Readcube’s benefits end. The enhanced PDF viewing feature is nice (it shows all the reference in the sidebar), but not really worth the slow-down in scrolling performance. The program is just clunky still. (I thought Adobe was slow!) And there’s no iOS/Android app yet. It’s on its way, allegedly, but I need it now! Readcube is really taking off, so maybe in a year it will be perfect. But not yet.

Edit: Readcube has a new version of their desktop application. Maybe it’s faster? Wait, did the references sidebar disappear? No, wait, it’s there. Just not on by default.

2013 Nobel predictions

September 26, 2013 at 10:46 am | | nobel

The Curious Wavefunction, Thompson-Reuters, ChemBark, and In the Pipeline have all started making Nobel Prize predictions for 2013. Last year, I correctly predicted Kobilka for GPCRs. In 2010, I got Heck and Suzuki. (You can find my previous predictions here: 2012, 2011, 2010, all Nobel posts.) Here’s this year’s stab at it…

Chemistry

Moerner and Orrit for single-molecule spectroscopy. Zare could easily be #3. Now that single-molecule imaging is effectively a routine tool in biophysics and single-molecule superresolution techniques like PALM/STORM are all the rage, it’s high time for a prize for this science. [FULL DISCLOSURE: I did my PhD with Moerner.]

Kris Matyjaszewski and Jean Frechet for polymer synthesis. Frechet invented chemically-amplified photoresists and developed dendrimer synthesis. Matyjaszewski was awarded the 2011 Wolf Prize. (Of course, others were involved in both discoveries.)

Al Bard and Harry Gray for bioinorganic chemistry and electron transfer. Both won Wolf prizes in the last decade.

Medicine

Gero Hütter for curing AIDS. Once.

Art Horwich & Franz-Ulrich Hartl for chaperonins. Unlikely a chemistry Prize, because GPCR won last year, and they probably won’t do another biomolecule this year. They won the 2011 Lasker Prize.

Ron ValeJim Spudich, and Mike Sheetz for biomolecular motors. Remember, they won the 2012 Lasker Prize! Maybe a chemistry prize, but same issue as with Horwich and Hartl above.

Carl Djerassi for the Pill. Unlikely, because they gave a prize for test-tube babies a couple years ago, and that would have been a perfect time to include Carl.

Jim AllisonEllis Reinherz, John Kappler, and Philippa Marrack for the discovery of the T-cell receptor. Oops, that’s too many people. Might not happen for that reason.

Physics

John Pendry and Steve Harris for cloaking and nonlinear optics.

Peter Higgs for that boson.

Peace

Bill and Malinda Gates Foundation for malaria and vaccine work.

George W. Bush for PEPFAR funding in Africa, now that AIDS rates in children are lower.

readcube and deepdyve update

June 6, 2013 at 7:48 am | | literature, science community, software

I just wanted to reiterate how great the ReadCube recommendations are. I imported all my PDFs and now check the recommendations every day. I often find great papers (and then later find them popping up in my RSS feeds).

Also, I wanted to let folks know that DeepDyve, the article rental site, is now allowing free 5-min rental of journal articles. Try it out!

block?

April 29, 2013 at 9:15 am | | science and the public

Sidewalk infographic fail.

2013-03-22 14.55.14

You think Stanford would know how to spell Felix Bloch’s name.

PubReader review

April 14, 2013 at 7:52 pm | | literature, software

I’ve reviewed several PDF reader/organizers, like ReadCube, Papers, and Mendeley. Currently, I use Papers for organizing my PDF library on my computer. I also like Papers a lot for reading PDFs, because it displays in full screen so well. But I’ve started using Mendeley for adding citations to Word documents, because it makes it really easy to collaborate with other people who have Mendeley.

Now check out PubReader! It’s really cool. Pubmed has the advantage that it requires all research publications resulting from NIH funding to be uploaded to their depository. And they don’t just grab a PDF; they get the raw text and figures and they format it their own way. I used to think that was silly and overkill, but now I see that that approach was genius: it now allows Pubmed to reformat the papers into more readable shapes and sizes … and they can reformat in the future when the old format becomes antiquated. You can’t really do that with a PDF.

It’s always been nearly impossible to read PDFs on a phone or an e-ink tablet like the basic Kindle. Now, with PubReader and the beta option to download the article in an ePub format (for reading in iBooks or Kindle or something), that option is here. Or on its way, at least.

PubReader on a computer:

pubreader

PubReader on iPad:

pubreader on ipad

ePub in iBooks:

ebook epub

Now PubReader just needs to display the references in an elegant way like ReadCube, and it will be the best!

It makes me think the future of reading and storing scientific papers is not the hard drive, but simply reading on online depositories. Pubmed allows you to create collection and star favorites, so you can just use Pubmed to store your collection of papers and never have to download a PDF again in your life!

readcube review

April 10, 2013 at 11:45 am | | literature, software

I recently tried Readcube, which is a PDF reader and organizer. I did so because Nature has been using it built into their site, and I like how it displaying PDFs. The article data downloads seamlessly for most papers, and  interface is quite beautiful:

readcube1

The really cool feature is that Readcube automatically downloads the references and the supporting information documents and can display them at a click of a button. More importantly, it displays the references in the sidebar. It makes an excellent reading experience!

readcube2 readcube3

The final interesting feature is that Readcube offers recommendations based on your library. From my quick scan, the recommendations seem pretty good.

Other than that, Readcube is quite feature poor. It doesn’t have a way to insert citations into a Word document, like Papers and Mendeley does, although you can export to Endnote. I don’t see a way to read in full screen nor does it let you view two pages simultaneously, like Papers does.

papers fullscreen

The screenshot above is from Papers fullscreen view, which is how I really like to read PDFs.

But Readcube is still in beta, and they’re starting from a really nice starting point. I’m not ready to give up on Papers for reading (and I’ve been using Mendeley for Word citations, because it has really nice collaborative features). But I might try Readcube some more, mainly because of the awesome ability to see all the references and the paper simultaneously. I really wish I could mash Papers, Mendeley, and Readcube all together into one feature-rich program…

ActiveView PDF

April 10, 2013 at 10:38 am | | everyday science, literature, news

Does anyone else love ACS’s ActiveView PDF viewer for reading PDFs and seeing reference? And Nature’s ReadCube, too. Great stuff.

Of course, after I scan the ActiveView, I still download the old-fashioned PDF and use Papers (or Mendeley) to read and manage my library.

google reader alternatives

April 3, 2013 at 8:12 am | | everyday science, literature, science community, software

Now that Google Reader is going the way of the dodo Google Gears, how am I going to keep up with the literature?!? I read RSS feeds of many journal table of contents, because it’s one of the best ways to keep up with all the articles out there (and see the awesome TOC art). So what am I to do?

There are many RSS readers out there (one of my favorites was Feeddler for iOS), but the real problem is syncing! Google servers took care of all the syncing when I read RSS feeds on my phone and then want to continue reading at home on my computer. The RSS readers out there are simply pretty faces on top of Google Reader’s guts.

But now those RSS programs are scrambling to build their own syncing databases. Feedly, one of the frontrunners to come out of the Google Reader retirement, claims that their project Normandy will take care of everything seamlessly. Reeder, another very popular reader, also claims that syncing will continue, probably using Feedbin. Feeddler also says they’re not going away, but with no details. After July 1, we’ll see how many of these programs actually work!

So what am I doing? I’ve tried Feedly and really like how pretty it is and easy it is to use. The real problem with Feedly is that its designed for beauty, not necessarily utility. For instance look how pretty it displays on my iPad:

feedly

But note that its hard to distinguish the journal from the authors and the abstract. And it doesn’t show the full TOC image. Feedly might be faster (you can swipe to move to the next articles), but you may not get as much full information in your brain and might miss articles that might actually interest you.

Here’s Reeder, which displays the title, journal, authors, and TOC art all differently, making it easy to quickly scan each  article:

reeder

 

And Feeddler:

feeddler

I love that Feeddler lets me put the navigation arrow on the bottom right or left, and that it displays a lot of information in nice formatting for each entry. That way, I can quickly flip through many articles and get the full information. The major problem is that it doesn’t have a Mac or PC version, so you’ll be stuck on your phone.

I think I’ll drop Feeddler and keep demoing Reedler and Feedly until July 1 rolls around.

are fuel economy gauges doing math wrong?

March 26, 2013 at 3:27 pm | | stupid technology

A few years ago, there was a piece in Science magazine about how we should all be using GPM instead of MPG. Here’s a link to my post about it back then. The main point is that the relevant unit for fuel use should be fuel divided by distance, and than MPG is inverse, which is harder wrap our puny brains around.

Back then, I looked into how fleet fuel economy averages were calculated, because I was worried that one single crazy-high MPG model could artificially skew the average high without actually making the fleet more fuel efficient. It turns out that the US requires automakers to calculate their fleet average fuel economy the correct way: convert each model’s economy to GPM, find the mean, then take the inverse again. Phew.


(not my car)

But now I wonder if the computer programmers at the automakers know how to calculate an average. My computer fuel gauge is always inflated compared to what I calculate from the fuel pump amount and odometer reading. Every time. And I’m not alone. So, either the gas stations are messing with their pump readings, or the average MPG on my dash is miscalculated. I wonder if the computer just takes a continuous average of the measured MPG values, which would definitely result in an inflated number at the end of a gas tank. (That’s because 10 miles of driving at 35 MPG after 10 miles at 25 MPG does not average to 20 miles at 30 MPG. It’s actually 29 MPG.*) If the computer just averages the MPG numbers, it will be 2% inflated from the actual value. That inflation would get worse if you drive down a hill for a mile and go 50 MPG, then back up that hill and drop down to 10 MPG: instead of an average of 30 MPG, the true average is only 17 MPG!

Of course, if the computer just takes the total miles driven and divides by the total gallons of fuel used (since the reset), than the average would be calculated correctly. But is that what’s happening?

Does anyone know anyone who works at an automaker who can check how they do the math?

 

* Here’s my math. Driving 10 miles at 25 MPG uses 0.4 gal of fuel. Driving 10 miles at 35 MPG uses around 0.29 gal of fuel. That’s 20 miles driven and 0.69 gal fuel used, or 29 MPG. Not 30 MPG. For the hill example, down the hill uses 0.02 gal for the mile, and up uses 0.1 gal. That’s 2 miles and 0.12 gal, or 16.7 MPG.

great chemophobia article in Slate

February 11, 2013 at 10:02 am | | pseudoscience, science and the public

I’ve argued in the past that the Precautionary Principle is logically flawed, even dangerous. A recent article on Slate gives a great job giving an example of when the Precautionary Principle goes bad. In response to a NYT article on alternative medicine, the Slate article compares the FDA-approved drugs to the alternative medicine that a mother is more comfortable giving her son. (Surprise! the alternative medicine also contains chemicals.)

The reality is this. [The NYT author] has been tricked by the language, maliciously or not, into considering switching her child from a carefully measured weekly dose of this molecule:

Chemical structure of four marvels.

To four doses a day of an unknown amount of this chemical:

Chemical structure of a drug.

Really?

I want to be absolutely clear. Neither of these chemicals is benign or nontoxic. The LD-50 (the “lethal dose” amount that kills 50 percent of mice fed the chemical) is about the same for quercetin as it is for methotrexate, roughly 150 milligrams per kilogram of body weight.

Berberine, one of the drugs found in four-marvels powder, has been documented to cause brain damage in infants. Hello? Exactly how much of this have you been giving your son?

[The NYT author's] “better the molecule I don’t know, than the molecule I do” stance may help her sleep better, but it is ignorance nonetheless. The chemicals are still there, even when you squint your eyes closed so you can’t see them.

This is really scary to me, that parents are giving their children unknown doses of potentially dangerous drugs. This is exactly the danger of the Precautionary Principle: people seem more comfortable with unknown dangers than known and carefully quantified risks. That’s a silly approach to risk, but I think it might just be how our brains work. And knowing that, we should be careful to guard against it.

Another concern not mentioned in either the Slate or NYT article is the drug interactions when taking a prescribed medicine with unknown alternative drugs: because they aren’t tested, alternative medicines have the potential for devastating interactions. The FDA should require at least safety testing (if not efficacy) of all medicines, both modern-medicine and alternative. NIH has an alternative medicines institute, but I wonder how quickly they can test all the options out there.

I want to also add that I completely understand the NYT mother’s concern about giving her son drugs every day. And I completely agree with the mom’s effort to find diet changes that help: the body is a complicated network, and diet can have a huge effect on health. And the immune system is in some senses a black box that we’re only beginning to understand. A variety of alternative treatments and diet changes should be tried, but eating a bunch of unknown chemicals because they have prettier names is really concerning.

I really feel for the boy and his mom, and I wish there was a magic wand to take away his pain. But even if there were, we should probably ask about the side effects of the wand.

no ensemble averaging

February 7, 2013 at 12:24 pm | | nerd

I’ve been making these nerdy CafePress products for many years. The most “popular” idea I came up with was a pin that denounced ensemble averaging in favor of single-molecule spectroscopy. (At some point in 2006, I saw random science folks wearing my buttons and they claimed that someone their lab made them, so I added the copyright. But I’m more than happy to have other people “borrow” the design.)

newnoEA_copyright sms-bio

For the 2010 Single-Molecule Approaches to Biology Gordon Conference, we made a slightly different design and W.E. handed them out to attendees.

I used to own a car with several of these bumper stickers on it, and I thought I was a super-nerd. Well, I’ve been way out-nerded: a friend (Jan Lipfert via Adam Cohen) emailed me these photos from BPS in Philly.

no ea car1no ea car2

That really cracked me up! Does anyone know who this super-nerd is?

So, to keep up with the times, I’m creating a new product. It celebrates the state-of-the-art efforts to break the diffraction limit of light microscopy.

no lambda over 2na

I’m inspired to detail my car, but I don’t think my wife would appreciate it.

Update: It’s Yale E. Goldman. Apparently, he needed to cover a big scratch! Best. Reason. Ever. A tractor trailer veered into his lane and the wheel scrapped away his paint. He sent me this before-and-after:

no ea car3 no ea car4

laser pointer and a fluorescent lanyard

January 8, 2013 at 8:24 pm | | nerd

This is one of the coolest things I’ve seen all year! I have a habit of shining my 405 nm laser pointer at fun things. But I was really surprised when I donned my safety goggles and the beam hit this Chroma lanyard:

Wow! I think what’s happening is that the fibers are acting as light guides—like fiber optics. So you see the fluorescence travel along the fibers, which are weaved diagonally up along the strap, over the edge, then diagonally back down. Super cool. Chroma should use this for marketing.

urine biophysics

October 17, 2012 at 1:50 pm | | literature

The Shape of the Urine Stream — From Biophysics to Diagnostics.

Definitely an Ig Nobel contender.

lion hunter?

October 11, 2012 at 1:16 pm | | nerd

What are the chances that the only person cc’d on this email would be “LHunter”?

Also, anyone wanna go get coffee? I know a shortcut through the woods. Here, put this antler hat on.

2012 nobel in chemistry: Kobilka and Lefkowitz

October 10, 2012 at 9:52 am | | news, nobel

Well, I predicted G-protein coupled receptors (GPCRs) and Brian Kobilka, but not Robert Lefkowitz. Congrats to both!

GPCRs are cell-surface receptors that translate signal from an extracellular ligand to a G-protein, a molecular “switch” turned on and off by GTP. (The discovery of the G-protein was awarded the 1994 Nobel in Medicine). GPCRs are very important in a variety of signaling in the human body, and most modern drugs target GPCRs.

Kobilka and Lefkowitz first had inklings of the structure of GPCRs in the 80s, when they began isolating and purifying the β2-adrenergic receptor (βAR). They eventually realized that the protein had seven transmembrane helices; to their surprise, that hinted at a very similar structure to rhodopsin—the component in the eye responsible for detecting light—another GPCR. This discovery implied that all the receptors that couple to G-proteins might have a conserved structure! Over the last few decades, Kobilka, Lefkowitz, and others have produced a bunch of structures for GPCRs, which should aid in future drug design.

I think it’s fascinating is that Kobilka was a postdoc with Lefkowitz many years ago. I wonder how often it happens that both the professor and a student/postdoc share a Nobel? Of course, Kobilka has performed enough work during his independent career to earn a Nobel, but I still think it’s cool that he won the award with his former professor. I’m not sure why Stevens or Palczewski were not also included in the prize, but it seems that the committee (given only three available slots, of course) stuck to the early discoveries that lead to the GPCR structures.

And I must discuss the concern from many corners that this is not “chemistry.” Why did it not win the medicine prize, instead? Well, I don’t know. It certainly could have won the prize in the medicine category, because of GPCR’s huge role in medicine! But the Nobel Committee seems to often place protein structures into the chemistry category [Update: see this great history]. I think that is reasonable: the task of isolating, purifying, crystallizing, and determining the structure of a protein is basically biochemistry, not medicine. And many of the individuals in the lab performing the tasks are probably chemists and biochemists. Maybe the lab isn’t located in a chemistry building, but neither is the lab that I work in, and I am certainly a chemist performing chemistry. (Well, right now I’m blogging.) I continue to think that these type of discoveries being labeled “chemistry” is great for the field of chemistry. Maybe I feel this way because I don’t perform “traditional” chemistry synthesizing small organic molecules. My research has spanned polymer physics, spectroscopy, optics, and cell biology. But I have applied my skills and knowledge of a physical chemist to all those sciences. As I said in my interview with Slate.com (where I did not predict GPCRs):

The line between chemistry and other fields (especially biology) is often blurred, and that’s a wonderful thing; but this fact sometimes results in a chemistry Nobel Prize being awarded for a decidedly biological discovery (like the 2009 prize for the structure of the ribosome). This may be exacerbated by the fact that the physiology or medicine prize tends to go to things directly related to health, and the chemistry prize often is used to cover the more basic biological science feats. Personally, I think it is a testament to the central position the field of chemistry holds in the Venn diagram of science.

Biology is the next frontier for the physical sciences! There is so much to learn about how biomolecule, cells, and organisms work. Let’s embrace biology’s commingling with chemistry with all our hearts!

You can read more about GPCRs here:

http://www.nature.com/news/2011/110824/full/476387a.html

http://cen.acs.org/articles/89/i11/Picture-Pill.html

http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2012/advanced-chemistryprize2012.pdf

http://cen.acs.org/articles/90/web/2012/10/Robert-Lefkowitz-Brian-Kobilka-Share.html

http://blogs.scientificamerican.com/the-curious-wavefunction/2012/10/10/
g-protein-coupled-receptors-gpcrs-win-2012-nobel-prize-in-chemistry/

Other bloggy commentary here:

http://blog.chembark.com/2012/10/09/liveblogging-the-2012-nobel-prize-in-chemistry/

http://www.coronene.com/blog/?p=1569

http://wavefunction.fieldofscience.com/2012/10/gpcrs-win-2012-nobel-prize-in-chemistry.html

http://wavefunction.fieldofscience.com/2012/10/crystallography-chemistry-and-nobel.html

http://pipeline.corante.com/archives/2012/10/10/
the_2012_nobel_in_chemistry_yes_chemistry.php

http://cenblog.org/terra-sigillata/2012/10/10/lefkowitz-and-kobilka-win-2012-chemistry-nobel-for-gpcrs/

slate

October 3, 2012 at 2:39 pm | | news, nobel, science and the public, science community

Paul and I were interviewed for a Slate.com article about Nobel Prize predictions. More details back at my original post on the 2012 Prize.

the precautionary principle is flawed

October 1, 2012 at 10:28 am | | news, science and the public

I’ve always warned against the Precautionary Principle, mainly because it has a fatal flaw: no one applies the same principle to the alternatives. The Precautionary Principle assumes a product (or medicine or technology) is harmful until it is proven to be safe, instead of the other way around. This sounds nice, but the problem is that it doesn’t take into account the dangers of the alternative products (or medicines or technologies). That is, at least how most consumers apply the principle.

I warned against this when the BPA kerfuffle emerged. Many people started to get concerned about bisphenol A, which is a monomer for polycarbonate used in many plastic bottles. Some BPA can leach from the plastic into food or liquids, and there has been some evidence that it may mimic hormones in the human body and may have negative health effects especially in children. So everyone started banning BPA bottles and switching to other materials. The main alternative is “BPA-free” plastics. When this happened, I asked, “But what are those plastics made of??”

Basically, everyone switched over from a known product (polycarbonate) that might have some deleterious effects, to a proprietary polymer (Eastman’s Tritan) that we knew nothing about. And everyone felt safe.

But what if Tritan is a thousand times more dangerous? What if the glass bottles that some people switched to leaches lead (although I doubt many parents are giving their kids crystal to drink out of)? What if those steel water bottles put chromium into your water? (The aluminum ones like Sigg are coated with a plastic, anyway.) It doesn’t really make tons of sense to throw away your old water bottles to buy brand new ones that have a new, proprietary plastic that can leach new, unknown chemicals into your water.

C&E News has a story about Eastman’s Tritan and it’s possible health dangers. We should all throw away our new water bottles and start drinking out of another unknown material so another company can make billions off of our fears. Or just start drinking directly from the faucet.

The only correct application of the Precautionary Principle is to have someone measure the safety of all the materials used to make water bottles and baby sippy cups and weigh the dangers against each other. Maybe Eastman should pay for that. ;)

(That said, I must admit that I drink out of glass, a coffee mug made in China, and a steel water bottle. Who knows what I have in my body.)

Thanks for the tip, Chemjobber.

2012 nobel prize predictions

September 10, 2012 at 1:35 pm | | nobel, science community

It’s time again for my annual blog post Nobel Prize predictions. This year I’m limiting to the chemistry prizes. Of course there are many more individuals and discoveries that should be listed below and even more who deserve a Nobel Prize!

 

Single-Molecule Spectroscopy

Moerner, Orrit

Single-molecule imaging has matured to an important technique in biophysics. Just go to a Biophysical Society meeting and see all the talks and posters with “single molecule” in the title! Single-molecule techniques have begun to answer biological questions that would be obscured in traditional imaging. Moreover, super-resolution techniques such as PALM and STORM rely directly on detecting single molecules and the spectroscopic techniques developed in the late 80s and 90s. W.E. Moerner won the 2008 Wolf Prize in Chemistry.

 

Electrochemistry/Bioinorganic Electron Transfer

Bard, Gray

Al Bard won the 2008 Wolf Prize in Chemistry; Harry Gray won it in 2004.

 

Polymer Synthesis

Matyjaszewski, Frechet

Jean Frechet invented chemically-amplified photoresists and developed dendrimer synthesis. Kris Matyjaszewski won the 2011 Wolf Prize in Chemistry for ATRP polymerization. Of course, others were involved in both discoveries.

 

GPCR Structure

Kobilka, Stevens, and Palczewski

Biomolecule structures have won chemistry Nobels in the past, so I’m including G-protein coupled receptors here. A lot of buzz in the last couple years about GPCRs and Nobel. Good article here.

Update 10/10/12: Kobilka wins.

 

Chaperonins

Horwich, Hartl

Although these are biological molecules, they are still molecules. And many Chemistry Nobels have gone to bio-related discoveries in the last couple decades. Both won the Lasker Award in 2011.

 

Biomolecular Motors

Vale, Spudich, Sheetz

Another bio subject, but you really never know with the Chemistry prize. All three just won the Lasker Award this year.

 

(BTW, check out other predictions at ChemBark and The Curious Wavefunction and Thompson. And my prior predictions.)

(P.S. W.E. Moerner was my PhD advisor. Also, I worked in a collaboration with Kris Matyjaszewski when I was an undergrad.)

Update 9/11/12: I added chaperonins and biomolecular motors because I figure this year’s Chemistry Nobel might be more biological.

Update 10/3/12: Paul and I were interviewed for a Slate.com piece on Nobel Prize predictions. I like Paul’s section, especially about Djerassi. Anyway, here is what I said:

The line between chemistry and other fields (especially biology) is often blurred, and that’s a wonderful thing; but this fact sometimes results in a chemistry Nobel Prize being awarded for a decidedly biological discovery (like the 2009 prize for the structure of the ribosome). This may be exacerbated by the fact that the physiology or medicine prize tends to go to things directly related to health, and the chemistry prize often is used to cover the more basic biological science feats. Personally, I think it is a testament to the central position the field of chemistry holds in the Venn diagram of science.

My top prediction is for single-molecule spectroscopy. In 1989, W.E. Moerner at IBM (now at Stanford) was the first to use light (lasers) to perform measurements on single molecules. Before this, millions or trillions of molecules or more were measured together to detect an average signal. His amazingly difficult feat required ultrasensitive detection techniques, perfect samples, and temperatures just above absolute zero! A year later, Michel Orrit in France observed the fluorescent photons from a single molecule. With those early experiments, Moerner and others laid the experimental groundwork for imaging single molecules.

Single-molecule spectroscopy and imaging has become a subfield unto itself. I performed my Ph.D. research in the Moerner lab, and I know firsthand that the technique reveals events that would otherwise be hidden in averages of “bulk” measurements. Biophysics, the field of understanding how cells and biomolecules operate on a physical level, is particularly aided because rare events can have major effects in biology. (Think of a single cell mutating and then dividing into a tumor.) For example, Sunney Xie at the Pacific Northwest National Laboratory (now at Harvard) performed the early work on how individual enzymes experience multiple states, which otherwise would be averaged away in a bulk experiment. More recently, imaging single molecules has been instrumental in novel “super-resolution” techniques that reveal structures in cells at tenfold higher resolution than ever available before. Several companies (Pacific Biosciences, Helicos, Illumina, Life Technologies) have either released or are developing products that use single-molecule imaging to sequence individual strands of DNA. My prediction is bolstered by others along the same vein. In 2008, Moerner won the Wolf Prize in Chemistry, which is often considered a harbinger for the Nobel. More importantly, The Simpsons were betting on Moerner in 2010. Of course, that was Milhouse’s prediction, and maybe it’s more reasonable to go with Lisa.

My other prediction is for biomolecular motors (aka molecular motors). These are proteins in cells that move important cargo around, and on a more practical level, make muscles contract. Ron Vale (now at University of California, San Francisco) and Michael Sheetz (now at Columbia) discovered kinesin, a protein that walks along tiny tubes and pulls cargo to different parts of the cell. This is supremely important because it would take far too long (months in some cases) for diffusion alone to bring nutrients and signaling molecules to all parts of the cell. (Interestingly, kinesin was discovered from the neurons of squids because they are extraordinarily long cells!) Jim Spudich (at Stanford), Sheetz, Vale, and others have developed many important techniques for studying the actions of these tiny machines. Spudich shared this year’s Lasker Award, which many see portending a Nobel, with Vale and Sheetz.

It’s hard not to allow hope to creep into almost anything we humans do, and I have clearly failed to prevent my own desires from influencing my predictions: I would be thrilled to see either of the above discoveries—or any that I list on my blog—win a prize. But there are many, many deserving scientists who have discovered amazing things and helped millions of people. Unfortunately, only a handful of these amazing individuals will be awarded the ultimate recognition in science. So it goes.

DIY spectrometer

August 30, 2012 at 1:44 pm | | hardware, science@home, wild web

A Kickstarter project is aiming to make a kit for simple DIY spectroscopy. For spectra-nerds, this is pretty cool.

(Hat tip Austin.)

Atoms and Molecules – A Child’s Guide to Chemistry

June 27, 2012 at 2:22 pm | | literature, science and the public, teaching

My labmate wrote a chemistry book for children … and his daughter did the illustrations. It succinctly describes atoms, orbitals, bonding, molecules, and biomolecules.

I highly recommend it.

the matrix begins

June 27, 2012 at 10:56 am | | literature

Implanted Biofuel Cell Operating in a Living Snail.”

Implantable biofuel cells have been suggested [BY MACHINES] as sustainable micropower sources operating in living organisms, but such bioelectronic systems are still exotic and very challenging to design.

One thing I never understood about the Matrix was how the machines were getting more power in electricity out of the human farms than they had to put in as food. Don’t the machines know the three laws of thermodynamics? Or just the three laws of robotics?

PeerJ

June 8, 2012 at 9:39 am | | literature, science and the public, science community

This is an interesting idea. PeerJ sounds like it’s going to be an open access journal, with a cheap publication fee ($99 for a lifetime membership). I wonder if it will be selective?

I’m more excited about HHMI’s new journal eLife.

walking with coffee

May 23, 2012 at 8:40 am | | literature, nerd, science@home

I love this paper: H. C. Mayer and R. Krechetnikov. Walking with coffee: Why does it spill? Phys. Rev. E 2012, 85, 046117.

In our busy lives, almost all of us have to walk with a cup of coffee. While often we spill the drink, this familiar phenomenon has never been explored systematically. Here we report on the results of an experimental study of the conditions under which coffee spills for various walking speeds and initial liquid levels in the cup. These observations are analyzed from the dynamical systems and fluid mechanics viewpoints as well as with the help of a model developed here. Particularities of the common cup sizes, the coffee properties, and the biomechanics of walking proved to be responsible for the spilling phenomenon. The studied problem represents an example of the interplay between the complex motion of a cup, due to the biomechanics of a walking individual, and the low-viscosity-liquid dynamics in it.

Genius. Here’s a great figure from the paper:

Fun stuff. It would be especially cool if they designed a new cup shape to minimize coffee oscillations.

chemicals ad campaign

May 16, 2012 at 9:41 am | | science and the public, science@home

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

May 15, 2012 at 4:05 pm | | literature

(hat tip to efdm and brsmblog.com.)

3d FtsZ

April 28, 2012 at 2:56 pm | | literature, single molecules

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

April 25, 2012 at 7:52 am | | literature, science community, scientific integrity

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

March 21, 2012 at 3:25 pm | | hardware

(Other photos here.)

An optical parametric oscillator and related optics:















Enjoy.

refocusable images of microscope and laser table

March 21, 2012 at 2:51 pm | | hardware

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 photos here.

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

SPRAIPAINT

October 26, 2011 at 4:52 pm | | literature

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

October 12, 2011 at 4:09 pm | | everyday science, lab safety

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

September 8, 2011 at 7:28 am | | news, nobel

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

ChemistryMatyjaszewski, 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

July 13, 2011 at 11:13 am | | hardware, nerd, stupid technology

Fancy electron microscope…

 

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

405 nm laser fun

May 26, 2011 at 5:39 pm | | nerd, science and the public, science@home

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

May 3, 2011 at 5:31 pm | | crazy figure contest, literature, scientific integrity

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?

April 18, 2011 at 10:06 am | | hardware, science@home

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 screwing/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 a screwing/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 screwing force from precession (on a reverse-thread on the right pedal) 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 animated figure from Wikipedia:

Animation_of_mechanical_precession

Animation of mechanical precession” by Chris ShannonOwn work. Licensed under CC BY-SA 3.0 via Wikimedia Commons.

wtf?! acs fall meeting deadline is already passed?

March 25, 2011 at 3:41 pm | | conferences, news, science community

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

March 24, 2011 at 10:49 am | | literature, science@home

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 20116(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.

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