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

Paul and I were interviewed for a 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 [awarded in 2014], 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.



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 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?


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

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:


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. :)


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.

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