Everyday Scientist

the simpsons have their own nobel predictions

This was on The Simpsons last night:

(the screenshot is from 1 min 22 sec on Hulu)

I may update my predictions to reflect the venerated opinions of cartoon writers.

By the way, seeing my PhD advisor and a member of my dissertation committee listed on The Simpsons feels really strange.

(My/our real predictions are here.)

i have a seminal contribution for you…

I really think this is a joke: old-man baiting, if you will.

In response to the discussion on whether the word “seminal” is sexist as well as sexual, there are two points to be made, and I would also like to offer a potential solution. First, seminal carries forward the homocentric view of scientific research from a time when males were predominant and considered more important researchers in science. Consequently, it is a sexist term unless one is talking about physiological or related dynamics.

As for seminal being seen as a sexual term, I am not sure that we should necessarily eliminate all such terminology from the dialog in science just because it refers to “sexuality.” One need only look at the extensive literature that conflates birth sex with gender. The question “What is your gender?” is incorrect unless you are doing research on gender identity. The correct question is “What is your sex?”

Many individuals incorrectly conflate the word “sex” with sexuality. Consequently, numerous scientific papers, research surveys and discussions misuse gender as an equivalent to birth sex or natal sex in response to the aforementioned difficulty.

I propose the following solution, that I have used for years. When suggesting that a particular piece of research is “seminal” simply replace the word “seminal” with the word “seminovarian.” Everyone gets equal play. Of course, we could take up the question of which should go first, but that’s another letter to the editor altogether.

Tarynn M. Witten
Richmond, VA

I mean, this is getting hilarious.

But maybe this isn’t a joke. First of all, it turns out that the first letter was serious (see “Only Males Respond“). Also, this second letter makes be think that it’s from some liberal-arts student, mostly because it is terribly written. The rambling tangent on “sex” vs. “gender” is very academic, and I can tell that the author likes using the thesaurus: what “dynamics” are related to sperm physiology? Flagellum switching?

Maybe I should be more sensitive. I don’t like the fact that females have been second-class citizens (if citizens at all) throughout our history. But when it comes down to it, sexual references are funny. And I will giggle like a middle-school boy every time.

UPDATE: Oh shit. Dr. Witten is a bio prof at VCU. Which means she probably knows a lot more about dynamics than I ever will. Oops.

2010 nobel predictions

In previous years, I’ve awarded Edsel-Nobels, which no one really cared about. Maybe this is the year I’ll make predictions for the actual Nobel. Paul at Chembark already started his predictions, and everyone else will be buzzing about it soon enough.

In no particular order (and without much forethought):

1. Solar: Grätzel
2. Super-resolution optical microscopy: Betzig [awarded in 2014], Hell [awarded in 2014], Zhuang, Hess
3. Cloaking: Pendry
4. Birth control: Djerassi
5. Laser-induced fluorescence: Zare
6. Inorganic: Gray, Lippard
7. Single-molecule spectroscopy: Moerner [awarded in 2014], Orrit, Rigler, Xie
8. Chaperonins and protein folding: Horwich, Hartl, Lindquist, Ellis
9. DNA fingerprinting: Jefferys
10. Electrochemistry: Bard, Nocera
11. Polymer synthesis: Matyjaszewski, Wang
12. NMR and membranes: McConnell
13. Discovery of kinesin: Sheetz, Vale, Brady
14. Nano: Whitesides
15. Peace: Twitter
16. Cross-coupling: Suzuki, Heck, [awarded in 2010] Sonogashira
17. Electron Transfer in DNA/Electrochemical DNA Damage Sensors: Barton, Giese, Schuster
18. Pd-catalyzed Alkyne/Alkene Coupling and Atom-Economy: Trost
19. Nuclear hormone receptors: Chambon, Evans, Jensen, O’Malley
20. Two-photon microscopy: Webb, Denk, Strickler
21. DNA microarrays: Brown
22. NLO: Harris (as predicted by The Simpsons)

So there. The only one I’m confident about is Twitter.

Please feel free to add more in the comments. I will probably continue to update this…

UPDATE: Paul now has updated odds. Very impressive. He’s put a lot more thought into this than I. I’ve added cross-coupling to the list. Additions are in italics.

UPDATE: Can you name all the Chemistry Nobel winners?

UPDATE: Thompson has released their predictions.

UPDATE: The Simpsons also have some predictions.

economic stimulus via science

Senators McCain and Coburn (who is a physician!) released a political report complaining about stupid stimulus projects. Now, it’s not surprising that Republicans are calling for cutting science funding and mocking silly-sounding science, so of course there are several science programs funded by stimulus money that this report calls out. Here are a couple:

“A Better Way to Freeze Rat DNA”

[S]cientists at the University of Missouri received stimulus funds ““to develop freezing protocols for epididymal rat sperm which would allow reconstitution of genetics by using standard artificial insemination and in-vitro fertilization methods.”” The scientists note that“ “[o]ver the last few years, our laboratory has generated ample amount of data related with optimal sperm handling.”

“Reducing Menopausal Hot Flashes Through Yoga”

“Weather Predictions for Other Planets”

“In a time when jobs are hard to come by, several high school and college students have gotten federal funding to inspire their scientific curiosity.”

OK OK, I understand that some of these seem silly, but when Senators start mocking scientific programs without acknowledging the broader context, those Senators come across as ignorant and foolish. The rat DNA one is especially annoying: Hehe, it says sperm! What, do they get middle-schoolers to write this stuff?

We could make any scientific project sounds silly if we wanted: Scientists try to send light down a tiny glass tube; federal government spending billions to develop satellites that will see where your phone is; some nut is trying to make a horseless carriage.

The point of gov’t stimulus is to get money flowing and jumpstart the economy. Most economists acknowledge that Federal spending has a significant multiplier effect, so spending money on construction projects, scientific research, and infrastructure isn’t really that silly. I can understand how some would question how studying rat DNA could make any money flow back into the economy, but those people would be forgetting about scientific-supply companies like Nalgene (originally of Rochester NY), ThermoFisher (of Waltham MA), Invitrogen (of Carlsbad CA), Sigma-Aldrich (St. Louis MO), etc. I’m sure those and many other companies that employ Americans are very happy about stimulus money going to scientific research!

Still, I do agree that these spending projects should not be beyond reproach. I’m not convinced that science funding is always the most efficient approach to stimulating a national economy in the short run. We should check up on our stimulus funding and try to measure how well each project is benefitting American taxpayers. But what McCain and Coburn have done is lazy—and ignorant. Instead of mocking science because it involves sperm or yoga (or even both), step up and take a mature approach to critiquing our spending policies!

(via Nature)

dangerous laser pointers

NIST is warning us that some cheapo green laser pointers might be unfiltered and dangerous. Some manufacturers skip installing the IR filter, thus making a laser pointer that has a high-power invisible beam along with the green light.

The “green” of green laser pointers is 532 nm, doubled frequency of the 1064 nm emission from a neodymium (e.g. Nd:YAG, Nd:YLF, or Nd:YVO4) laser. A diode (e.g. 800 nm) pumps the neodymium laser, which emits 1064 nm light; a doubling crystal produces the green 532 nm light. But the doubling crystal is not 100% efficient, so an IR filter is necessary to block the remaining 1064 nm light that isn’t doubled (as well as block the 800 nm pumping light). The plot above shows how much 1064 nm light escapes if the filter is removed: it’s much more than the green light—if the 532 nm is 20 mW, the IR might be as high as 100 mW, certainly potentially damaging to the eye!

IR is especially dangerous laser light. First, it is invisible, so it is more difficult to identify and avoid stray beams. In this case, that’s less of a worry, because the green beam coaligned is visible. However, the second reason IR is dangerous is that, because it is invisible, you can’t tell how bright it is (see below). The final reason IR is dangerous is the biology of the eye, which is transparent to IR light, and focuses it to the retina (the nerves). IR can easily burn the retina permanently (causing blindness), or burn other parts of the eye or skin.

The simple method NIST suggests we can use to test our laser pointers is described in the announcement. Basically, they use a CD as a diffraction grating and a cheap webcam. The sensor of a digital camera is sensitive to IR light, but usually has a filter to see only visible; it is simple to remove the IR filter of a cheap webcam to make an IR sensitive detector. (Unfortunately, the sensitivity cuts out before 1064 nm, so the camera can only see the 800 nm pump light). The picture above shows the diffraction of the visible light with a normal digital camera; the bottom image is using the IR webcam. You can see the extra diffraction spots from the 800 nm light. Note also how much brighter the IR light is from the laser: even though you can’t see it with your eyes, it is very bright and dangerous.

By the way, my favorite line in the NIST report is the following: “The infrared light spreads out beyond the green, which could be injurious, for example, to a cat closely chasing a spot of green light.” Actually, that’s kinda sad: I hope the NIST folks didn’t discover this problem after they blinded their pet.

TARDIS

One of my labmates attended Comic-Con last week in San Diego and decided to dress up as a TARDIS (a sort of time-machine from Dr. Who) in what can only be described as an epically awesome costume.

While there is a side-on photo of her with writer/director Joss Whedon (Firefly, Serenity, Buffy the Vampire Slayer, the Avengers, etc.) that’s been circulating on Twitter, below is an EXCLUSIVE photo from her own camera.

In addition to attracting the attention of the famous and powerful, she also managed to attract the very sketchy. Link

Creatine, a popular sports supplement

Creatine, a small-molecule found naturally in red meat (and biosynthesized in our bodies), is a popular supplement for weight lifters. To understand how it works, one needs to know that ATP (adenosine triphosphate) is the body’s energy molecule.  It gives muscles the energy they need to function, but in the process, it loses a phosphate group and is converted to ADP (adenosine diphosphate).

Creatine monophosphate has the ability to convert this low-energy ADP molecule back into the super-charged ATP molecule that muscles crave.

Creatine monophosphate

As a consequence, lifters that supplement with creatine can do more reps, which can lead to better results in the gym on a shorter timescale.  Creatine supplementation also has the effect of increasing water volume in the muscles, causing them to swell and look bigger; this effect subsides quickly once creatine supplementation is stopped.

It is well known that consumption of simple sugars with creatine increases creatine absorption.  When you consume sugar, your blood-sugar level increases, and your body releases insulin in response (assuming you don’t have type 1 diabetes).  Insulin instructs the cells to take up sugar from the bloodstream.  Insulin also has the nice effect of stimulating creatine transporters, which transport creatine from the blood into cells.

Now that the background is finished…

I was at GNC yesterday buying some creatine.  I looked at the ingredients on the GNC-brand creatine and gasped.  Creatine and sucralose!?!?!?!  Sucralose???  OK- a little more background.  Sucralose is a zero-carbohydrate, synthetic, sugar mimic.  As you can see below, it looks a lot like sucrose, only it has some chlorine groups that basically make it unrecognizable by the body’s enzymes.  So your tongue recognizes it, but your waistline doesn’t because it’s not metabolized.

“Sucralose”

Sucrose

Now to the remarkable part.  Sucralose has no effect on the blood sugar level. So this GNC-brand product that I bought containing 17% sucralose/83% creatine is ridiculous.  Uninformed weightlifters don’t want “sugar” calories so the industry introduces 1 g calorie-free sucralose per 5 g creatine, which has no effect on creatine uptake and actually tastes quite disgusting (sucralose is 600x sweeter than sucrose, which is regular sugar).

So who is the bigger idiot?

Inappropriate Labware

We have these Al bases floating all over the place.  I guess when Stanford sanitized their mascot, we never got around to PCing our opto-mechanics.

cleaning-chemicals industry takes on the final frontier…

…invisible stains. Finally, there are cleaners on the market that can clean up stains that are undetectable by any of the human senses.

Have you seen that commercial for a toilet-bowl cleaner? They say, “Bleach only hides stains.” Then they pour some purple stuff on the ceramic to reveal the hidden “stains.”

Um, what? Isn’t hiding a stain mean you get rid of the stain? By definition? I think it’s nuts that the cleaning-chemicals industry is inventing the problem of invisible stains. I have a solution to this problem: don’t pour that purple stuff in your toilet!

And then there are those “chemical residues” that watch you shower. The invisible, undetectable residues. How do we know that invisible residues are there at all? The TV tells us that they are there, of course. But wait, how do we know that the alternative cleaner doesn’t leave an invisible residue?

All this reminds me of the Emperor’s New Clothes. Or, more aptly, that old joke about the elephant repellant (“You don’t see any elephants around here do you? It must be working, then!”) People need to ignore these silly commercials and relax a little bit about cleaning. Just scrub the toilet bowl every week or two with a brush, then wipe the seat etc. with diluted bleach and be done with it! Jeez!

temperatures infograph

A graphic designer emailed me this cool “infotaining charticle” she made:

Cool. (get it?)

Although she did forget to include the temperature of my cold heart.

liquid oxygen

Not a good idea:

I don’t think putting liquid oxygen on your tongue is so smart. Fortunately, it’s not really liquid O2, it’s just salt water:

“The chemical components in Liquid Oxygen are distilled water, sodium chloride, dissolved oxygen and essential and trace minerals. The species of oxygen found in Liquid Oxygen include O2, and O4. The active ingredient in Liquid Oxygen is a relatively stable nascent molecule of oxygen in the form of O4. All other oxygen type supplements bond their active oxygen to salt molecules forming oxychlorine or oxy-halogen compounds driving up the pH to levels that could be dangerous to the skin and delicate membranes in the oral cavity if taken improperly. In addition, additional stomach acid activity is required to break these molecules down to release the oxygen.”

Huh?

evidence-based medicine

What is the greatest medical invention of all time? Bob Park says that it was the double-blind study. That may be an exaggeration, but I think we all can agree that applying scientific, fact-based methods to healthcare sounds like a good thing.

But many people don’t like science. The GOP and others are all upset that it turns out that maybe too many tests (mammograms, prostate exams, and pap smears) actually cause harm to patients. Sorry, ’bout that. I know you look forward to having fingers shoved up your ass every year, but it might do you better to get that test every other year.

(Al Gore should make a new movie about evidence-based medicine and call it A Convenient Truth.)

Here’s a good NPR news story about it. Slate has a great analysis, encouraging journalists to actually report facts. Interesting stuff.

UPDATE: Quoting from the Slate article:

So consider the actual numbers: For the average 40-year-old woman, annual mammography for a decade increases one’s overall chance of breast cancer survival from roughly 99.7 percent to 99.8 percent. That is, it increases the final batting average by only 0.001. According to the National Cancer Institute, there’s also a downside. During this time, half of all screened women will have at least one suspicious mammogram, and one-quarter of them will end up getting a biopsy. Mammograms in women from 40 to 50 years old cause a huge number of false positives, resulting in about 100 biopsies for every life saved. Even more worrisome: It’s possible the radiation from those mammograms may end up causing more cancers than they prevent.

ribosomes are cool

There’s a lot of complaining on the chem blogosphere and in chemistry departments around the world about this year’s Nobel Prize in Chemistry. What? Going to biologist again!?!?

Personally, I don’t find this year’s chemistry prize at all offensive. We chemists love to tout chemistry as the nexus of all fields of science, from physics to biology. So we shouldn’t be too upset when researchers outside our personal subfield wins a chemistry prize.

Moreover, the chemistry Prize has always been awarded a range of experiments. (Think nuclear physics in the early part of the 20th century.) Biology is today a maturing field with amazing breakthroughs daily, so it’s not surprising that biological chemistry wins prizes.

And ribosomes are very cool.

what do CCDs and optical fibers have in common?

Answer: they’re both super important. (And they both won this year’s Nobel Prize in Physics.)

Upon hearing this prize announcement, just about everyone I know thought, Yup, those are important. Some people also thought, Why are they sharing the same prize? And at least one person thought, How did they shoot live video before the CCD?

They used basically a reverse television, the pickup tube:

Get it?

energy flow charts

Here are some cool energy flow charts:

(source: LLNL and Whitesides review)

(source: GCEP)