Wednesday, January 30, 2013

Quantum sense of smell?

I had been meaning to write a blog post about this for some time, and the recent news article from the BBC and post by ZapperZ inspired me. There is a debate going on in the bio literature about the physical basis for the sense of smell. The traditional idea is that the olfactory receptors in your nose rely on a combination of binding motifs, including molecular shape (think lock-and-key), to identify analytes. However, it is possible for some animals such as fruit flies to tell the difference between a molecule and a deuterated version of that molecule. Since replacing hydrogen with deuterium should not affect chemical binding mechanisms (generally), and since the shapes of the molecules are the same, this would seem to suggest that something else is going on. A new paper has shown that people can also distinguish isotopic ally labeled molecules via smell, in double blind experiments.

 

The suggested candidate is inelastic electron tunneling. As I've discussed elsewhere, electrons can traverse a molecule through a second order tunneling process, and if enough energy is available to those electrons and the microscopic couplings work out right, they can leave behind a vibrational quantum of energy. In so doing, there is a kink in the current as a function of voltage, signifying the onset of this process.

I am very skeptical that true inelastic tunneling of that type is at work in your nose. First, the natural linewidth of IETS features is several times kT. At room temperature, that is several times 26 meV. The energetic difference between, e.g., the CH and CD stretch vibrations is around 125 meV. Basically, even with a laboratory setup and far higher currents than present in biological systems, and with the benefit of phase-sensitive detection, it would be very difficult if not impossible to use IETS to resolve that isotopic difference. That doesnt even take into account the complicated nature of electronic motion in biological conditions. That being said, I suppose there could be some weird physics where that vibrational frequency makes itself known through the noise in electronic motion - I am thinking along the lines of a fluctuation-dissipation effect like this one. Any mechanism has to be robust in the presence of environmental and thermal noise, and IETS is not, in my view. Still, it's a neat mystery!

 

 

Wednesday, January 23, 2013

Why whiskey stones don't cool as well as ice.

While they sound like something you might find in the Skymall catalog, whiskey stones have been touted as a way to cool drinks without the annoyance of dilution that you get from melting ice cubes.  It's true that they don't dilute your beverage of choice, and you get to make jokes about having drinks "on the rocks".  However, for real physics reasons these stones just aren't that effective at cooling your drink down.  To see this, let's consider how much energy it takes to warm four of these stones from -40 \(^{\circ}\)C to room temperature (25 \(^{\circ}\)C).  Each stone is around 8 cm3, and granite has a density of 2.7 g/cm3, and the specific heat of granite is 0.79 J/gK.  Combining, that means that warming four of those stones to room temperature would take around 4400 J.

Now consider an equivalent volume of ice starting at 40 \(^{\circ}\)C.  Ordinary ice has a density of 0.917 g/cm3, and a specific heat of roughly 2.05 J/gK.  Warming four 8 cm3 ice cubes up to 0 \(^{\circ}\)C takes 2400 J.  However, converting ice from solid to liquid requires a latent heat, in this case 334 J/g.  So, just melting those ice cubes requires 9800 additional Joules.  Without even worrying about warming up the resulting water, the ice cubes are able to take up almost three times as much energy just by warming up to the melting point and melting.  So, while it's true that ice can dilute your beverage, it is much better at cooling things (if that's what you want to do), thanks to the latent heat, the energy required to change phases. 

A lack of understanding of specific heats and so forth is quite common.  Even the article I linked above about whiskey stones says "Another obscure advantage of whiskey stones is they freeze quickly. Granite ice cubes are ready to go after 20 to 30 minutes in the freezer, whereas water needs hours to freeze into ice cubes."  That's not an advantage - it tells you that the heat capacity of your whiskey stones is low compared to the water equivalent.

Monday, January 21, 2013

FSP's fake CV contest

Sorry about the blogging lull.  More to come soon.

In the meantime, this is hilarious, distressing, and insightful in equal portions.  I encourage you to read each one (and the comments). 

Friday, January 11, 2013

Black holes, information, and "fire walls"

It's not my area, but I always take notice when part of the physics community is abuzz about a thought experiment that seems to expose flaws in our understanding.  At issue is whether something dramatic (involving quantum gravitational effects) takes place at the event horizon of a black hole, from the point of view of an infalling observer.  Way back when I took a general relativity course, I learned that, because of the way spacetime works, the more massive the black hole, the more mild the actual curvature of spacetime at the horizon.  Tiny blackholes = tightly curved spacetime at the horizon; galactic-mass blackholes = nearly flat spacetime at the horizon.  (The horizon is the location where, in the usual Schwarzchild treatment, the sign of the metric components flips; that's another way of saying that once you cross the horizon, classically you are inevitably going to hit the singularity.  Avoiding it is mathematically as hard as avoiding next Tuesday in flat spacetime, as my professor had said.)  So, the old-school classical picture says, a freely falling observer can cross the event horizon and not even realize it.  Moreover, classically, an observer at rest relative to the black hole outside the horizon never actually sees anything cross the horizon - from such a perspective, a clock falling toward the horizon gets progressively more red-shifted and runs slower and slower, stopping altogether at the horizon after being infinitely red-shifted.

I freely admit that I don't understand Hawking radiation beyond a handwave level.  Still, I would be grateful if someone could explain to me, even more clearly than the article linked above, what the big deal is.  Arguments about entanglement across the horizon sound almost theological to me - if it's by definition impossible to check to see if measurements inside the horizon are quantum-correlated with measurements outside the horizon, then such discussions don't seem scientifically meaningful.  

Thursday, January 10, 2013

Workshop on Surface Plasmons, Metamaterials, and Catalysis

Three of my colleagues and I are helping to organize a workshop at Rice University on May 20-22, 2013.  The goal of this ARO-sponsored workshop is to explore the opportunities for chemical catalysis arising from recent advances in the fields of metamaterials and plasmonics.  The workshop will bring together scientists from the disciplines of electrochemistry, catalysis, and plasmonics, which have not traditionally had a common platform.

Topics include:
  • The state of the art in plasmonics, metamaterials, and chemical catalysis
  • Areas of catalysis that could benefit from enhanced optical/electromagnetic concepts
  • Concepts for nanophotonic- and metamaterials-driven catalysis and heat generation
  • Surface nanoengineering to merge nanophotonics and catalysis
  • Quantum plasmonics
  • Hot electrons driving chemistry
  • Chemical sensing using nanophotonic and plasmonic concepts
  • Nanophotonic characterization of catalytic structures:  Where do the reactions happen, and how fast?
The deadline for abstract submission is Feb. 14, 2013, and space is limited.  The workshop website is here:  http://PlasEnhCat2013.rice.edu  .

Please feel free to distribute this information to people that would be interested!

Saturday, January 05, 2013

Blogs as a way to deal with bad or fraudulent science

Thanks to a colleague, in addition to the controversy discussed here, I have been following closely the saga of science-fraud.org . That website, the content of which has now been taken down (but remains available through google's cache, if you know what you're doing), had been a clearing house where an anonymous primary poster (assisted by anonymous colleagues) reported on biomedical research papers that had what looked like some serious problems with image manipulation. For context, in that research area, a common tool is a Western Blot, where stained or tagged proteins are identified by the position of bands in digital images of electrophoresis gels. Because this data is basically shown in papers just as an image, it is ripe for manipulation by unscrupulous researchers with photoshop. While it might be ok to crank up the contrast, for example, it is definitely not ok to copy and paste sections of image, or erase inconvenient bands, or duplicate images from paper to paper and pretend that they are from different proteins. That site highlighted many many very suspicious images in the literature, and outright accused a number of bio researchers of fraud - the poster contacted the deans of many of these people, as well as their institutional research integrity officers and the national Office of Research Integrity.

That blogger has now been revealed as Paul Brookes, a scientist at the University of Rochester med center. His anonymity was broken when a very angry individual spammed a large number of relevant researchers with an email claiming the Brookes was responsible for that page, which the angry person (pseudonymous, ironically), claimed was a hate site. Brookes has come under serious legal threats; at issue is whether some of the posts were libelous, since they often went well beyond pointing out suspicious figures and directly accused people, in public and to their institutions and grant agencies, of deliberate research misconduct.

There are several lessons to draw from all this, as has been pointed out both by Brookes (in a post that he took down) and others.

  • There is a very serious problem with image manipulation out there in that community. It involves investigators and labs at some major places (as well as minor ones).
  • Anecdotally, it looks like some journal editors in this field are reluctant to look at this issue as closely as it needs.
  • Science-fraud.org did identify serious problems with a number of papers and prompted ORI investigations that uncovered research misconduct.
  • There does seem to be a communal need for a better means of identifying suspicious papers, and blogs could serve this role. I'm reluctant to take page views as a direct measure of that need, though - a lot of people click on articles about Kim Kardashian's pregnancy and the latest celebrity trainwrecks, but that doesn't mean that there is a need for those articles.
  • There really is no such thing as online anonymity. That's why I've never bothered to obscure my identity.
  • Do not post anything online or email anything that you would be ashamed to see on the front page of the New York Times.
  • Publicly accusing people of fraud is a serious business - it's not something that should be done without a lot of consideration of the consequences. The university's lawyers are also unlikely to protect a faculty member who makes public accusations like that without consulting them first.
  • It does make me wonder whether there are similar issues in the physical sciences on this scale.
On a related note, getting caught up on last year's news, I see that a Columbia economist involved in Freakonomics has somehow ended up with $240k in "lost" research money, and had to write a check to the university for $13k. Wow. I'm pretty sure that I would be fired if I couldn't account for $240k of research funds, and claiming that I just wasn't good at bookkeeping would be considered a laughable response.

All in all, a rather depressing roundup. Remember, it's this kind of fraud and poor behavior that just give ammunition to the anti-science parts of society.






Thursday, January 03, 2013

Ahh, poor journalism and high energy physics. Again.

Well, apparently I should just retire.  According to this article at the National Post, "Higgs boson discovery may signal the world’s last physics experiment as scientists struggle to come up with next big question". This isn't just a case of poor headline scripting by some editor. The article itself says:
What modern physics knows about the matter in the universe (better at the end of 2012 than the beginning) is that it is basically shrapnel, strange bits that endure from an ancient explosive nativity, known as the Big Bang. What Melissa Franklin knows about modern physics (likewise better than ever, or pretty much anyone) is that it is finished. Done. Kaput.
I am going to assume that this is just a case of poor journalism, and that Prof. Franklin, the chair of Harvard's physics department, does not really think that all of modern physics is encompassed by collider-based high energy work.

Wednesday, January 02, 2013

Review about quantum coherence

Happy 2013 to all!  The Proceedings of the Royal Society A has a special issue from this past fall about the issue of decoherence in quantum mechanics.  When last I looked, the content from this issue was free (!) for download.  I need to read through the rest of it, but I enjoyed Philip Stamp's article about decoherence and the possibility of intrinsic decoherence.  The point is, in ordinary quantum mechanics the state function of a quantum system evolves with time according to the Schroedinger equation, also called unitary time evolution.  However, that seems at odds with what happens when we perform measurements - in that situation, it seems like the state of the system "collapses" into an eigenstate of a measured observable, so that coherence appears to be lost, and we don't observed, e.g., Schroedinger's cat to be in a superposition of alive and dead.  The now standard treatment says that the apparent decoherence of a quantum system of interest when we "perform a measurement" results from  the coupling of the system with many environmental degrees of freedom (a "bath"), the states of which we then "trace over".  When we do this, looking only at the system, we see what looks like decoherence of the system, but the idea is that this is an approximation of the true situation, in which the whole system + environment is still obeying the Schroedinger equation.  (This skirts other aspects of the "measurement problem", like what really picks out the particular classical states that we seem to observe.)  Intrinsic decoherence would imply either that there is something genuinely wrong with unitary time evolution (i.e., quantum mechanics is incomplete), or there are environmental degrees of freedom out there in the very fabric of the universe that are impossible to avoid, such as the quantum degrees of freedom of curved spacetime itself.