Monday, February 25, 2013

The human machine: probing the mechanics

The previous post in this series can be found here.

This week, inspired by Shaun's most recent post covering exciting new results in cosmology, I have decided to also take a quick look at one of the fascinating recent findings of molecular biology. I hope to give some insight into how this work is done, and why it is not only intellectually interesting, but also potentially practically useful. 

What do we know?

Those of you who have been following this series for a while might remember a post that I wrote last year (biological batteries and motors) where I discuss how energy is converted from myriad chemical forms in your food into the single energy currency of the cell, ATP. The system by which this is achieved is quite beautiful, chemical energy is converted into an electrical current within the mitochondria of your cells, which is in turn converted into a current of protons. This proton current drives a motor (ATP synthase) that churns out ATP, thereby converting it back into chemical energy. I'm not going to go into the whole process again here, but if you'd like a quick refresher then just hop back to my older post here, go on - you know you want to! I don't mind waiting.

So, a key player in this whole process is the so-called respiratory complex I (or NADH dehydrogenase), which is the first link in the chain that converts electrical current into proton current. Complex I takes electrons from a molecule known as NADH, which is produced from energy in your food by a range of complex metabolic chemical reactions. It moves the electrons that it takes from NADH and sticks them onto a molecule called ubiquinone, which then moves on to the next stage in the process: the perhaps confusingly named complex III.

Tuesday, February 12, 2013

David J. Wineland: trapping ions for clocks and computers

Simon Thwaite recently completed a D.Phil. in Atomic & Laser Physics at the University of Oxford, and is currently a postdoctoral researcher at the Ludwig Maximilian University in Munich. The first part of his post series commenting on the 2012 Nobel Prize in Physics can be found here.

In this post he gives an overview of the field of trapped ions, describes two of its most important applications, and describes what goes on behind the scenes when a trapped ion interacts with a laser beam.

David J. Wineland – probing trapped atoms with light

David Wineland, an experimental physicist at the National Institute for Standards and Technology (NIST) in Boulder, Colorado, is one of the leading researchers in the field of trapped ions: that is, the study of how positively-charged ions (i.e. atoms stripped of one or more electrons) may be trapped, cooled, and manipulated.  This field shares many similarities with experiments on neutral atoms (laser cooling, for example, is just as useful for ions as it is for neutral atoms), but also has a number of significant differences. The most important difference that distinguishes ions from atoms is, obviously enough, the fact that ions have a non-zero net electrical charge. This has two very important consequences.

Trapped ions: trapping and interactions

A string of trapped ions (red dots) lined up in a Paul trap
can be imaged with a tightly-focused laser beam and CCD camera.

Image credit: Rainer Blatt experimental group, University of Innsbruck.

Applying an electric field to an ion produces a force on the ion: positive ions are drawn in the direction of the field. [In contrast, applying an electric field to a neutral atom changes the ‘shape’ of the atom slightly, since the positively-charged nucleus and negatively-charged electron cloud are drawn in opposite directions, but produces no net force.] Consequently, whereas traps for neutral atoms must rely on combinations of laser light and magnetic fields, ions can be trapped just by electric fields. Most of the recent trapped-ion experiments use some variation on the Paul trap (a.k.a. the quadrupole ion trap) which uses a combination of static (DC) and oscillating (AC) electric fields to trap ions along a 1-dimensional line.

Tuesday, February 5, 2013

The “ISW mystery” deepens considerably (II)

[... continued from yesterday]

[Note added April 29: Through correspondence with some of the authors from what I label as the "French group" below I have learned that the density threshold was actually applied in their work as well. This makes things rather confusing as it means that their methods and the methods of "the DHB" are much more similar. However, they have also updated their paper to reflect new knowledge about the void catalogues and see a slightly more significant signal, similar to what Planck find (see note below). Everything is rather confusing right now. Again, once the dust has settled, I will write a post clearing everything up.]

[Note added March 21: Wow, sometimes science moves quickly. Today Planck released its data. They appear to confirm the anomalous spots in the original "Granett" (Hawaiian) result. They also appear to confirm the new anomalous result that was present in the paper that is now retracted (see the note below from March 19), albeit with a slightly reduced significance. It is unclear exactly what is going on, but it is clear that it is something interesting. I will keep you informed as things progress.]

[Noted added March 19: The paper described in the second half of this post (I called its authors the DHB) has been withdrawn from the journal it was submitted to (see the new abstract at this link: It is unclear whether the problems that the authors found in their analysis will affect their conclusions. However, I suggest you are cautious regarding how you interpret the conclusions I have drawn below based on this paper. I will keep you informed as/when things progress.]

A really neat figure from arXiv:1301.5849 showing the locations and sizes of the various catalogues of voids being examined. A larger redshift means the void is further away from us and one Megaparsec (Mpc) corresponds to three million light years. The purple "Granett et al." box is the original catalogue used by the Hawaiian group back in 2008. 

Isn't this just "a posteriori" statistics?

There is another possible explanation for the mystery. The probability of ZOBOV picking out these lines of sight at random is exceedingly small (less than 0.003), but it isn't zero. Might this have just been a crazy fluke?

Suppose 100 different groups of physicists look for unexpected, but interesting, signals in cosmological data. Then, even if each group is very careful you still expect one of them to find something that would seem to them to be unlikely. Unfortunately, they would be the only ones to publish their results. So we wouldn't see one “detection” paper and ninety-nine papers consistent with no detection. We would just see the one “detection” paper.

The best way to determine whether this is what happened is to look for the signal in other surveys.  If the original measurement was a fluke, it won't show up anywhere else. But, if it does show up again, then the chances that it was a fluke will significantly diminish.

The Friday before last a paper appeared that did exactly this. A French group took two catalogues of voids (so no over-densities), which have been produced by applying ZOBOV to a new catalogue of galaxies (these ones are closer to us). The French group then did more or less the same thing as the Hawaiians did. They examined images of the CMB along the lines of sight of these voids, averaged the temperature in all the images and checked whether the resulting signal could have happened at random.

They found no significant result.

This was quite sobering to read on the day. The paper did verify the significance of the original measurement, but not finding it in the new catalogues was highly suggestive that the story I painted above of a sort of community wide “look elsewhere effect” was true.

Hold on though!

Things at this date in time did look bad for the anomaly, but there was one important piece missing from the French group's analysis. The Hawaiians only used the most extreme over and under-dense regions in their analysis. ZOBOV found many more than 50 regions for them and if they had used all of them, they also wouldn't have obtained a statistically significant signal. This was always a crucial part of their analysis because we already knew from other observations that the observed ISW effect from most of the universe is as small as the predicted signal.

What would the French group have seen if they had only examined the most extreme voids?

A new observation

Apparently it is a rule of thumb for observers, that the more interesting your observation is, the more boring you are meant to make your title. These guys probably deserve a promotion. The paper is here.

Three days later (last Monday) a mixture of physicists from Durham, Hawaii and Baltimore (the DHB) released a paper. It answered the question posed above. For anybody interested in finding new physics, the answer is very exciting.

Monday, February 4, 2013

The “ISW mystery” deepens considerably

Other than my initials, what secrets does the CMB hide that are waiting to be seen only when the CMB is examined in just the right way?

This time last year I wrote a few posts describing what I called the “ISW mystery” (Part I, II, III and IV). A year has passed, it is time for an update on the mystery.

The very short summary is that things are starting to get more than a little bit exciting. All of the plausible ways in which the calculation of the expected ISW signal could have been wrong have been checked and eliminated as possibilities; if the measured signal is real, it is too large for the standard cosmological model. Much, much more excitingly, the observation that generated the mystery has now been repeated in another region of the universe and a very similar and equally anomalous signal was found; the apparent anomaly was not a statistical fluke.

The preprint of the paper describing this new observation was released just a week ago.

What is the “ISW mystery”?

The image that began the mystery. Why is that spot so hot, and how did it get that cold ring around it?

A quick recap will probably be useful. The integrated Sachs-Wolfe (ISW) effect describes the heating and cooling of light as it passes through gravitational peaks and valleys late in the evolution of the universe. In the standard cosmological model, these peaks and valleys decay with time, so a light ray gains (or loses) more energy entering an over-dense (or under-dense) region of the universe than it loses (or gains) leaving it. The effect is very, very small. Almost every source of light in the universe is not known well enough to be used to detect it. Only the cosmic microwave background (CMB) is uniform enough that these tiny fluctuations could ever be detected.

However, even then, the primary fluctuations in the the temperature of the CMB are bigger than the secondary ones created by the ISW effect. We can measure these fluctuations but we could never know how much is due to the ISW effect and how much is primordial. The only thing we can do is look at the structures in the universe nearby and see if on average the CMB is slightly hotter (colder) along lines of sight where the nearby universe is over-dense (under-dense). The bigger, primordial fluctuations in the CMB should have nothing to do with local structures (the CMB has come from much further away). Therefore, if this signal were to be found in the CMB, the most plausible explanation would be an ISW effect.

A group in Hawaii decided to look for this signal in a slightly unusual way. Firstly, they made a catalogue of significant over and under-dense regions in a particular survey of galaxies. Then, they only examined patches of the CMB that existed along the line of sight of each of these regions. They then found that the patches aligned with over-densities were hotter on average than a randomly selected patch and those aligned with under-densities were colder (with more than “\(4\sigma\)” significance). This is what one would expect from an ISW effect. The “ISW mystery” is that these patches were too hot and too cold. The ISW effect simply shouldn't be that big.

The importance of checking the anomaly from every angle