Proton is Smaller Than Previously Thought

Did someone mess up physics? The size of proton, long thought to be understood, turns out to be wrong according to new research:

Speaking [...] at the April meeting of the American Physical Society, researchers said they need more data to understand why new measurements of proton size don't match old ones.

"The discrepancy is rather severe," said Randolf Pohl, a scientist at the Max Planck Institute of Quantum Optics. The question, Pohl and his colleagues said, is whether the explanation is a boring one — someone messed up the measurements — or something that will generate new physics theories. [...]

The proton is a positively charged particle in the nucleus of atoms, the building blocks of everything. Years of measurements pegged the proton at 0.8768 femtometers in radius (a femtometer is a millionth of a billionth of a meter).

But a new method used in 2009 found a different measurement: 0.84087 femtometers, a 4 percent difference in radius.

LiveScience has the report: Link

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My guess (or bet...) would be that it is a mistake in the calculations involved in getting the result from the measurements. The result depends on the charge distribution within a proton, which is not a point particle due to the three quarks it is composed on, and the occasional other interloper and gluon holding them together. Calculations involving just electrons and EM fields tend to be incredibly accurate using quantum electrodynamics, and there has been a lot of success with that theory. Unfortunately, the way the universe is, makes the equivalent involving quarks, quantum chromodynamics, much more difficult to mathematically compute. Getting accurate enough QED results is just a matter of having a large enough army of graduate students to work out smaller and smaller corrections, while getting accurate results with QCD takes a bit more forethought and is still being worked on. It seems possible there is room from "old physics" for something to be forgotten here.

And if my guess turns out to be true, it would be unfortunate, as the alternative of being due to "new physics" would probably yield great hints at which extension of the Standard Model is on the right path. It would be great if there were small experiments that could easily and cheaply separate the wheat from the chaff with such post-SM theories, but nature doesn't seem to be too kind in that regard so far.

(This isn't my field of work, and it has been a few months since I read over couple papers on the topic, so I could easily be misremembering something...)
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Thanks for the additional insight, Plasmagryphon! Why do you think the two techniques yield differing results? Is it just experimental artefact or is there something fundamentally weird going on?
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When I pay for three pounds of chicken at Sam's Club, I only get 2 lbs, 10 oz. A one terabyte hard drove only show 931 gigabytes on my computer. Now I know why.
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That seems like a decent article on the topic. Although, last time some of the research on the topic came up in the news, I saw some confusion (possibly due to some of the headlines used), that some people were asking me if the it was possible the proton had physically shrunk or is smaller than it was a couple years ago. The old methods for measuring the charge radius of a proton still give the same value, so it is down to a discrepancy between two methods.

Even more interesting is that the new method actually produces two different radii related to the proton from the same set of measurements: the average radius of the charge, and an average radius of magnetic effects. The latter is in agreement with older methods, while the former is the one with the 4% difference. So the same set of results both agree and disagree with results from different methods.
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