As someone who is currently only able to use my left foot I must say I
like your way of thinking, Steve. (I broke my right ankle Mar 5).
Still can't walk, but at least I have one leg to stand on...
I myself am a left-handed human, and I admit I do find some devious
pleasure in this "reversal of fortunes". Perhaps it is some deep-seated
suppressed anger from my days in kindergarten searching through piles of
scissors for those few "lefty" ones that the oppressive "rightist"
majority tossed into the pile to placate us. Perhaps it is my
frustration with "chirally prejudiced" pointing devices that has led me
to hate GUIs so much. Perhaps it was learning the etymology of words
like "sinister" and how us lefties were nearly driven to extinction in
the middle ages. Whatever the case, it does now appear that "right" is
not "right". So. Ha Ha! Chalk up one for the lefties! One day we
will rise up and take back what is leftfully ours!
Or maybe I've been watching too much TV.
Happy April Fool everyone!
-James Holton
MAD Scientist
Steve Lane wrote:
> James:
>
> I have been unable to find any logical flaw in your great chain of
> reasoning, in spite of the several minutes I spent contemplating it over
> a mug of lukewarm tea. Given that you are doubtless also correct that,
> "Inverting the 'hand of the world' is going to be very hard for a lot of
> people to accept", I propose a radical divergence from the entire "hand"
> concept, a sort of "starting over from scratch" methodology, to avoid
> (as much as possible) any further confusion.
>
> Given that Google (in particular) has shown great interest in digitizing
> all forms of recorded media, I suggest a simple search+replace algorithm,
> locating all crystallography papers of the past 60 years in the great
> Googlebase (by the simple expedient of assuming that anything with the
> word "crystallography" in the title qualifies; the Google people may
> wish to participate in this effort), and then replacing any instances
> of the string "right hand" with the string "left foot". I believe the
> concept of "footedness" will, in this way, catch on quickly, and readily
> address all of the problems brought forth by your research.
>
> I would hesitate to refer to this as my left footedness concept, but
> one is tempted...
>
> --
> Steve Lane
> System, Network and Security Administrator
> Doudna Lab
> Biomolecular Structure and Mechanism Group
> UC Berkeley
>
>
> On Tue, Apr 01, 2008 at 10:59:34AM -0700, James Holton wrote:
>
>> Dear CCP4BB,
>>
>> I think it prudent at this point for me to announce what could be a
>> very old, but serious error in the fundamental mathematics of
>> crystallography. To be brief, I have uncovered evidence that the "hand"
>> of the micro-world is actually the opposite of what we have believed
>> since Bijvoet's classic paper in 1951.
>>
>> Those of you who know me know that I have been trying to lay down
>> the whole of x-ray diffraction into a single program. This is harder
>> than it sounds. We all know what anomalous scattering is, but a
>> detailed description of the math behind translating this "dynamical
>> theory" effect all the way to the intensity of a particular detector
>> pixel is hard to find all in one place. Most references in the
>> literature about how anomalous scattering is connected to absolute
>> configuration point to the classic Nature paper: Bijvoet et. al.
>> (1951). Unfortunately, since this is a Nature paper, it is too short to
>> describe the math in detail. For the calculations, the reader is
>> referred to another paper by Bijvoet in the Proc. Roy. Acad. Amsterdam
>> v52, 313 (1949). Essentially, the only new information in Bijvoet et.
>> al. (1951) is the assertion that Emil Fischer "got it right" in his
>> initial (arbitrary) assignment of the "R" and "S" reference compounds
>> for the absolute configuration of molecules.
>>
>> I decided to follow this paper trail. The PRAA document was hard to
>> come by and, to my disappointment, again referenced the "real"
>> calculation to another work. Eventually, however, all roads lead back
>> to R. W. James (1946). This is the definitive textbook on scattering
>> theory (originally edited by Sir Lawrence Bragg himself). It is
>> extremely useful, and I highly recommend that anyone who wants to really
>> understand scattering should read it. However, even this wonderful text
>> does not go through the full quantum-mechanical derivation of
>> scattering, but rather rests on J. J. Thompson's original classical
>> treatment. There is nothing wrong with this because the the exact value
>> of the phase lag of the scattering event does not effect anything as
>> long as the phase lag from all the atoms is the same. The only time it
>> does become important is anomalous scattering. Even so, changing the
>> sign of the phase lag will have no effect on any of the anomalous
>> scattering equations as long as all the anomalous contributions have the
>> same sign. The only time the sign of the phase lag is important is in
>> the assignment of absolute configuration. Unfortunately, a full quantum
>> mechanical treatment of the scattering process DOES produce a phase lag
>> with the opposite sign of the classical treatment. This is not the only
>> example of this sort of thing cropping up. One you can find in any
>> quantum text book is the treatment of "tilting" a quantum-mechanical
>> spin (such as an electron). It was shown by Heisenberg that a "tilt" of
>> 360 degrees actually only turns an electron upside-down. You have to
>> "tilt" it by 720 degrees to restore the initial state, or get it
>> "right-side-up" again. This is very counterintuitive, but true, and
>> unfortunately a similar treatment of scattering results in a phase lag
>> of +270 degrees to "restore" the electron after the scattering event,
>> not +90 degrees as was derived classically. To be brief, there is a
>> sign error.
>>
>> Perhaps the reason why noone caught this until now is not just that
>> the quantum calculations are a pain, but that it was very tempting to
>> accept that the large body of literature following Fischer's convention
>> would not have to be "corrected" by inverting the hand of every chiral
>> center described up to that time. Unfortunately, we now have an even
>> larger body of literature (including the PDB) that must now be "corrected".
>>
>> It is an under-appreciated fact in chemistry that anomalous scattering
>> is arguably the only direct evidence we have about the "hand" of the
>> micro-world. There are other lines of evidence, such as the morphology
>> of macroscopic crystals and some recent STEM-type microscope
>> observations of DNA. However, as someone with a lot of experience in
>> motor control I don't mind telling you how easy it is to make a sign
>> error in the direction of an axis. This is especially easy when the
>> range of motion of the axis is too small to see by eye. You end up just
>> swapping wires and flipping bits in the axis definitions until you "get
>> it right". The "right" configuration (we have all assumed) is the one
>> asserted in Bijvoet et. al. (1951). Apparently, the STEM observations
>> fell prey to such a "mistake". But can you blame them? Inverting the
>> "hand of the world" is going to be very hard for a lot of people to
>> accept. Indeed, if anyone can find an error in my math, please tell
>> me! I would really like to be wrong about this.
>>
>> -James Holton
>> MAD Scientist
>>
>
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