I take exception to the "NMR results [are] more vague than X-Ray crystallography". If you do NMR structure determination, you would know that it doesn't have to be that way. It depends on how much information you can get from the NMR NOESY spectra, which is basically a map that tells you which hydrogen atoms are close to other hydrogen atoms. The "vague" statement may refer to the simulations that are required to transform the NMR spectrum into a structure. However, X-ray crystallography also requires computer manipulation in order to interpret the diffraction pattern into a structure. If the pattern is not well defined, one gets a structure with large errors. This, in my opinion, could be called "vague".
In fact, there is extra information that may be discerned from NMR that x-ray cannot easily determine: fluxionality. A well-known, but somewhat new theory, describes the "breathability" of proteins and its importance in protein function. Good crystals, by definition, may mistakenly label a fluxional part of the protein as well-defined and not moving. NMR structure determination, however, does not make those mistakes. Why does this matter? In some proteins, the moving parts are central to answering how the protein functions.
It's also my feeling that non-native solution is more pertinent to nature than a crystalline solid, so it's a mistake to equate the two shortcomings. The only thing that x-ray has going for it is it's ability to easily determine the structure of large proteins. However, as magnets get larger, and the technology gets better (including hydrogen-assignment computer algorithms?), magnet jockeys may close the size gap on crystallographers.
Knowing how bees fly does not refute ID. Knowing how bees fly refutes the ID proponents who say, "Science is bogus; they don't even know how bees fly!"
Although I do agree with you in that the research is wonderful without the mention of the controversial 'theory', it is the prerogative of the researcher (Douglas Altshuler) to talk about ID if he wishes. Please note that the "pissed-off researcher" is the scientist that did the research. Actually, he's the first author on the paper, which probably means he did most of the work (while Dickinson was his research advisor). He may have been extra-motivated to do this particular research in order to 'stick it' to the ID'ers. If that's the case, he deserves his podium. Research is a form of truth. Truth cannot be cheapened no matter how politicized the discussion is. My own personal opinion is that this research is extra interesting since ID'ers do talk about the bee-flying phenomenon as an example of the wonder of God. With that in mind, this experiment and its connection to ID is a very dangerous precedent. Are we playing into the hands of ID'ers? Are we now obligated to prove scientific logic for every question ID 'theory' poses? That's going to take a while...
Even so, why is it so bad if its the ranting of a "pissed-off researcher" or a "reporter with an agenda"? Is the science/research any less truthful?
-j
Slashdot Mirror
The computer programs that predict protein structure from its primary structure are getting better. So there is a way....
I take exception to the "NMR results [are] more vague than X-Ray crystallography". If you do NMR structure determination, you would know that it doesn't have to be that way. It depends on how much information you can get from the NMR NOESY spectra, which is basically a map that tells you which hydrogen atoms are close to other hydrogen atoms. The "vague" statement may refer to the simulations that are required to transform the NMR spectrum into a structure. However, X-ray crystallography also requires computer manipulation in order to interpret the diffraction pattern into a structure. If the pattern is not well defined, one gets a structure with large errors. This, in my opinion, could be called "vague".
In fact, there is extra information that may be discerned from NMR that x-ray cannot easily determine: fluxionality. A well-known, but somewhat new theory, describes the "breathability" of proteins and its importance in protein function. Good crystals, by definition, may mistakenly label a fluxional part of the protein as well-defined and not moving. NMR structure determination, however, does not make those mistakes. Why does this matter? In some proteins, the moving parts are central to answering how the protein functions.
It's also my feeling that non-native solution is more pertinent to nature than a crystalline solid, so it's a mistake to equate the two shortcomings. The only thing that x-ray has going for it is it's ability to easily determine the structure of large proteins. However, as magnets get larger, and the technology gets better (including hydrogen-assignment computer algorithms?), magnet jockeys may close the size gap on crystallographers.
Knowing how bees fly does not refute ID. Knowing how bees fly refutes the ID proponents who say, "Science is bogus; they don't even know how bees fly!"
In other words, "Nuh-uh! They started it!"
-j
Although I do agree with you in that the research is wonderful without the mention of the controversial 'theory', it is the prerogative of the researcher (Douglas Altshuler) to talk about ID if he wishes. Please note that the "pissed-off researcher" is the scientist that did the research. Actually, he's the first author on the paper, which probably means he did most of the work (while Dickinson was his research advisor). He may have been extra-motivated to do this particular research in order to 'stick it' to the ID'ers. If that's the case, he deserves his podium. Research is a form of truth. Truth cannot be cheapened no matter how politicized the discussion is. My own personal opinion is that this research is extra interesting since ID'ers do talk about the bee-flying phenomenon as an example of the wonder of God. With that in mind, this experiment and its connection to ID is a very dangerous precedent. Are we playing into the hands of ID'ers? Are we now obligated to prove scientific logic for every question ID 'theory' poses? That's going to take a while... Even so, why is it so bad if its the ranting of a "pissed-off researcher" or a "reporter with an agenda"? Is the science/research any less truthful? -j