Re: [ccp4bb] PNAS on fraud
This gets us more into the philosophy of science but I've always felt authors had a right to speculate in the discussion sections of their papers on what it all means. And speculate even past the information in the actual data (see for example the wonderfully prescient final lines of the Watson Crick paper). As long as the experiments are fully described and the confidence of the data is clearly spelled out. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8611 (voice) (716) 480-8615 (mobile) (716) 898-8660 (fax) deti...@hwi.buffalo.edu www.hwi.buffalo.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: Friday, October 19, 2012 1:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud This is worth looking at as well. Suggests most papers should be retracted! http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124 Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter, Charlie Sent: 19 October 2012 17:55 To: ccp4bb Subject: Re: [ccp4bb] PNAS on fraud Dom, You've opened a pandora's box here, which I won't try to contain. The short answer is both of the above. I feel it is becoming increasingly difficult as a referee to be on top of every paper I review, and as an editor it is becoming increasingly difficult to find willing referees. Both phenomena are diagnostic of the cost of eliminating fraudulent publications, which gall me pretty much as much as they do many others, but which do not drive me apoplectic, either. I've been amused over the years by the frantic efforts to bring crystallographic charlatans to justice, even as I've been angered by publication in high-impact journals of material I myself view as fraudulent, but which obviously survives peer review. On the second of your alternatives, I'll give you two examples of highly celebrated frauds that wound up moving science forward, despite their scurrilous background. The first is the story of Hasko Paradies, whose only legitimate publication, as far as I know, was a first-author paper on the crystallization of tRNA. In that paper, he was, I think, the first author to describe the use of spermine/spermidine and Mg++ ions in improving crystallization conditions. These two contributions proved useful in the actual generation by others of suitable crystals. Paradies apparently went on to make a habit of filching precession photographs from dark rooms and then presenting them elsewhere and at meetings as if he had taken them and as if they were from hot problems of the day. His story was chronicled by Wayne Hendrickson, Ed Lattman, and others in Nature many years later. He dropped out of science and became a pediatrician, I believe in Munich, where, despite not having attended medical school, he was much beloved by his patients and their families. Paradies had been an associate of my own post-doctoral mentor, Sir Aaron Klug. I've no way of knowing whether or not he actually faked the data in his report of tRNA crystallization. His crystals did not diffract in any case, which may have driven him to short cuts. The other celebrated Fraud was Mark Spector, who embarrassed (and indeed victimized) Ephraim Racker at Cornell by using 125Iodine to construct gel autoradiographs to support his remarkable notion of the use of phosphorylation and dephosphorylation in cell signaling. His data were entirely fictitious, but it turned out that his ideas were pregnant indeed. I still view the cross-checking he provoked in serious students of signaling as having stimulated the entire field and actually accelerated it. Both Paradies and Spector are gifted fakes. Their work deserves appreciation for the intelligence that went into the tales they told. A lay homolog was Ferdinand Waldo Demara, who had very little formal education, but who established himself as outstanding in several fields, including open heart surgery, which he performed on a Japanese sailor rescued from after a battle, and who had shrapnel very close to his heart. Apparently, the sailor lived, and Demara saved his life. His story is told in a wonderful film with Tony Curtis in the roll, called The Great Imposter. I hope I've answered your question about what I meant to say on the subject. Charlie On Oct 19, 2012, at 11:25 AM, dom.bell...@diamond.ac.ukmailto:dom.bell...@diamond.ac.uk wrote: Dear Charlie, Do you mean that small doses of fraud should be accepted as a form of natural evolution? Or perhaps you were suggesting that genuine errors/mistakes are acceptable in 1/1 due to the high costs of spotting them? D From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter, Charlie Sent: 19 October 2012 13:09 To: ccp4bb Subject: [ccp4bb] Fwd:
[ccp4bb] Herbert Hauptman Memorial Date Venue Set
A memorial to honor the life of Herb Hauptman, co-winner of the 1985 Nobel Prize in Chemistry for the development of mathematical methods that would become the basis of direct methods, will be held on Monday 21 November 2011 at 4PM in the UB Center for the Arts on the UB north campus. The scientific community is invited. If you plan to attend from out of town or out of country please give us a heads-up by mailing to Walter Pangborn (pangb...@hwi.buffalo.edumailto:pangb...@hwi.buffalo.edu). You can also check the HWI web site (see below for link) for further details and updates. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8611 (voice) (716) 898-8660 (fax) deti...@hwi.buffalo.edumailto:deti...@hwi.buffalo.edu www.hwi.buffalo.eduhttp://www.hwi.buffalo.edu
[ccp4bb] Phantom Crystals - a recap
Thanks to all who replied regarding experiences with phantom crystals (objects with crystal-like morphologies but NO diffraction). The answers were more fascinating than the original poorly worded inquiry deserved. Here is a recap. The observation of phantoms may be rare but not so rare: a number of people replied with first hand experience. Classes of compounds that may lead to these bad actors: membrane-associated proteins and RNAs. NO diffraction may be interpreted as no OBSERVABLE Bragg diffraction, but beware of behind-the-beamstop diffraction; i.e. a few Bragg peaks that are not typically observed unless care is taken to insure a small beamstop. I think of a mental image as follows. Say proteins are spherically shaped and present as cats' eyes marbles. You might be able to lay them down in a perfect HCP lattice but rotationally the eyes might point in all directions. The object at macroscopic dimensions would look like a crystal but at atomic dimensions there would be no buildup of scattering from cooperative effect of many atoms at the same lattice spacing. Thanks to all. George George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor and Chairman Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8600 (voice) (716) 898-8660 (fax) www.hwi.buffalo.edu http://www.hwi.buffalo.edu
[ccp4bb] Phantom Crystals
I'd appreciate it if people could tell me their experiences with what I would call phantom crystals, or ghost crystals. These are objects that display the seeming morphology of crystals (clear facets, sharp edges) but do not diffract X-rays AT ALL. I would not count objects that diffract to 30 A in this category. I mean objects that don't show a single Bragg spot. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor and Chairman Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8600 (voice) (716) 898-8660 (fax) www.hwi.buffalo.edu http://www.hwi.buffalo.edu
Re: [ccp4bb] microbatch vs hanging drop
It may be worth noting that unless rigorous efforts to retard water transfer are made, most microbatch experiments become vapor diffusion experiments. A most common situation arises when microbatch is undertaken in polystyrene containers. Water can then diffuse from the crystallization droplet through the polystyrene. Normally this diffusion process through the plastic takes some time to be significant but it's worth noting that the conditions in the droplet are not invariant in time. If you want to keep the conditions more or less unchanged you will probably be best off undertaking your experiments in glass vessels - and sealing with silicone grease. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor and Chairman Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8600 (voice) (716) 898-8660 (fax) www.hwi.buffalo.edu http://www.hwi.buffalo.edu From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kris Tesh Sent: Wednesday, April 22, 2009 12:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] microbatch vs hanging drop The obvious difference is that the ratio of drop volume to well volume can be potentially greater in non-microbatch wells, and can accommodate higher solvent volume transfers...which is generally in dehydration, but can be for hydration too. Other considerations are the slower rate of temperature change with larger volumes, the distance between the drop and reservoir, rate of drop dehydration when opened, and (for practical use) the ease of withdrawing crystals. And, although many crystals show evidence of crystallization in both systems, some will only grow in one or the other. Kris - Kris F. Tesh, Ph D Director, Macromolecular Products Rigaku Americas Corporation 9009 New Trails Drive The Woodlands, TX 77381 USA 001 281 362 2300 x 144 From: rui ruis...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Date: 04/22/2009 11:09 AM Subject: [ccp4bb] microbatch vs hanging drop Hi, I have a question about the method for crystallization. With traditional hanging drop(24 wells), one slide can also hold for multiple drops but it requires the buffer quite a lot, 600uL? Microbatch can save buffers,only 100uL is required, and also can hold up to three samples in the sitting well. Other than saving the buffer, what's the advantage of microbatch? Which method will be easier to get crystals or no big difference? Thanks for sharing. R
