What about the possibility of double-blind review? I have actually wondered why the reviewers should be given the author info--does that determine the quality of the work? Am I missing some obvious reason why reviewers should know who the authors are?
JPK On Wed, Oct 27, 2010 at 5:50 PM, Phoebe Rice <pr...@uchicago.edu> wrote: > Journal editors need to know when the reviewer they trusted is completely out > to lunch. So please don't just silently knuckle under! > It may make no difference for Nature, but my impression has been that > rigorous journals like JMB do care about review quality. > Phoebe > > ===================================== > Phoebe A. Rice > Dept. of Biochemistry & Molecular Biology > The University of Chicago > phone 773 834 1723 > http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 > http://www.rsc.org/shop/books/2008/9780854042722.asp > > > ---- Original message ---- >>Date: Wed, 27 Oct 2010 15:13:03 -0700 >>From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> (on behalf of "Bernhard >>Rupp (Hofkristallrat a.D.)" <hofkristall...@gmail.com>) >>Subject: Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree) >>To: CCP4BB@JISCMAIL.AC.UK >> >>> Surely the "best" model is the one that the referees for your paper are >>happy with? >> >>That may be the sad and pragmatic wisdom, but certainly not a truth we >>should accept... >> >>> I have found referees to impose seemingly random and arbitrary standards >> >>a) Reviewers are people belonging to a certain population, characterized by >>say a property 'review quality' that follows a certain distribution. >>Irrespective of the actual shape of that parent distribution, the central >>limit theorem informs us that if you sample this distribution reasonably >>often, the sampling distribution will be normal. That means, that half of >>the reviews will be below average review quality, and half above. >> >>Unfortunately, the mean of that distribution is >>b) a function of journal editor quality (they pick the reviewers after all) >>and >>c) affected by systematic errors such as your reputation and the chance that >>you yourself might sit on a reviewer's grant review panel >>By combining a, b, c you can get a fairly good assessment of the joint >>probability of what report you will receive. You do notice that model >>quality is not a parameter in this model, because we can neglect marginal >>second order contributions. >> >>> Mind you discussions on this email list can be a useful resource for >>telling referee's why you don't think you should comply with their "rule of >>thumb". >> >>I agree and sympathize with your optimism, but I am afraid that those who >>might need this education are not the ones who seek it. I.e., reading the bb >>complicates matters (simplicity being one benefit of ROTs) and you can't >>build an empire wasting time on such things. >> >>Good luck with your reviews! >> >>BR >> >>Simon >> >> >> >>On 27 Oct 2010, at 20:11, Bernhard Rupp (Hofkristallrat a.D.) wrote: >> >>> Dear Young and Impressionable readers: >>> >>> I second-guess here that Robbie's intent - after re-refining many many >>> PDB structures, seeing dreadful things, and becoming a hardened cynic >>> - is to provoke more discussion in order to put in perspective - if >>> not >>> debunk- >>> almost all of these rules. >>> >>> So it may be better to pretend you have never heard of these rules. >>> Your >>> crystallographic life might be a happier and less biased one. >>> >>> If you follow this simple procedure (not a rule) >>> >>> The model that fits the primary evidence (minimally biased electron >>> density) >>> best and is at the same time physically meaningful, is the best model, >>> i. >>> e., all plausibly accountable electron density (and not more) is >>> modeled. >>> >>> This process of course does require a little work (like looking >>> through all of the model, not just the interesting parts, and thinking >>> what makes sense) but may lead to additional and unexpected insights. >>> And in almost all cases, you will get a model with plausible >>> statistics, without any reliance on rules. >>> >>> For some decisions regarding global parameterizations you have to >>> apply more sophisticated test such as Ethan pointed out (HR tests) or >>> Ian uses (LL-tests). And once you know how to do that, you do not need >>> any rules of thumb anyhow. >>> >>> So I opt for a formal burial of these rules of thumb and a toast to >>> evidence and plausibility. >>> >>> And, as Gerard B said in other words so nicely: >>> >>> Si tacuisses, philosophus mansisses. >>> >>> BR >>> >>> -----Original Message----- >>> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of >>> Robbie Joosten >>> Sent: Tuesday, October 26, 2010 10:29 PM >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree) >>> >>> Dear Anthony, >>> >>> That is an excellent question! I believe there are quite a lot of >>> 'rules of thumb' going around. Some of them seem to lead to very >>> dogmatic thinking and have caused (refereeing) trouble for good >>> structures and lack of trouble for bad structures. A lot of them were >>> discussed at the CCP4BB so it may be nice to try to list them all. >>> >>> >>> Rule 1: If Rwork < 20%, you are done. >>> Rule 2: If R-free - Rwork > 5%, your structure is wrong. >>> Rule 3: At resolution X, the bond length rmsd should be < than Y (What >>> is the rmsd thing people keep talking about?) Rule 4: If your >>> resolution is lower than X, you should not >>> use_anisotropic_Bs/riding_hydrogens >>> Rule 5: You should not build waters/alternates at resolutions lower >>> than X Rule 6: You should do the final refinement with ALL reflections >>> Rule >>> 7: No >>> one cares about getting the carbohydrates right >>> >>> >>> Obviously, this list is not complete. I may also have overstated some >>> of the rules to get the discussion going. Any addidtions are welcome. >>> >>> Cheers, >>> Robbie Joosten >>> Netherlands Cancer Institute >>> >>>> Apologies if I have missed a recent relevant thread, but are lists of >>>> rules of thumb for model building and refinement? >>>> >>>> >>>> >>>> >>>> >>>> Anthony >>>> >>>> >>>> >>>> Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076 >>>> >>>> >>>> = >
