> > HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt > > > -- Prof. Dr. Andreas Klamt CEO / Gesch�ftsf�hrer COSMOlogic GmbH & Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt*o*cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] Join us at the 4th-COSMO-RS-Symposium April 2013 Details at www.cosmologic.de/symposium2013 HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt --------------090809020808040605090108 Content-Type: text/html; charset=ISO-8859-15 Content-Transfer-Encoding: 8bit

Hi Gerard,

I agree regarding the inadequate balance of being authors disclosed vs. reviewers being anonymous. But I would go the other direction: Disclose the reviewers.
Two arguments:
- an expert in the field will anyway recognize the authors after reading the abstract and 10 lines.
- and after a while you also identify 50% of the reviewers based on their style and arguments.
Hence let us operate with open face. If we have good arguments we should be sufficiently able to justify a rejection of a paper even if we know and like a certain colleague. Indeed, I several times put my name into a review, because based on my specific knowledge and arguments the authors anyway would have easily know who I am.

But if you suggest to disclose the reviewers in the final publication header, you need to add also the recommendation given by the reviewer, i.e. whther he/she suggested to accept/reject the paper.� His would be a good thing in the way that a reviewer wold have to be more cautious in rejection: If he suggests to reject a good paper, which is finally accepted, it would be finally known to the community that he had recommended rejection. Now if he has good arguments, he needs not be afraid of this. But if he does not, he would be ashamed.

Does someone know how such suggestions about improvements of the peer review system can be brought into panels who finally decide on that?

Andreas

Am 18.08.2012 21:50, schrieb Gerard JP van Westen gerard.vanwesten]![gmail.com:

Dear All,

I should say I agree with Andreas Klamt, to me it sometimes seems peer review sets the boundary low. However I have also had experiences where a referee could not always substantiate negative comments which seemed subjective rather than objective. I can therefore understand that one can get frustrated. But would still argue that the scientific method as it is, is the best available (at least I cannot think of a better way).�

That said however, to me it seems strange that referees are anonymous but authors are not. Perhaps I am over�simplifying the situation, but a paper should be about the science. The science should be sound and as you said, the authors should be able to respond to questions and defend their paper. BUT it should not matter who they are. When authors are disclosed on a manuscript it always indirectly includes their full career in the form of previously published papers, conferences, personal encounters etc. This will always influence an objective judgement (wether negative or positive it is difficult to remain completely objective). I would therefore argue that authors should also be anonymous on a manuscript (it should only be known to the editor who is who).�

In addition, I would argue to add the referees that reviewed a paper to all published papers (perhaps added to the header as the�editor�is added to the header in PLoS ONE). This will allow authors to continue the discussion with a referee after a paper has been accepted. I concur that discussion if a good thing, and in�particular�post publication discussion as this orm of discussion allows the whole field to be involved rather than a select number of people. In addition it could perhaps lead to a reduction of papers that are accepted too easy as the referees responsible for this acceptance are also named on the paper. Likewise, referees that positively review a paper are also in some small way connected to it.�

In any case, just my $ 0.02.

Regards,

Gerard
On Sat, Aug 18, 2012 at 10:02 AM, Andreas Klamt klamt]*[cosmologic.de <owner-chemistry],[ccl.net> wrote:
Sergio,
as most other contributors, I think that you are seeing things too pessimistic here. Critical discussion and opposition really are important for the advancement of science. Indeed, I believe that we need more of that and that we have to find more open ways to oppone and discuss scientific results. We need more discussion in conferences after the talks, and we need a better way of discussion of scientific papers. Sometimes I have am considered as inpolite when I ask a really critical question after a scientific presentation. But how can that be? I think everybody who presents or publishes in sciences should have good arguments for all of his statements and results. If that is the case then he will be well prepared to reply to that question. If not then the question has disclosed some weekness in his research and it should help to improve. Discussion at the end of talks also are too much bilateral between speaker and opponent. Usually no real discussion between many of the experts in the room evolves. But that would be interesting and sometimes needed. Today mostly the discussion is just a question by an opponent and an answer by the speaker, and it ends a bit vague. If the question was unfair or the speaker not well able to find the right answer, he goes home with a bad feeling, and if on the other hand the reply was wrong or unfair, the opponent goes home with a bad feeling. It would be good if we would have the culture of discussion that in such a situation other people stand up in order to either support the speaker or the opponent, or have a third oppinion.

I think we need this culture even more in scientific literature. We need more "Comments on paper xyz", and we need comments on comments, but usually the latter are not allowed by the editors any more. Hence it is like in the conference room: The author has the last word, and if the reply on a comment is again misleading, the opponent has no way of replying any more. And we need the discussion on papers on a shorter time scale and at one place. Today each round takes 2 months at minimum. Nowadays it should be doable to do such discussion of a paper electronically, and it should be available online at the end of each article. Hence, when downlaoding an article you could have a quick look whether there has been a discussion and what the average opinion had been.

The reason why I think that we need such discussion culture and forum is that I am less optimistic about peer review meanwhile. No question, we need the peer review system to filter out some rubbish and to have a barrier which hinders unserious people to submit all rubbish as scientific papers. But I am afraid that much too many bad papers go through the system and after passing can claim to be peer reviewed. Some influencing people in the community who know the editors since long get everything published, even if one reviewer has detected substantial mistakes. In one case I proved mathmatically that some equation which was considered by the author as something new, was mathmatically identical with an earlier published equation of someone else. I suggest not to publish the paper with that wrong claim. The paper appeared essentially unchanged in an ACS journal. Asking the editor how this could happen, he answered that he had gotten two positive and one negative reports. Thus we had accepted it. Asking him, whether he had sent my substantial concerns to the other reviewers in order to reconsider their opinion, he answered that that would not be within the rules of the journal. And just yesterday I saw that a paper by an influencing author appeared online essentially unchanged, although I again had a raised a number of severe concerns.� Therefore I believe: We need more critical post-peer-review debates.

Andreas

Am 18.08.2012 02:43, schrieb Sergio Manzetti sergio.manzetti-$-gmx.com:

I think JJ and Amy are getting closer to the point I am stating. There are many cases where people with great ideas never make it to the surface, either because they are not "strong" enough to "battle" against opposition or criticism, or they simply don't want to. I know of one who had a great method to treat people, but because it was never scientifically validated, he received cold showers each time he opened up his method to scientist. In the meantime, his method treated a lot of people, and they recovered. Scientists ARE trained to validate, annihilate, exclude, disregard and eventually accept. This trait of the scientist is to me a little stupidious, it seems like House in the series at the hospital. He goes through a bunch of hypotheses and tests them all on the patient, meanwhile the patient suffers and at the end after hitting the right hypothesis he calls himself a great doctor (or at least appears to be one). Same thing are scientists, they are recognized as great after they have learned on how to tramp down opposition as the first step in their life as scientists, then they have to defend their research to grant-organization, and fill up the applications with "why this is so important for the future and society". Still in a near pseudo-darwinistic�� behavior, the scientist fights through the hierarchy of late nights and hard work, and at the age of 70 reaches the Emeritious stage. To many this is "life at its best", and many are also good examples of nice events, but at the end of the day, the way scientist DO science is build on that everything has to be bullet and water proof before he even discusses the theory with others, otherwise the classical debates begin. I have also heard from previous Senior Scientists passing the age of 50 of witnessing and ENJOYING debates where scientist where verbally annihilating each other, and I recall particularly what this professor said in the context with the debate he saw "it was blood on the dance floor". At the end of the day it is a litigious procedure that scientists have to "survive" through, and it creates FRICTION. This friction is my whole point of the discussion: It is energy and can be used to do great science (pr other positive things), and not wasted on discussions and debates. Those are just for entertaining the competitive nature in people. Competition, debate and discussion requires energy, again, that energy can be used for other things and is valuable.
Therefore, the quite and contemplating scientist who doesn't bother about debating or showing his results before reaching a full final format, and perhaps not even showing them then but wait till people are not so interested in debating him, is a calm and relaxing scientist, that cares about the object of science, not the subject behind it or those around it.

Sergio

�

----- Original Message -----

From: j j robinson jameschums^^^yahoo.com

Sent: 08/17/12 09:48 PM

To: Manzetti, Sergio

Subject: CCL: On "defending" and "opposing" science

Dear CCLers,

�

might I suggest the original correspondent watches the film "Insignificance". We all have knowledge... but I prefer insight, understanding..I suspect I am simply too stupid to find the truth.. Experiment, observation, hypothesis. The debates are not battles of gladiators, nor personal feuds..science and/or natural philosophy - is patient observation, measurement, correlation, verification of experimental facts, comparison, perspective, understanding..we debate with others to make sure we are not simply deluding ourselves or that other are not deluded. We can agree to differ, review papers, admit mistakes..we are human too. Results and conclusion do not simply result from pressing the return key and waiting to see how many "hartree's" come out at the end.

�

J J Robinson - personal email - opinions are personal only.

�

�
-- 
Prof. Dr. Andreas Klamt
CEO / Gesch�ftsf�hrer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt##cosmologic.de
web    	www.cosmologic.de

[University address:      Inst. of Physical and
Theoretical Chemistry, University of Regensburg]

Join us at the 4th-COSMO-RS-Symposium April 2013
Details at www.cosmologic.de/symposium2013 

HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt

-- 
Prof. Dr. Andreas Klamt
CEO / Gesch�ftsf�hrer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt*o*cosmologic.de
web    	www.cosmologic.de

[University address:      Inst. of Physical and
Theoretical Chemistry, University of Regensburg]

Join us at the 4th-COSMO-RS-Symposium April 2013
Details at www.cosmologic.de/symposium2013 

HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt

--------------090809020808040605090108-- From owner-chemistry@ccl.net Sun Aug 19 13:10:00 2012 From: "George Fitzgerald George.Fitzgerald*|*accelrys.com" To: CCL Subject: CCL: Well... Message-Id: <-47404-120819101412-23093-oV/HMGKZ5WJ4WuqSfBbeFw..server.ccl.net> X-Original-From: George Fitzgerald Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 19 Aug 2012 07:13:49 -0700 MIME-Version: 1.0 Sent to CCL by: George Fitzgerald [George.Fitzgerald:+:accelrys.com] Sergio, There is little that I can add to the excellent comments of my peers. I wanted to comment, though, on your recent post. You wrote It is the "guerrier" aspect of science which generates the contiguous debates of science that never end, and that cost billlions of tax payers money, as in the case of CFC gases in the 80s and ozone, DDTs in the 70s and infertility in birds and animals, dioxins in the 60s at industrial sites destroying entire ecosystems, Lead in the pain in the 50s damaging health and one can nearly go back in 10-year cycles to see the absurdities of science caused by endless debate and not following "a straight-ling between two points" in order to conclude if something is working or not. This is the collision between science and politics. Along with the examples I mentioned earlier - cigarettes and acid rain - these debates were NOT prolonged by serious scientists but by professional obfuscators who were in the pockets of the corporations. They couldn't refute the evidence, but they could - and did - prolong the debate. I agree that this is a horrible state of affairs, and I wish I knew what to do about it. -george -----Original Message----- > From: owner-chemistry+gfitzgerald==accelrys.com ~~ ccl.net [mailto:owner-chemistry+gfitzgerald==accelrys.com ~~ ccl.net] On Behalf Of Sergio Manzetti sergio.manzetti=gmail.com Sent: Saturday, August 18, 2012 6:20 AM To: George Fitzgerald Subject: CCL: Well... Sent to CCL by: "Sergio Manzetti" [sergio.manzetti]![gmail.com] Irenes notion is an example, however the effects on the clouds can be so many and derive from so many sources that the path to explaining a phenomenon is diverging from the path of observing it. When science becomes argumentative, and unnecessary iterative it fails as much as when it fails to provide a sound and reproducible explanation to a phenomenon. The problem is often the absence of reason in science, which is not dependent on education and number of publications. A person can have a far more clear understanding and reason than a scientist even not being a scientist, if that person has contemplated phenomena for long enough time, and has interests in what she/he observes. The scientist however can go to length of debating the evident and perhaps even neglecting crucial facts until the next generation comes and replaces them with new views. It is not the the reproducibility of science and its methods that I question, it is the reaction of the scientist to anything new. Two types of scientist result mainly: One that attacks the new findings with doubt, skepticism and criticism, the second with openness and calmness. I think the former is a necessary scientist for revelaing fraud-related "science" such as promises of things that cannot be true in commercial and self-evident environmental problems. However, when ideas are generated, the presence of such critical scientist is devastating, because their sole response is to kill whatever is new, without even being inspired. This is where egos of scientist emerge, and resemble egos of musicians and artists. They may be critical of others inventions, however if enough time passes the inventions have suddenly migrated over to the the skepticists as "ideas to be tested". If the ideas survive, they even generate new sub-ideas and projects in the original scientist who was formerly critical and skeptical. Thus, criticism and blind neglection of new ideas is a waste of energy and time, because if an idea is right, it will survive with or without the criticism. The role of these destructive scientists is in defending the borders of sound science, but they have nothing to do in the developing of science, because developments come from ideas that rarely agree with contemporary views. The scientist have therefore a personal responsibility to disseminate science with patience and openness, and accept other views without going to war all the time. It is the "guerrier" aspect of science which generates the contiguous debates of science that never end, and that cost billlions of tax payers money, as in the case of CFC gases in the 80s and ozone, DDTs in the 70s and infertility in birds and animals, dioxins in the 60s at industrial sites destroying entire ecosystems, Lead in the pain in the 50s damaging health and one can nearly go back in 10-year cycles to see the absurdities of science caused by endless debate and not following "a straight-ling between two points" in order to conclude if something is working or not. Sergiohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sun Aug 19 13:45:00 2012 From: "Fatima Mons fatima.mons^^^yahoo.com" To: CCL Subject: CCL: On "defending" and "opposing" science Message-Id: <-47405-120819104220-24111-zUfUj5h9O5ZahE99Nz7NbA^server.ccl.net> X-Original-From: "Fatima Mons" Date: Sun, 19 Aug 2012 10:42:19 -0400 Sent to CCL by: "Fatima Mons" [fatima.mons]~[yahoo.com] There still is *an* amount of bias with referees, especially those that have a vested interest. I know of one case involving the aquatic toxicity of ionic liquids that was rejected for publication (the paper showed that the ionic liquids tested were more toxic in the aquatic environment than most commonly used molecular solvents). It turned out that one of the referees had a vested interest in ionic liquids (I believe that they didn't have a background in environmental toxicity either). Editors have to do more to ensure that referees do not have bias due to vested interests. Gerard's point about hiding author and organization affiliations from referees during the first review is a good point. The names of the authors and referees should be published for complete transparency after the review process. Furthermore, if a paper is rejected and the author feels that this is not justified, the board of editors should review the rejection to see if this is genuinely justified and when appropriate seek additional referees. In some cases, such as the aforementioned ionic liquid paper, calling upon referees with an environmental background would be key here. It can be all to easy for an author to make 'grand claims' about benefits of a technology when they have next to no knowledge of that field. The scientific community have to do more to genuinely challenge these claims and journal editors have a moral and scientific duty to ensure that the science is of an appropriate standard and that there is no adverse bias or vested interested involved in the publishing process. May be there is a novel way to deal with this type of situation. Publish the paper along with the referees' comments. In that way, the whole scientific community can see the debate in a transparent manner, which prompts discussion and further scientific research. Clearly the editors will have to manage this process appropriately and on a case-by-case basis. Fatima. Btw., the paper was published in another journal and subsequently a number of other studies have been published by other groups which have come to similar conclusions. So the science was indeed valid! From owner-chemistry@ccl.net Sun Aug 19 15:46:01 2012 From: "Mezei, Mihaly mihaly.mezei###mssm.edu" To: CCL Subject: CCL: On "defending" and "opposing" science Message-Id: <-47406-120819154158-8327-l9dfurI4W3mgSAt2ug0olQ###server.ccl.net> X-Original-From: "Mezei, Mihaly" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 19 Aug 2012 19:41:52 +0000 MIME-Version: 1.0 Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei-.-mssm.edu] Greetings, This thread has touched upon many important issues so I feel justified to include one more: the abdication of responsibilities of many editors. Like one of the posters' experience where an editor ignored a referee suggestion because of two other referees' opposing view, I had editor ignoring my specific arguments against a referee's (negative) argument and telling me that I have to convince that referee (not him). I suggest that the community insist of the editors being more than simple vote counters; instead they should actively arbitrate the discussion between the author(s) and referees. This way there would be less need for a post-publication discussion. There is, of course, always the avenue of publishing a comment on a paper in the traditional way. Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Sun Aug 19 16:21:00 2012 From: "Sergio Manzetti sergio.manzetti###gmx.com" To: CCL Subject: CCL: Suggestion Message-Id: <-47407-120819133653-7109-OPYBOhNxxiooABKVUCTQww.@.server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary73281345397799501288" Date: Sun, 19 Aug 2012 19:36:39 +0200 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti(!)gmx.com] --========GMXBoundary73281345397799501288 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Let more women in science, particularly the heavy sciences such as QM, Particle Physics and theoretical astrophysics. Shift the subject away from peer-review issues and problems in dissemination, this has to do with traditions that are male-made and derive from the 12th century and need to be rounded and merged with new ways of thinking, with a maintenance of the strict demands of correctness, precision and collective evaluation of scientific works. Also, leave the innovators alone and let students and young newcomers test their "stupid" theories not matter how stupid they sound. They need to try. Sergio --========GMXBoundary73281345397799501288 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Let more= women in science, particularly the heavy sciences such as QM, Particle Phy= sics and theoretical astrophysics. Shift the subject away from peer-review = issues and problems in dissemination, this has to do with traditions that a= re male-made and derive from the 12th century and need to be rounded and me= rged with new ways of thinking, with a maintenance of the strict demands of= correctness, precision and collective evaluation of scientific works. Also= , leave the innovators alone and let students and young newcomers test thei= r "stupid" theories not matter how stupid they sound. They need to try.
=20
=20 Sergio --========GMXBoundary73281345397799501288-- From owner-chemistry@ccl.net Sun Aug 19 16:55:00 2012 From: "Gerard JP van Westen gerard.vanwesten * gmail.com" To: CCL Subject: CCL: On "defending" and "opposing" science Message-Id: <-47408-120819155625-12393-2/seb8LrI7I1vdV4ipGQNQ ~~ server.ccl.net> X-Original-From: Gerard JP van Westen Content-Type: multipart/alternative; boundary=bcaec51d2a383902af04c7a3c90f Date: Sun, 19 Aug 2012 20:55:46 +0100 MIME-Version: 1.0 Sent to CCL by: Gerard JP van Westen [gerard.vanwesten~~gmail.com] --bcaec51d2a383902af04c7a3c90f Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Andreas and Fatima, Indeed I agree with you on the statement that it is easy to reverse engineer who your referee was. In particular in a highly specialized fields the real experts are usually little in number, hence there is a lot of 'inbreeding' in the review process. While one can already extrapolate from the comments who the referee is, the same is the case for manuscripts. Even if the authors would be hidden it can become clear after reading a few paragraphs, in particular when authors cite their own work. However, what I was hoping to achieve was to influence the first impression. Preventing a biased first impression would already mean a significant difference in my view (after all, the first thing you see after the title is usually the authors, even before the abstract!). So I agree that keeping authors hidden will not be the ideal solution, I just think it would add to making things a little less biased. Indeed Fatima, a possible compromise could be that this anonymity is dropped after the first round of reviews. A very good suggestion indeed. I also agree that the final recommendation by the referee should be added in the header. This transparency would add to a more balanced judgement I would say... I am not aware of any location to propose these recommendations, however I would guess that the more or less crowd sourced PLoS ONE might be open for suggestions? Perhaps they are willing to implement these ideas? After all little coding should be needed for them to make these changes as they are already a fully electronic journal. What are your ideas on this? Regards, Gerard On Sun, Aug 19, 2012 at 9:54 AM, Andreas Klamt klamt(_)cosmologic.de < owner-chemistry:_:ccl.net> wrote: > Hi Gerard, > > I agree regarding the inadequate balance of being authors disclosed vs. > reviewers being anonymous. But I would go the other direction: Disclose t= he > reviewers. > Two arguments: > - an expert in the field will anyway recognize the authors after reading > the abstract and 10 lines. > - and after a while you also identify 50% of the reviewers based on their > style and arguments. > Hence let us operate with open face. If we have good arguments we should > be sufficiently able to justify a rejection of a paper even if we know an= d > like a certain colleague. Indeed, I several times put my name into a > review, because based on my specific knowledge and arguments the authors > anyway would have easily know who I am. > > But if you suggest to disclose the reviewers in the final publication > header, you need to add also the recommendation given by the reviewer, i.= e. > whther he/she suggested to accept/reject the paper. His would be a good > thing in the way that a reviewer wold have to be more cautious in > rejection: If he suggests to reject a good paper, which is finally > accepted, it would be finally known to the community that he had > recommended rejection. Now if he has good arguments, he needs not be afra= id > of this. But if he does not, he would be ashamed. > > Does someone know how such suggestions about improvements of the peer > review system can be brought into panels who finally decide on that? > > Andreas > > Am 18.08.2012 21:50, schrieb Gerard JP van Westen gerard.vanwesten]![ > gmail.com: > > Dear All, > > I should say I agree with Andreas Klamt, to me it sometimes seems peer > review sets the boundary low. However I have also had experiences where a > referee could not always substantiate negative comments which seemed > subjective rather than objective. I can therefore understand that one can > get frustrated. But would still argue that the scientific method as it is= , > is the best available (at least I cannot think of a better way). > > That said however, to me it seems strange that referees are anonymous > but authors are not. Perhaps I am over simplifying the situation, but a > paper should be about the science. The science should be sound and as you > said, the authors should be able to respond to questions and defend their > paper. BUT it should not matter who they are. When authors are disclosed = on > a manuscript it always indirectly includes their full career in the form = of > previously published papers, conferences, personal encounters etc. This > will always influence an objective judgement (wether negative or positive > it is difficult to remain completely objective). I would therefore argue > that authors should also be anonymous on a manuscript (it should only be > known to the editor who is who). > > In addition, I would argue to add the referees that reviewed a paper to > all published papers (perhaps added to the header as the editor is added = to > the header in PLoS ONE). This will allow authors to continue the discussi= on > with a referee after a paper has been accepted. I concur that discussion = if > a good thing, and in particular post publication discussion as this orm o= f > discussion allows the whole field to be involved rather than a select > number of people. In addition it could perhaps lead to a reduction of > papers that are accepted too easy as the referees responsible for this > acceptance are also named on the paper. Likewise, referees that positivel= y > review a paper are also in some small way connected to it. > > In any case, just my $ 0.02. > > Regards, > > Gerard > > On Sat, Aug 18, 2012 at 10:02 AM, Andreas Klamt klamt]*[cosmologic.de < > owner-chemistry],[ccl.net> wrote: > >> Sergio, >> as most other contributors, I think that you are seeing things too >> pessimistic here. Critical discussion and opposition really are importan= t >> for the advancement of science. Indeed, I believe that we need more of t= hat >> and that we have to find more open ways to oppone and discuss scientific >> results. We need more discussion in conferences after the talks, and we >> need a better way of discussion of scientific papers. Sometimes I have a= m >> considered as inpolite when I ask a really critical question after a >> scientific presentation. But how can that be? I think everybody who >> presents or publishes in sciences should have good arguments for all of = his >> statements and results. If that is the case then he will be well prepare= d >> to reply to that question. If not then the question has disclosed some >> weekness in his research and it should help to improve. Discussion at th= e >> end of talks also are too much bilateral between speaker and opponent. >> Usually no real discussion between many of the experts in the room evolv= es. >> But that would be interesting and sometimes needed. Today mostly the >> discussion is just a question by an opponent and an answer by the speake= r, >> and it ends a bit vague. If the question was unfair or the speaker not w= ell >> able to find the right answer, he goes home with a bad feeling, and if o= n >> the other hand the reply was wrong or unfair, the opponent goes home wit= h a >> bad feeling. It would be good if we would have the culture of discussion >> that in such a situation other people stand up in order to either suppor= t >> the speaker or the opponent, or have a third oppinion. >> >> I think we need this culture even more in scientific literature. We need >> more "Comments on paper xyz", and we need comments on comments, but usua= lly >> the latter are not allowed by the editors any more. Hence it is like in = the >> conference room: The author has the last word, and if the reply on a >> comment is again misleading, the opponent has no way of replying any mor= e. >> And we need the discussion on papers on a shorter time scale and at one >> place. Today each round takes 2 months at minimum. Nowadays it should be >> doable to do such discussion of a paper electronically, and it should be >> available online at the end of each article. Hence, when downlaoding an >> article you could have a quick look whether there has been a discussion = and >> what the average opinion had been. >> >> The reason why I think that we need such discussion culture and forum is >> that I am less optimistic about peer review meanwhile. No question, we n= eed >> the peer review system to filter out some rubbish and to have a barrier >> which hinders unserious people to submit all rubbish as scientific paper= s. >> But I am afraid that much too many bad papers go through the system and >> after passing can claim to be peer reviewed. Some influencing people in = the >> community who know the editors since long get everything published, even= if >> one reviewer has detected substantial mistakes. In one case I proved >> mathmatically that some equation which was considered by the author as >> something new, was mathmatically identical with an earlier published >> equation of someone else. I suggest not to publish the paper with that >> wrong claim. The paper appeared essentially unchanged in an ACS journal. >> Asking the editor how this could happen, he answered that he had gotten = two >> positive and one negative reports. Thus we had accepted it. Asking him, >> whether he had sent my substantial concerns to the other reviewers in or= der >> to reconsider their opinion, he answered that that would not be within t= he >> rules of the journal. And just yesterday I saw that a paper by an >> influencing author appeared online essentially unchanged, although I aga= in >> had a raised a number of severe concerns. Therefore I believe: We need >> more critical post-peer-review debates. >> >> Andreas >> >> Am 18.08.2012 02:43, schrieb Sergio Manzetti sergio.manzetti-$-gmx.com: >> >> I think JJ and Amy are getting closer to the point I am stating. There >> are many cases where people with great ideas never make it to the surfac= e, >> either because they are not "strong" enough to "battle" against oppositi= on >> or criticism, or they simply don't want to. I know of one who had a grea= t >> method to treat people, but because it was never scientifically validate= d, >> he received cold showers each time he opened up his method to scientist.= In >> the meantime, his method treated a lot of people, and they recovered. >> Scientists ARE trained to validate, annihilate, exclude, disregard and >> eventually accept. This trait of the scientist is to me a little >> stupidious, it seems like House in the series at the hospital. He goes >> through a bunch of hypotheses and tests them all on the patient, meanwhi= le >> the patient suffers and at the end after hitting the right hypothesis he >> calls himself a great doctor (or at least appears to be one). Same thing >> are scientists, they are recognized as great after they have learned on = how >> to tramp down opposition as the first step in their life as scientists, >> then they have to defend their research to grant-organization, and fill = up >> the applications with "why this is so important for the future and >> society". Still in a near pseudo-darwinistic behavior, the scientist >> fights through the hierarchy of late nights and hard work, and at the ag= e >> of 70 reaches the Emeritious stage. To many this is "life at its best", = and >> many are also good examples of nice events, but at the end of the day, t= he >> way scientist DO science is build on that everything has to be bullet an= d >> water proof before he even discusses the theory with others, otherwise t= he >> classical debates begin. I have also heard from previous Senior Scientis= ts >> passing the age of 50 of witnessing and ENJOYING debates where scientist >> where verbally annihilating each other, and I recall particularly what t= his >> professor said in the context with the debate he saw "it was blood on th= e >> dance floor". At the end of the day it is a litigious procedure that >> scientists have to "survive" through, and it creates FRICTION. This >> friction is my whole point of the discussion: It is energy and can be us= ed >> to do great science (pr other positive things), and not wasted on >> discussions and debates. Those are just for entertaining the competitive >> nature in people. Competition, debate and discussion requires energy, >> again, that energy can be used for other things and is valuable. >> Therefore, the quite and contemplating scientist who doesn't bother abou= t >> debating or showing his results before reaching a full final format, and >> perhaps not even showing them then but wait till people are not so >> interested in debating him, is a calm and relaxing scientist, that cares >> about the object of science, not the subject behind it or those around i= t. >> >> >> Sergio >> >> >> >> ----- Original Message ----- >> >> From: j j robinson jameschums^^^yahoo.com >> >> Sent: 08/17/12 09:48 PM >> >> To: Manzetti, Sergio >> >> Subject: CCL: On "defending" and "opposing" science >> >> Dear CCLers, >> >> might I suggest the original correspondent watches the film >> "Insignificance". We all have knowledge... but I prefer insight, >> understanding..I suspect I am simply too stupid to find the truth.. >> Experiment, observation, hypothesis. The debates are not battles of >> gladiators, nor personal feuds..science and/or natural philosophy - is >> patient observation, measurement, correlation, verification of experimen= tal >> facts, comparison, perspective, understanding..we debate with others to >> make sure we are not simply deluding ourselves or that other are not >> deluded. We can agree to differ, review papers, admit mistakes..we are >> human too. Results and conclusion do not simply result from pressing the >> return key and waiting to see how many "hartree's" come out at the end. >> >> J J Robinson - personal email - opinions are personal only. >> >> >> >> >> >> >> >> -- >> Prof. Dr. Andreas Klamt >> CEO / Gesch=E4ftsf=FChrer >> COSMOlogic GmbH & Co. KG >> Burscheider Strasse 515 >> D-51381 Leverkusen, Germany >> >> phone +49-2171-731681 >> fax +49-2171-731689 >> e-mail klamt##cosmologic.de >> web www.cosmologic.de >> >> [University address: Inst. of Physical and >> Theoretical Chemistry, University of Regensburg] >> >> Join us at the 4th-COSMO-RS-Symposium April 2013 >> Details at www.cosmologic.de/symposium2013 >> >> HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt >> Komplementaer: COSMOlogic Verwaltungs GmbH >> HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt >> >> >> >> > > > -- > Prof. Dr. Andreas Klamt > CEO / Gesch=E4ftsf=FChrer > COSMOlogic GmbH & Co. KG > Burscheider Strasse 515 > D-51381 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > > e-mail klamt()cosmologic.de > > web www.cosmologic.de > > [University address: Inst. of Physical and > Theoretical Chemistry, University of Regensburg] > > Join us at the 4th-COSMO-RS-Symposium April 2013 > Details at www.cosmologic.de/symposium2013 > > HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt > > > > --bcaec51d2a383902af04c7a3c90f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Andreas and Fatima,

Indeed I agree with you on the = statement that it is easy to reverse engineer who your referee was. In part= icular in a highly specialized fields the real experts are usually little i= n number, hence there is a lot of 'inbreeding' =A0in the review pro= cess. While one can already extrapolate from the comments who the referee i= s, the same is the case for manuscripts. Even if the authors would be hidde= n it can become clear after reading a few paragraphs, in particular when au= thors cite their own work. However, what I was hoping to achieve was to inf= luence the first impression. Preventing a biased first impression would alr= eady mean a significant difference in my view (after all, the first thing y= ou see after the title is usually the authors, even before the abstract!).= =A0

So I agree that keeping authors hidden will not be the = ideal solution, I just think it would add to making things a little less bi= ased. Indeed Fatima, a possible compromise could be that this=A0anonymity= =A0is dropped after the first round of reviews. A very good suggestion inde= ed.=A0

I also agree that the final recommendation by the refer= ee should be added in the header. This=A0transparency=A0would add to a more= balanced judgement I would say...

I am not aware = of any location to propose these recommendations, however I would guess tha= t the more or less crowd sourced PLoS ONE might be open for suggestions? Pe= rhaps they are willing to implement these ideas? After all little coding sh= ould be needed for them to make these changes as they are already a fully e= lectronic journal.=A0

What are your ideas on this?

R= egards,

Gerard=A0

On Sun, Aug 19, 2012 at 9:54 AM, Andreas Klamt klamt(_)cosmologic.de <owner-chemistry:_:ccl.net= > wrote:

=20 =20 =20
Hi Gerard,

I agree regarding the inadequate balance of being authors disclosed vs. reviewers being anonymous. But I would go the other direction: Disclose the reviewers.
Two arguments:
- an expert in the field will anyway recognize the authors after reading the abstract and 10 lines.
- and after a while you also identify 50% of the reviewers based on their style and arguments.
Hence let us operate with open face. If we have good arguments we should be sufficiently able to justify a rejection of a paper even if we know and like a certain colleague. Indeed, I several times put my name into a review, because based on my specific knowledge and arguments the authors anyway would have easily know who I am.

But if you suggest to disclose the reviewers in the final publication header, you need to add also the recommendation given by the reviewer, i.e. whther he/she suggested to accept/reject the paper.=A0 His would be a good thing in the way that a reviewer wold have to be more cautious in rejection: If he suggests to reject a good paper, which is finally accepted, it would be finally known to the community that he had recommended rejection. Now if he has good arguments, he needs not be afraid of this. But if he does not, he would be ashamed.

Does someone know how such suggestions about improvements of the peer review system can be brought into panels who finally decide on that?

Andreas

Am 18.08.2012 21:50, schrieb Gerard JP van Westen gerard.vanwesten]![gma= il.com:
Dear All,

I should say I agree with Andreas Klamt, to me it sometimes seems peer review sets the boundary low. However I have also had experiences where a referee could not always substantiate negative comments which seemed subjective rather than objective. I can therefore understand that one can get frustrated. But would still argue that the scientific method as it is, is the best available (at least I cannot think of a better way).=A0

That said however, to me it seems strange that referees are anonymous but authors are not. Perhaps I am over=A0simplifying the situation, but a paper should be about the science. The science should be sound and as you said, the authors should be able to respond to questions and defend their paper. BUT it should not matter who they are. When authors are disclosed on a manuscript it always indirectly includes their full career in the form of previously published papers, conferences, personal encounters etc. This will always influence an objective judgement (wether negative or positive it is difficult to remain completely objective). I would therefore argue that authors should also be anonymous on a manuscript (it should only be known to the editor who is who).=A0

In addition, I would argue to add the referees that reviewed a paper to all published papers (perhaps added to the header as the=A0editor=A0is added to the header in PLoS ONE). This will allow authors to continue the discussion with a referee after a paper has been accepted. I concur that discussion if a good thing, and in=A0particular=A0post publication discussion as this orm of discussion allows the whole field to be involved rather than a select number of people. In addition it could perhaps lead to a reduction of papers that are accepted too easy as the referees responsible for this acceptance are also named on the paper. Likewise, referees that positively review a paper are also in some small way connected to it.=A0

In any case, just my $ 0.02.

Regards,

Gerard
On Sat, Aug 18, 2012 at 10:02 AM, Andreas Klamt klamt]*[cosmologic.de <owner-chemistry],[ccl.net> wrote:

Sergio,
as most other contributors, I think that you are seeing things too pessimistic here. Critical discussion and opposition really are important for the advancement of science. Indeed, I believe that we need more of that and that we have to find more open ways to oppone and discuss scientific results. We need more discussion in conferences after the talks, and we need a better way of discussion of scientific papers. Sometimes I have am considered as inpolite when I ask a really critical question after a scientific presentation. But how can that be? I think everybody who presents or publishes in sciences should have good arguments for all of his statements and results. If that is the case then he will be well prepared to reply to that question. If not then the question has disclosed some weekness in his research and it should help to improve. Discussion at the end of talks also are too much bilateral between speaker and opponent. Usually no real discussion between many of the experts in the room evolves. But that would be interesting and sometimes needed. Today mostly the discussion is just a question by an opponent and an answer by the speaker, and it ends a bit vague. If the question was unfair or the speaker not well able to find the right answer, he goes home with a bad feeling, and if on the other hand the reply was wrong or unfair, the opponent goes home with a bad feeling. It would be good if we would have the culture of discussion that in such a situation other people stand up in order to either support the speaker or the opponent, or have a third oppinion.

I think we need this culture even more in scientific literature. We need more "Comments on paper xyz",= and we need comments on comments, but usually the latter are not allowed by the editors any more. Hence it is like in the conference room: The author has the last word, and if the reply on a comment is again misleading, the opponent has no way of replying any more. And we need the discussion on papers on a shorter time scale and at one place. Today each round takes 2 months at minimum. Nowadays it should be doable to do such discussion of a paper electronically, and it should be available online at the end of each article. Hence, when downlaoding an article you could have a quick look whether there has been a discussion and what the average opinion had been.

The reason why I think that we need such discussion culture and forum is that I am less optimistic about peer review meanwhile. No question, we need the peer review system to filter out some rubbish and to have a barrier which hinders unserious people to submit all rubbish as scientific papers. But I am afraid that much too many bad papers go through the system and after passing can claim to be peer reviewed. Some influencing people in the community who know the editors since long get everything published, even if one reviewer has detected substantial mistakes. In one case I proved mathmatically that some equation which was considered by the author as something new, was mathmatically identical with an earlier published equation of someone else. I suggest not to publish the paper with that wrong claim. The paper appeared essentially unchanged in an ACS journal. Asking the editor how this could happen, he answered that he had gotten two positive and one negative reports. Thus we had accepted it. Asking him, whether he had sent my substantial concerns to the other reviewers in order to reconsider their opinion, he answered that that would not be within the rules of the journal. And just yesterday I saw that a paper by an influencing author appeared online essentially unchanged, although I again had a raised a number of severe concerns.=A0 Therefore I believe: We need more critical post-peer-review debates.

Andreas

Am 18.08.2012 02:43, schrieb Sergio Manzetti sergio.manzetti-$-gmx.com:

I think JJ and Amy are getting closer to the point I am stating. There are many cases where people with great ideas never make it to the surface, either because they are not "strong" enough to "bat= tle" against opposition or criticism, or they simply don't want to. I know of one who had a great method to treat people, but because it was never scientifically validated, he received cold showers each time he opened up his method to scientist. In the meantime, his method treated a lot of people, and they recovered. Scientists ARE trained to validate, annihilate, exclude, disregard and eventually accept. This trait of the scientist is to me a little stupidious, it seems like House in the series at the hospital. He goes through a bunch of hypotheses and tests them all on the patient, meanwhile the patient suffers and at the end after hitting the right hypothesis he calls himself a great doctor (or at least appears to be one). Same thing are scientists, they are recognized as great after they have learned on how to tramp down opposition as the first step in their life as scientists, then they have to defend their research to grant-organization, and fill up the applications with "why this is so important fo= r the future and society". Still in a near pseudo-darwinistic=A0=A0 behavior, the scientist fights through the hierarchy of late nights and hard work, and at the age of 70 reaches the Emeritious stage. To many this is "life at its best", and many are also good examples of nice events, but at the end of the day, the way scientist DO science is build on that everything has to be bullet and water proof before he even discusses the theory with others, otherwise the classical debates begin. I have also heard from previous Senior Scientists passing the age of 50 of witnessing and ENJOYING debates where scientist where verbally annihilating each other, and I recall particularly what this professor said in the context with the debate he saw "it was blood on the dance floor". At= the end of the day it is a litigious procedure that scientists have to "survive" through, and= it creates FRICTION. This friction is my whole point of the discussion: It is energy and can be used to do great science (pr other positive things), and not wasted on discussions and debates. Those are just for entertaining the competitive nature in people. Competition, debate and discussion requires energy, again, that energy can be used for other things and is valuable.
Therefore, the quite and contemplating scientist who doesn't bother about debating or showing hi= s results before reaching a full final format, and perhaps not even showing them then but wait till people are not so interested in debating him, is a calm and relaxing scientist, that cares about the object of science, not the subject behind it or those around it.

Sergio

=A0

----- Original Message -----

From: j j robinson jameschums^^^yahoo.com

Sent: 08/17/12 09:48 PM

To: Manzetti, Sergio

Subject: CCL: On "defending" and "opposing&qu= ot; science

Dear CCLers,

=A0

might I suggest the original correspondent watches the film "Insignificance". We all have knowledge... but I prefer insight, understanding..I suspect I am simply too stupid to find the truth.. Experiment, observation, hypothesis. The debates are not battles of gladiators, nor personal feuds..science and/or natural philosophy - is patient observation, measurement, correlation, verification of experimental facts, comparison, perspective, understanding..we debate with others to make sure we are not simply deluding ourselves or that other are not deluded. We can agree to differ, review papers, admit mistakes..we are human too. Results and conclusion do not simply result from pressing the return key and waiting to see how many "hartree'= ;s" come out at the end.

=A0

J J Robinson - personal email - opinions are personal only.

=A0

=A0

--=20 Prof. Dr. Andreas Klamt CEO / Gesch=E4ftsf=FChrer COSMOlogic GmbH & Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt##= cosmologic.de web www.cosmolog= ic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] Join us at the 4th-COSMO-RS-Symposium April 2013 Details at www.cosmologic.de/symposium2013=20 HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
--=20
Prof. Dr. Andreas Klamt
CEO / Gesch=E4ftsf=FChrer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt()co=
smologic.de
web    	www.cosmolog=
ic.de

[University address:      Inst. of Physical and
Theoretical Chemistry, University of Regensburg]

Join us at the 4th-COSMO-RS-Symposium April 2013
Details at www.cosmologic.de/symposium2013=20

HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt

--bcaec51d2a383902af04c7a3c90f-- From owner-chemistry@ccl.net Sun Aug 19 17:30:01 2012 From: "Amy Austin amy_jean_austin[-]yahoo.com" To: CCL Subject: CCL: On "defending" and "opposing" science Message-Id: <-47409-120819161455-20331-HSousDVu3R/KX8CEMIoTbA/./server.ccl.net> X-Original-From: Amy Austin Content-Type: multipart/alternative; boundary="1073417382-128454288-1345407287=:19353" Date: Sun, 19 Aug 2012 13:14:47 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Amy Austin [amy_jean_austin],[yahoo.com] --1073417382-128454288-1345407287=:19353 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =0A=0AI think Fatima makes raises some excellent concerns here, and I agree= that vested interest does enter into the equation when it comes to peer re= view. Apparently, this isn't limited to journal submissions alone. I apolog= ize for the third party information, but I have heard of a reviewer rejecti= ng a grant proposal, and later plagiarizing it. Fortunately, that particula= r party was held accountable from what I understand.=0A=0ABest,=0A=0AAmy=0A= =0A=0A________________________________=0A From: Fatima Mons fatima.mons^^^y= ahoo.com =0ATo: "Austin, Amy J " =0ASent: Sunday, August 19, 2012 10:42 AM=0ASubject: CCL= : On "defending" and "opposing" science=0A =0A=0ASent to CCL by: "Fatima=A0= Mons" [fatima.mons]~[yahoo.com]=0AThere still is *an* amount of bias with = referees, especially those that have a vested interest.=A0 I know =0Aof one= case involving the aquatic toxicity of ionic liquids that was rejected for= publication (the paper =0Ashowed that the ionic liquids tested were more t= oxic in the aquatic environment than most =0Acommonly used molecular solven= ts).=A0 It turned out that one of the referees had a vested interest in =0A= ionic liquids (I believe that they didn't have a background in environmenta= l toxicity either).=A0 Editors =0Ahave to do more to ensure that referees d= o not have bias due to vested interests.=A0 Gerard's point =0Aabout hiding = author and organization affiliations from referees during the first review = is a good =0Apoint.=A0 The names of the authors and referees should be publ= ished for complete transparency after =0Athe review process.=A0 Furthermore= , if a paper is rejected and the author feels that this is not justified, = =0Athe board of editors should review the rejection to see if this is genui= nely justified and when =0Aappropriate seek additional referees.=A0 In some= cases, such as the aforementioned ionic liquid paper, =0Acalling upon refe= rees with an environmental background would be key here.=0A=0AIt can be all= to easy for an author to make 'grand claims' about benefits of a technolog= y when they =0Ahave next to no knowledge of that field.=A0 The scientific c= ommunity have to do more to genuinely =0Achallenge these claims and journal= editors have a moral and scientific duty to ensure that the =0Ascience is = of an appropriate standard and that there is no adverse bias or vested inte= rested involved =0Ain the publishing process.=0A=0AMay be there is a novel = way to deal with this type of situation.=A0 Publish the paper along with th= e =0Areferees' comments.=A0 In that way, the whole scientific community can= see the debate in a transparent =0Amanner, which prompts discussion and fu= rther scientific research.=A0 Clearly the editors will have to =0Amanage th= is process appropriately and on a case-by-case basis.=0A=0AFatima.=0A=0ABtw= ., the paper was published in another journal and subsequently a number of = other studies have =0Abeen published by other groups which have come to sim= ilar conclusions.=A0 So the science was indeed =0Avalid!=0A=0A=0A=0A-=3D Th= is is automatically added to each message by the mailing script =3D-=0ATo r= ecover the email address of the author of the message, please change=0Athe = strange characters on the top line to the .. sign. You can also=0Alook up th= e X-Original-From: line in the mail header.=0A=0AE-mail to subscribers: CHE= MISTRY..ccl.net or use:=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_cc= l_message=0A=0A= =0A=A0 =A0 =A0=0A=0ASubscri= be/Unsubscribe: =0A=A0 =A0 =A0= =0A=0A=0A=0AJob: http= ://www.ccl.net/jobs =0AConferences: http://server.ccl.net/chemistry/announc= ements/conferences/=0A=0ASearch Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml=0A=0AIf your mail bounces from CCL with 5.7.1 error, chec= k:=0A=A0 =A0 =A0=0A=0ARTFI: http://www.ccl.= net/chemistry/aboutccl/instructions/ --1073417382-128454288-1345407287=:19353 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

I think Fatima makes raises some excellent concerns here, and I= agree that vested interest does enter into the equation when it comes to p= eer review. Apparently, this isn't limited to journal submissions alone. I = apologize for the third party information, but I have heard of a reviewer r= ejecting a grant proposal, and later plagiarizing it. Fortunately, that par= ticular party was held accountable from what I understand.

Best,

Amy

= From: Fatima Mons fatima.mons^^^yahoo.com <owner-chemistry..ccl.net>
To: "Austin, Amy J " <amy_jea= n_austin..yahoo.com>
Sent: Sunday, August 19, 2012 10:42 AM
Subject: CCL: On "defending" and "opposing" science
=

=0A
Sent to CCL by: "Fatima Mons" [fatima.mons]= ~[yahoo.com]
There s= till is *an* amount of bias with referees, especially those that have a ves= ted interest. I know
of one case involving the aquatic toxicity o= f ionic liquids that was rejected for publication (the paper
showed tha= t the ionic liquids tested were more toxic in the aquatic environment than = most
commonly used molecular solvents). It turned out that one of= the referees had a vested interest in
ionic liquids (I believe that th= ey didn't have a background in environmental toxicity either). Editor= s
have to do more to ensure that referees do not have bias due to veste= d interests. Gerard's point
about hiding author and organization = affiliations from referees during the first review is a good
point.&nbs= p; The names of the authors and referees should be published for complete t= ransparency after
the review process. Furthermore, if a paper is rejected and the = author feels that this is not justified,
the board of editors should re= view the rejection to see if this is genuinely justified and when
appro= priate seek additional referees. In some cases, such as the aforement= ioned ionic liquid paper,
calling upon referees with an environmental b= ackground would be key here.

It can be all to easy for an author to = make 'grand claims' about benefits of a technology when they
have next = to no knowledge of that field. The scientific community have to do mo= re to genuinely
challenge these claims and journal editors have a moral= and scientific duty to ensure that the
science is of an appropriate st= andard and that there is no adverse bias or vested interested involved
= in the publishing process.

May be there is a novel way to deal with = this type of situation. Publish the paper along with the
referees' comments. In that way, the whole scientific community = can see the debate in a transparent
manner, which prompts discussion an= d further scientific research. Clearly the editors will have to
m= anage this process appropriately and on a case-by-case basis.

Fatima= .

Btw., the paper was published in another journal and subsequently = a number of other studies have
been published by other groups which hav= e come to similar conclusions. So the science was indeed
valid!

-=3D This is automatically added to each message by the maili= ng script =3D-
To recover the email address of the author of the message= , please change
the strange characters on the top line to the .. sign. Yo= u can also
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--1073417382-128454288-1345407287=:19353-- From owner-chemistry@ccl.net Sun Aug 19 18:05:00 2012 From: "Kira Armacost kza0004-*-auburn.edu" To: CCL Subject: CCL: Bio3D Endian error Message-Id: <-47410-120819165212-14878-bvUGZXQ54wNX6W7bCBH09w|*|server.ccl.net> X-Original-From: "Kira Armacost" Date: Sun, 19 Aug 2012 16:52:11 -0400 Sent to CCL by: "Kira Armacost" [kza0004|auburn.edu] I'm rather new to running Bio3D jobs, and I just received a strange error message which I can't tackle. I'm trying to read in my dcd trajectory generated from AMBER, which I changed from a .crd to a .dcd in VMD and this is the error I recieved: > trj <- read.dcd("/home/aubkaa/FMN/monooxygenase/FMR/apo/DCD/combine-LES.dcd", big=TRUE) [1] "PROBLEM with endian detection" Error in readChar(trj, nchars = 4) : invalid connection Calls: read.dcd -> dcd.header -> readChar Execution halted I tried searching and couldn't figure it out. I also reran it without the big=TRUE message and still got the error. Any help would be greatly appreciated. Thank you! From owner-chemistry@ccl.net Sun Aug 19 19:09:00 2012 From: "Irene Newhouse einew|*|hotmail.com" To: CCL Subject: CCL: Suggestion Message-Id: <-47411-120819185048-11205-rl53W/IfJH0c7jMcFnyjkg::server.ccl.net> X-Original-From: "Irene Newhouse" Date: Sun, 19 Aug 2012 18:50:45 -0400 Sent to CCL by: "Irene Newhouse" [einew_._hotmail.com] Sergio suggested 'let more women in science'... In my undergraduate senior seminar, I was the only women among about 20 students. I worked in industry for 6 years, then went back to graduate school in physical chemistry. My incoming class was 1/3 women. Things have change a LOT. Yes, departments could do significantly better in making things easier for young scientists to succeed - all my professional career, there has been an enormous imbalance in the number of applicants for fewer & fewer faculty positions, & I've observed something I'll call tenure abuse, but I can't judge whether it hits women worse than men. Even if does, are scientists more biased against women than society at large? I was part of a discussion among non-scientists yesterday in which the topic was, does the fact that Barack Obama is now president of the US while Hillary Clinton the Secretary of State mean that the US is more sexist than racist? And the clinching argument was, so many other countries have already had women heads of state, so yes. A large part of the problem begins long before a person chooses a career field, and we scientists should probably be more active in doing something about THAT. Girls are still not supposed to be good at math. Scientists are rarely if ever the heroes in entertainment & are generally pictured as ranging from outright evil to creepily dysfunctional. It's still common for Americans to react to learning I have a Ph D in chemistry by saying, "But you seem so normal". [Not the typical response for non-Americans, by the way]. There is a large anti-intellectual bias in the US. I tutor high school math part-time, and teenage boys regularly act sceptical about my ability to tutor them the first time - because I seem so normal, I guess. They're embarrassed to tell me when I ask after the tutoring session. Irene Newhouse From owner-chemistry@ccl.net Sun Aug 19 19:46:00 2012 From: "Amy J Austin amy_jean_austin__yahoo.com" To: CCL Subject: CCL: On "defending" and "opposing" science Message-Id: <-47412-120819191828-27590-u0X/E1NtS7r8YQSI0tOA4Q||server.ccl.net> X-Original-From: "Amy J Austin" Date: Sun, 19 Aug 2012 19:18:26 -0400 Sent to CCL by: "Amy J Austin" [amy_jean_austin]=[yahoo.com] IMHO, Fatima makes some excellent points here, as well. I feel it is important that I chime in. If the student were "rubbished academically" to the extent that they could no longer have a job in their chosen field, then why is it surprising that the individual does not have one currently? I enjoyed your post in reference to ionic liquids earlier today. I think it sounds reasonable that a person could be defamed by a subset of people but their ideas/proofs are valid - just like in your ionic liquid story. Ultimately, the proof of the pudding is in the eating. Certainly, one doesn't need to be a Mathematician to enjoy teaching Calculus, for example, nor should he/she claim to be one. I can say that I am a Computational Chemist who enjoys teaching Organic Chemistry since 1998. I invite readers of CCL to read my student success stories: http://www.wyzant.com/Tutors/NJ/Morganville/7792432/ http://www.linkedin.com/in/organontutoring Kind regards, Amy All my best, Amy > "Fatima Mons Fatima.mons]~[yahoo.com" wrote: > > Sent to CCL by: "Fatima Mons" [Fatima.mons^yahoo.com] > In any organization there can be some questionable practices and universities are no exceptions. I've > hear of academics unfairly damaging a student's career do personal conflicts, to the point that the > student is unable to pursue a career in their chosen field. One very unsavory incident I'm aware of > involved the academic rubbishing the student, then waiting an appropriate amount of time before > publishing the work in their own name. The whole governance system was flawed in that organization > for it to happen. > > There is another side to the equation. The student doesn't always make the grade for the academic to > approve them (usually again because of the failures of university system). We had an example of a > candidate claiming that their Ph.D. was a dual speciality that included organic chemistry. When they > were questioned about it, they couldn't solve problems that we would expect new graduates to be able > to answer. This individual's ego was writing checks that their minds couldn't cash. That person still > doesn't have a chemistry job, yet still claims to be an organic chemistry expert! > > For both sides of the coin it is really important that universities have appropriate processes in place to > protect the academic staff and the student body with equal fairness. However, the universities > themselves can have own interests. I'm sure most of you will have heard the news stories about a > football coach at an American university, where there have been claims that the university turned a > blind eye to some very disturbing activities. Vested interests and all that! > > Fatima. > > From owner-chemistry@ccl.net Sun Aug 19 21:19:01 2012 From: "Salter-Duke, Brian James - brian.james.duke*|*gmail.com" To: CCL Subject: CCL: On "defending" and "opposing" science Message-Id: <-47413-120819184207-5386-3uFaUYb1OFnr2jSzkwgdWg++server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 20 Aug 2012 08:41:52 +1000 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke]^[gmail.com] I would like to add another issue. It seems to have become common for the authors to be asked to nominate referees. The editor then takes the easy way out and uses the nominated referees at least in part. This should be stopped as it allows two groups to mutually support each other, even if subconsciously. However, authors should be allowed to nominate people who they do not want to act as referees, thus allowing them to not have their paper refereed by people they think are prejudiced against their ideas. Brian Duke. On Sun, Aug 19, 2012 at 07:41:52PM +0000, Mezei, Mihaly mihaly.mezei###mssm.edu wrote: > > Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei-.-mssm.edu] > Greetings, > > This thread has touched upon many important issues so I feel justified to include one more: the abdication of responsibilities of many editors. Like one of the posters' experience where an editor ignored a referee suggestion because of two other referees' opposing view, I had editor ignoring my specific arguments against a referee's (negative) argument and telling me that I have to convince that referee (not him). I suggest that the community insist of the editors being more than simple vote counters; instead they should actively arbitrate the discussion between the author(s) and referees. This way there would be less need for a post-publication discussion. There is, of course, always the avenue of publishing a comment on a paper in the traditional way. > > Mihaly Mezei > > Department of Structural and Chemical Biology, Mount Sinai School of Medicine > Voice: (212) 659-5475 Fax: (212) 849-2456 > WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > WWW (Department): http://atlas.physbio.mssm.edu > -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke() monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia From owner-chemistry@ccl.net Sun Aug 19 22:38:01 2012 From: "Eric Bennett ericb,pobox.com" To: CCL Subject: CCL: Well... Message-Id: <-47414-120819214827-22011-LT4yUGJDIkR05ykvq1/dug:server.ccl.net> X-Original-From: Eric Bennett Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=windows-1252 Date: Sun, 19 Aug 2012 21:48:05 -0400 MIME-version: 1.0 (Apple Message framework v1084) Sent to CCL by: Eric Bennett [ericb(_)pobox.com] George, There is obviously no shortage of what you call "professional obfuscators". However, I think there are too many scientists involved in politically charged research who get intellectually lazy and automatically try to lump all of their critics into that category. It's not a bad thing that additional studies have been done in the past couple years to rule out the possibility that global temperature measurements could have been skewed by bias of stations being located near cities, for example. Those studies have convinced some prior critics of global warming science to change their minds. Some pieces that are thoughtful, somewhat contrarian takes on cases where science and politics intersect: 1. http://online.wsj.com/article/SB10000872396390444772404577589270444059332.html 2. Environmental Alarmism, then and Now. Bjorn Lomberg. Foreign Affairs vol 91, no 4 (2012). 3. http://ngm.nationalgeographic.com/2007/07/malaria/finkel-text One snip from the second source: "[In 1980] economist Julian Simon, frustrated by incessant claims that the planet would run out of oil, food, and raw materials, offered to bet $10,000 that any given raw material picked by his opponents would drop in price over time. Simon�s gauntlet was taken up by the biologist [Paul] Ehrlich and the physicists John Harte and John Holdren (the latter is now U.S. President Barack Obama�s science adviser), saying 'the lure of easy money can be irresistible.' The three staked their bets on chromium, copper, nickel, tin, and tungsten, and they picked a time frame of ten years. When the decade was up, all five commodities had dropped in price, and they had to concede defeat (although they continued to stand by their original argument)." There is still legitimate debate about some of the topics you and Sergio mentioned. As the third article states, "In the face of the growing malaria toll, access to DDT is gradually becoming easier, and even the Sierra Club does not oppose limited spraying for malaria control." Sometimes scientifically political crusades to ban things that are harmful in a particular context go past their logical endpoint. There are scientific charlatans on both ends of the political spectrum. Cheers, Eric On Aug 19, 2012, at 10:13 AM, George Fitzgerald George.Fitzgerald*|*accelrys.com wrote: > > Sent to CCL by: George Fitzgerald [George.Fitzgerald:+:accelrys.com] > Sergio, > > There is little that I can add to the excellent comments of my peers. I wanted to comment, though, on your recent post. You wrote > > It is the "guerrier" aspect of science which generates the contiguous debates of science that never end, and that cost billlions of tax payers money, as in the case of CFC gases in the 80s and ozone, DDTs in the 70s and infertility in birds and animals, dioxins in the 60s at industrial sites destroying entire ecosystems, Lead in the pain in the 50s damaging health and one can nearly go back in 10-year cycles to see the absurdities of science caused by endless debate and not following "a straight-ling between two points" in order to conclude if something is working or not. > > This is the collision between science and politics. Along with the examples I mentioned earlier - cigarettes and acid rain - these debates were NOT prolonged by serious scientists but by professional obfuscators who were in the pockets of the corporations. They couldn't refute the evidence, but they could - and did - prolong the debate. I agree that this is a horrible state of affairs, and I wish I knew what to do about it. > > -george > > From owner-chemistry@ccl.net Sun Aug 19 23:13:01 2012 From: "Alavi, Saman Saman.Alavi:_:nrc-cnrc.gc.ca" To: CCL Subject: CCL: Suggestion Message-Id: <-47415-120819220801-30009-2vBO77S+gMROCdMQdnxKzg%a%server.ccl.net> X-Original-From: "Alavi, Saman" Content-Language: en-CA Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 19 Aug 2012 19:07:52 -0700 MIME-Version: 1.0 Sent to CCL by: "Alavi, Saman" [Saman.Alavi+*+nrc-cnrc.gc.ca] Dear Sergio, Some very good conversations have come up from this thread. I think its somewhat naive to expect that science, which is after all a human endeavor, would be any different from other fields of human activity. Can we point out any field of human activity which is not influenced by egos, power imbalances, vested interests, etc.? At least science has the advantage that its propositions have to be falsifiable by design, so are not absolute declarations. Also, scientific results must be verifiable regardless of location, prestige of lab, etc. They are not one-shot miracles observed by a select few. Can we say art, religion, or business hold up to these standards? The peer review system does at times become adversarial, which is unfortunate, but can anyone suggest a working model that would do things differently and better? Of course, the peer review system can be improved and reformed, for example, by editors automatically rejecting reviews which attack the authors rather than criticize a work. Many other excellent suggestions have been mentioned in this thread. Note that the anonymous peer review system is also there to protect a junior reviewer from the "expert" author (who may be wrong in this case). Would any junior reviewer want to be named as the person who rejected a work by a well-known scientist at a prestigious institution who is perhaps chair of a national granting committee? It would be great if everyone reached a level of maturity as to be able to accept criticism from others, regardless of their status. If we see the bickering and petty quarrels between some of the greatest minds of science, such as Newton and Hooke, its no surprise that these things go on now. Being a scientist is not a guard against the vices of human nature... :-) Hopefully you will continue in science and be involved in reviewing manuscripts. If your field involves physics, quantum mechanics, relativity, you will receive tens of manuscripts trying to prove Einstein was wrong about relativity, to propose a machine which can generate work out of nothing, and prove that the position and momentum of electrons can indeed be simultaneously determined. How much time should the science community have to spend on these "results". I do not know if having more patience with this type of "science" is beneficial. In the end, its the beauty of understanding nature which makes us all scientist. Its always good to keep this in mind when dealing with these other inevitable distractions. Best regards, Saman Alavi ________________________________________ > From: owner-chemistry+saman.alavi==nrc.ca+*+ccl.net [owner-chemistry+saman.alavi==nrc.ca+*+ccl.net] On Behalf Of Sergio Manzetti sergio.manzetti###gmx.com [owner-chemistry+*+ccl.net] Sent: August 19, 2012 1:36 PM To: Alavi, Saman Subject: CCL: Suggestion Let more women in science, particularly the heavy sciences such as QM, Particle Physics and theoretical astrophysics. Shift the subject away from peer-review issues and problems in dissemination, this has to do with traditions that are male-made and derive from the 12th century and need to be rounded and merged with new ways of thinking, with a maintenance of the strict demands of correctness, precision and collective evaluation of scientific works. Also, leave the innovators alone and let students and young newcomers test their "stupid" theories not matter how stupid they sound. They need to try. Sergio