Hello,

You cannot retrieve a checkpoin= t file if you did not state in your input that it should be saved (e.g., % = chk =3D example.chk)

If you ran the calculatio= n on a different machine, the checkpoint file cannot be used as it will be = hardware specific. In that case use the formchk utility:

http://www.gaussian.com/g_tech/g_ur/u_formchk.htm

Hope this helps.

Best,

Amy

From: "quantum chem qchem66,+,gmail= .com" <owner-chemistry%a%ccl.net>
To: "Austin, Amy J " <amy_jean_austin%a%yahoo.com&= gt;
Sent: Saturday, A= ugust 18, 2012 10:15 AM
Subject:<= /span> CCL:G: .chk from log

=0A
Sent to CCL b= y: "quantum chem" [qchem66 * gmail.com]
Dear members,
&nbs= p; I would greatly appreciate if someone helps me out in kno= wing
the following 2 things in a gaussian calculation:
1.How to retr= ieve .chk file from a log file in a gaussian calculation if .chk
keywor= d was not given in the input?
2.Suppose i have run a gaussian calculatio= n on a remote machine and the.chk
file has been generated there..then h= ow to open/read the .chk file on a
different system other than th= e remote one.

Thanks in advance and excuse me for such a naive= question.

QC

-=3D This is automatically added to eac= h message by the mailing script =3D-
To recover the email address of the= author of the message, please change
the strange characters on the top = line to the %a% sign. You can also
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---244526598-911069915-1345319960=:32389-- From owner-chemistry@ccl.net Sat Aug 18 17:18:00 2012 From: "Gerard JP van Westen gerard.vanwesten]![gmail.com" To: CCL Subject: CCL: On "defending" and "opposing" science Message-Id: <-47396-120818155048-29836-H3WD0z/jj3f2cbhdT+6u8Q##server.ccl.net> X-Original-From: Gerard JP van Westen Content-Type: multipart/alternative; boundary=f46d0438936f30a4dd04c78f971e Date: Sat, 18 Aug 2012 20:50:07 +0100 MIME-Version: 1.0 Sent to CCL by: Gerard JP van Westen [gerard.vanwesten~!~gmail.com] --f46d0438936f30a4dd04c78f971e Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 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 th= at > 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 h= is > 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 evolve= s. > 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 we= ll > 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 usual= ly > the latter are not allowed by the editors any more. Hence it is like in t= he > 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 a= nd > 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 ne= ed > 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 t= he > 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 t= wo > positive and one negative reports. Thus we had accepted it. Asking him, > whether he had sent my substantial concerns to the other reviewers in ord= er > to reconsider their opinion, he answered that that would not be within th= e > rules of the journal. And just yesterday I saw that a paper by an > influencing author appeared online essentially unchanged, although I agai= n > 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 ar= e > many cases where people with great ideas never make it to the surface, > either because they are not "strong" enough to "battle" against oppositio= n > 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, meanwhil= e > 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 h= ow > 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 u= p > 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", a= nd > many are also good examples of nice events, but at the end of the day, th= e > 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 th= e > classical debates begin. I have also heard from previous Senior Scientist= s > passing the age of 50 of witnessing and ENJOYING debates where scientist > where verbally annihilating each other, and I recall particularly what th= is > 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 use= d > 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 experiment= al > 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 > > > > --f46d0438936f30a4dd04c78f971e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 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 comm= ents which seemed subjective rather than objective. I can therefore underst= and 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 sit= uation, but a paper should be about the science. The science should be soun= d and as you said, the authors should be able to respond to questions and d= efend their paper. BUT it should not matter who they are. When authors are = disclosed on a manuscript it always indirectly includes their full career i= n 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 therefor= e argue that authors should also be anonymous on a manuscript (it should on= ly be known to the editor who is who).=A0

In addition, I would argue to add the referees that rev= iewed 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 publicat= ion discussion as this orm of discussion allows the whole field to be invol= ved rather than a select number of people. In addition it could perhaps lea= d to a reduction of papers that are accepted too easy as the referees respo= nsible 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.

R= egards,

Gerard

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

=20 =20 =20
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.co= m:

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" agai= nst opposition or criticism, or they simply don't want to. I know of one who ha= d 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&qu= ot;. 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" t= hrough, 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

=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" sc= ience

Dear CCLers,

=A0

might I suggest the original correspondent watches the film "Insignificance". We all hav= e 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. <= /div>
=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

--f46d0438936f30a4dd04c78f971e-- From owner-chemistry@ccl.net Sat Aug 18 22:32:01 2012 From: "Amy Austin amy_jean_austin||yahoo.com" To: CCL Subject: CCL:G: On "defending" and "opposing" science Message-Id: <-47397-120818174846-27274-XEugaK/bCZ5sy7q0aUb+Vw-$-server.ccl.net> X-Original-From: Amy Austin Content-Type: multipart/alternative; boundary="-15486822-32061779-1345326515=:40977" Date: Sat, 18 Aug 2012 14:48:35 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Amy Austin [amy_jean_austin ~~ yahoo.com] ---15486822-32061779-1345326515=:40977 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Greetings CCLer's:=0A=0AAlso in agreement with Andreas. I think that Gerard= 's point is valid. Let us assume that one is affiliated with Gaussian, and = one or more referree(s) in question is a part of the "Banned by Gaussian" m= ovement. Bias also has no place in science.=0A=0A=0AAmy.=0A=0A=0A=0A_______= _________________________=0A From: Gerard JP van Westen gerard.vanwesten]![= gmail.com =0ATo: "Austin, Amy J " =0ASent: Saturday, August 18, 2012 3:50 PM=0ASubject: C= CL: On "defending" and "opposing" science=0A =0A=0ADear All,=0A=0AI should = say I agree with Andreas Klamt, to me it sometimes seems peer review sets t= he boundary low. However I have also had experiences where a referee could = not always substantiate negative comments which seemed subjective rather th= an objective. I can therefore understand that one can get frustrated. But w= ould still argue that the scientific method as it is, is the best available= (at least I cannot think of a better way).=A0=0A=0AThat said however, to m= e 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 sci= ence. The science should be sound and as you said, the authors should be ab= le 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 indirec= tly includes their full career in the form of previously published papers, = conferences, personal encounters etc. This will always influence an objecti= ve judgement (wether negative or positive it is difficult to remain complet= ely objective). I would therefore argue that authors should also be anonymo= us on a manuscript (it should only be known to the editor who is who).=A0= =0A=0AIn 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 a= dded to the header in PLoS ONE). This will allow authors to continue the di= scussion with a referee after a paper has been accepted. I concur that disc= ussion if a good thing, and in=A0particular=A0post publication discussion a= s 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=0A=0AIn any c= ase, just my $ 0.02.=0A=0ARegards,=0A=0AGerard=0A=0AOn Sat, Aug 18, 2012 at= 10:02 AM, Andreas Klamt klamt]*[cosmologic.de = wrote:=0A=0ASergio,=0A>as most other contributors, I think that you are see= ing things too=0A pessimistic here. Critical discussion and opposition= really are=0A important for the advancement of science. Indeed, I bel= ieve that=0A we need more of that and that we have to find more open w= ays to=0A oppone and discuss scientific results. We need more discussi= on in=0A conferences after the talks, and we need a better way of=0A = discussion of scientific papers. Sometimes I have am considered as=0A = inpolite when I ask a really critical question after a scientific=0A = presentation. But how can that be? I think everybody who presents=0A = or publishes in sciences should have good arguments for all of his=0A = statements and results. If that is the case then he will be well=0A = prepared to reply to that question. If not then the question has=0A di= sclosed some weekness in his research and it should help to=0A improve= . Discussion at the end of talks also are too much=0A bilateral betwee= n speaker and opponent. Usually no real discussion=0A between many of = the experts in the room evolves. But that would be=0A interesting and = sometimes needed. Today mostly the discussion is=0A just a question by= an opponent and an answer by the speaker, and=0A it ends a bit vague.= If the question was unfair or the speaker not=0A well able to find th= e right answer, he goes home with a bad=0A feeling, and if on the othe= r hand the reply was wrong or unfair,=0A the opponent goes home with a= bad feeling. It would be good if we=0A would have the culture of disc= ussion that in such a situation=0A other people stand up in order to e= ither support the speaker or=0A the opponent, or have a third oppinion= . =0A>=0A>I think we need this culture even more in scientific literature.= =0A We need more "Comments on paper xyz", and we need comments on=0A = comments, but usually the latter are not allowed by the editors=0A = any more. Hence it is like in the conference room: The author has=0A = the last word, and if the reply on a comment is again misleading,=0A t= he opponent has no way of replying any more. And we need the=0A discus= sion on papers on a shorter time scale and at one place.=0A Today each= round takes 2 months at minimum. Nowadays it should be=0A doable to d= o such discussion of a paper electronically, and it=0A should be avail= able online at the end of each article. Hence, when=0A downlaoding an = article you could have a quick look whether there=0A has been a discus= sion and what the average opinion had been. =0A>=0A>The reason why I think = that we need such discussion culture and=0A forum is that I am less op= timistic about peer review meanwhile. No=0A question, we need the peer= review system to filter out some=0A rubbish and to have a barrier whi= ch hinders unserious people to=0A submit all rubbish as scientific pap= ers. But I am afraid that much=0A too many bad papers go through the s= ystem and after passing can=0A claim to be peer reviewed. Some influen= cing people in the=0A community who know the editors since long get ev= erything=0A published, even if one reviewer has detected substantial m= istakes.=0A In one case I proved mathmatically that some equation whic= h was=0A considered by the author as something new, was mathmatically= =0A identical with an earlier published equation of someone else. I=0A= suggest not to publish the paper with that wrong claim. The paper=0A = appeared essentially unchanged in an ACS journal. Asking the=0A e= ditor how this could happen, he answered that he had gotten two=0A pos= itive and one negative reports. Thus we had accepted it. Asking=0A him= , whether he had sent my substantial concerns to the other=0A reviewer= s in order to reconsider their opinion, he answered that=0A that would= not be within the rules of the journal. And just=0A yesterday I saw t= hat a paper by an influencing author appeared=0A online essentially un= changed, although I again had a raised a=0A number of severe concerns.= =A0 Therefore I believe: We need more=0A critical post-peer-review deb= ates.=0A>=0A>Andreas=0A>=0A>Am 18.08.2012 02:43, schrieb Sergio Manzetti=0A= sergio.manzetti-$-gmx.com:=0A>=0A>I think JJ and Amy are getting clos= er 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" en= ough 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 w= as never scientifically validated, he received cold showers each time he op= ened up his method to scientist. In the meantime, his method treated a lot = of people, and they recovered. Scientists ARE trained to validate, annihila= te, exclude, disregard and eventually accept. This trait of the scientist i= s to me a little stupidious, it seems like House in the series at the hospi= tal. He goes through a bunch of hypotheses and tests them all on the patien= t, meanwhile the patient suffers and at the end after hitting the right hyp= othesis he calls himself a great doctor (or at least appears to be one). Sa= me thing are scientists, they are recognized as great after they have learned on how to tramp down oppos= ition as the first step in their life as scientists, then they have to defe= nd 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 pseu= do-darwinistic=A0=A0 behavior, the scientist fights through the hierarchy o= f late nights and hard work, and at the age of 70 reaches the Emeritious st= age. 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 bu= ild on that everything has to be bullet and water proof before he even disc= usses the theory with others, otherwise the classical debates begin. I have= also heard from previous Senior Scientists passing the age of 50 of witnes= sing 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 e= nd 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 d= iscussion: It is energy and can be used to do great science (pr other posit= ive things), and not wasted on discussions and debates. Those are just for = entertaining the competitive nature in people. Competition, debate and disc= ussion requires energy, again, that energy can be used for other things and= is valuable.=0A>>Therefore, the quite and contemplating scientist who does= n't=0A bother about debating or showing his results before reachin= g a=0A full final format, and perhaps not even showing them then b= ut=0A wait till people are not so interested in debating him, is a= =0A calm and relaxing scientist, that cares about the object of=0A= science, not the subject behind it or those around it.=0A>>=0A>>= =0A>>Sergio=0A>>=0A>>=0A>>=A0=0A>>----- Original Message -----=0A>>>From: j= j robinson jameschums^^^yahoo.com=0A>>>Sent: 08/17/12 09:48 PM=0A>>>To: Ma= nzetti, Sergio =0A>>>Subject: CCL: On "defending" and "opposing" science=0A= >>>=0A>>>Dear CCLers, =0A>>>=A0=0A>>>might I suggest the original correspon= dent watches the film "Insignificance". We all have knowledge... but I pref= er insight, understanding..I suspect I am simply too stupid to find the tru= th.. Experiment, observation, hypothesis. The debates are not battles of gl= adiators, nor personal feuds..science and/or natural philosophy - is patien= t observation, measurement, correlation, verification of experimental facts= , comparison, perspective, understanding..we debate with others to make sur= e we are not simply deluding ourselves or that other are not deluded. We ca= n agree to differ, review papers, admit mistakes..we are human too. Results= and conclusion do not simply result from pressing the return key and waiti= ng to see how many "hartree's" come out at the end. =0A>>>=A0=0A>>>J J Robi= nson - personal email - opinions are personal only.=0A>>>=0A>>>=A0=0A>>=A0 = =0A>=0A>=0A>-- =0AProf. Dr. Andreas Klamt=0ACEO / Gesch=E4ftsf=FChrer=0ACOS= MOlogic GmbH & Co. KG=0ABurscheider Strasse 515=0AD-51381 Leverkusen, Germa= ny phone +49-2171-731681 fax +49-2171-731689 e-mail klamt##cosmologic.de we= b www.cosmologic.de [University address: Inst. of Physical and=0ATheor= etical Chemistry, University of Regensburg] Join us at the 4th-COSMO-RS-Sym= posium April 2013=0ADetails at www.cosmologic.de/symposium2013 HRA 20653 Am= tsgericht Koeln, GF: Prof. Dr. Andreas Klamt=0AKomplementaer: COSMOlogic Ve= rwaltungs GmbH=0AHRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt ---15486822-32061779-1345326515=:40977 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Greetings = CCLer's:

Also in agreeme= nt with Andreas. I think that Gerard's point is valid. Let us assume that o= ne is affiliated with Gaussian, and one or more referree(s) in question is = a part of the "Banned by Gaussian" movement. Bias also has no place in scie= nce.

Amy.

Fr= om: Gerard JP van Westen gerard.vanwesten]![gmail.com <owner-= chemistry- -ccl.net>
To:<= /b> "Austin, Amy J " <amy_jean_austin- -yahoo.com>
Sent: Saturday, August 18, 2012 3:50= PM
Subject: CCL: On "= defending" and "opposing" science

=0A
Dear = All,

I should say I agree with Andreas Klamt, to me it s= ometimes seems peer review sets the boundary low. However I have also had e= xperiences where a referee could not always substantiate negative comments = which seemed subjective rather than objective. I can therefore understand t= hat one can get frustrated. But would still argue that the scientific metho= d as it is, is the best available (at least I cannot think of a better way)= .
=0A=0A

That said however, to me it seems st= range that referees are anonymous but authors are not. Perhaps I am over&nb= sp;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 resp= ond to questions and defend their paper. BUT it should not matter who they = are. When authors are disclosed on a manuscript it always indirectly includ= es their full career in the form of previously published papers, conference= s, personal encounters etc. This will always influence an objective judgeme= nt (wether negative or positive it is difficult to remain completely object= ive). I would therefore argue that authors should also be anonymous on a ma= nuscript (it should only be known to the editor who is who).
=0A= =0A

In addition, I would argue to add the referees that = reviewed a paper to all published papers (perhaps added to the header as th= e editor is added to the header in PLoS ONE). This will allow aut= hors to continue the discussion with a referee after a paper has been accep= ted. I concur that discussion if a good thing, and in particular = post publication discussion as this orm of discussion allows the whole fiel= d to be involved rather than a select number of people. In addition it coul= d perhaps lead to a reduction of papers that are accepted too easy as the r= eferees responsible for this acceptance are also named on the paper. Likewi= se, referees that positively review a paper are also in some small way conn= ected to it.
=0A=0A

In any case, just my $ 0.= 02.

Regards,

Gerard
=

On Sat, Aug 18, = 2012 at 10:02 AM, Andreas Klamt klamt]*[cosmologic.de <<= a rel=3D"nofollow" ymailto=3D"mailto:owner-chemistry],[ccl.net" target=3D"_= blank" href=3D"mailto:owner-chemistry],[ccl.net">owner-chemistry],[ccl.net<= /a>> wrote:
=0A=0A
= =0A =0A =0A =0A
=0A
Sergio,
=0A as most other co= ntributors, I think that you are seeing things too=0A pessimistic here= . Critical discussion and opposition really are=0A important for the a= dvancement of science. Indeed, I believe that=0A we need more of that = and that we have to find more open ways to=0A oppone and discuss scien= tific results. We need more discussion in=0A conferences after the tal= ks, and we need a better way of=0A discussion of scientific papers. So= metimes I have am considered as=0A inpolite when I ask a really critic= al question after a scientific=0A presentation. But how can that be? I= think everybody who presents=0A or publishes in sciences should have = good arguments for all of his=0A statements and results. If that is th= e case then he will be well=0A prepared to reply to that question. If = not then the question has=0A disclosed some weekness in his research a= nd it should help to=0A improve. Discussion at the end of talks also a= re too much=0A bilateral between speaker and opponent. Usually no real= discussion=0A between many of the experts in the room evolves. But th= at would be=0A interesting and sometimes needed. Today mostly the disc= ussion is=0A just a question by an opponent and an answer by the speak= er, and=0A it ends a bit vague. If the question was unfair or the spea= ker not=0A well able to find the right answer, he goes home with a bad= =0A feeling, and if on the other hand the reply was wrong or unfair,= =0A the opponent goes home with a bad feeling. It would be good if we= =0A would have the culture of discussion that in such a situation=0A = other people stand up in order to either support the speaker or=0A = the opponent, or have a third oppinion.
=0A
=0A I think = we need this culture even more in scientific literature.=0A We need mo= re "Comments on paper xyz", and we need comments on=0A comments, but u= sually the latter are not allowed by the editors=0A any more. Hence it= is like in the conference room: The author has=0A the last word, and = if the reply on a comment is again misleading,=0A the opponent has no = way of replying any more. And we need the=0A discussion on papers on a= shorter time scale and at one place.=0A Today each round takes 2 mont= hs at minimum. Nowadays it should be=0A doable to do such discussion o= f a paper electronically, and it=0A should be available online at the = end of each article. Hence, when=0A downlaoding an article you could h= ave a quick look whether there=0A has been a discussion and what the a= verage opinion had been.
=0A
=0A The reason why I think t= hat we need such discussion culture and=0A forum is that I am less opt= imistic about peer review meanwhile. No=0A question, we need the peer = review system to filter out some=0A rubbish and to have a barrier whic= h hinders unserious people to=0A submit all rubbish as scientific pape= rs. But I am afraid that much=0A too many bad papers go through the sy= stem and after passing can=0A claim to be peer reviewed. Some influenc= ing people in the=0A community who know the editors since long get eve= rything=0A published, even if one reviewer has detected substantial mi= stakes.=0A In one case I proved mathmatically that some equation which= was=0A considered by the author as something new, was mathmatically= =0A identical with an earlier published equation of someone else. I=0A= suggest not to publish the paper with that wrong claim. The paper=0A = appeared essentially unchanged in an ACS journal. Asking the=0A e= ditor how this could happen, he answered that he had gotten two=0A pos= itive and one negative reports. Thus we had accepted it. Asking=0A him= , whether he had sent my substantial concerns to the other=0A reviewer= s in order to reconsider their opinion, he answered that=0A that would= not be within the rules of the journal. And just=0A yesterday I saw t= hat a paper by an influencing author appeared=0A online essentially un= changed, although I again had a raised a=0A number of severe concerns.= Therefore I believe: We need more=0A critical post-peer-review = debates.
=0A
=0A Andreas
=0A
=0A Am 18.08= .2012 02:43, schrieb Sergio Manzetti=0A sergio.manzetti-$-gmx.com:
=0A <= /div>
=0A
I think = JJ and Amy are getting closer=0A to the point I am stating. There = are many cases where people=0A with great ideas never make it to t= he surface, either because=0A they are not "strong" enough to "bat= tle" against opposition or=0A criticism, or they simply don't want= to. I know of one who had=0A a great method to treat people, but = because it was never=0A scientifically validated, he received cold= showers each time=0A he opened up his method to scientist. In the= meantime, his=0A method treated a lot of people, and they recover= ed. Scientists=0A ARE trained to validate, annihilate, exclude, di= sregard and=0A eventually accept. This trait of the scientist is t= o me a=0A little stupidious, it seems like House in the series at = the=0A hospital. He goes through a bunch of hypotheses and tests t= hem=0A all on the patient, meanwhile the patient suffers and at th= e=0A end after hitting the right hypothesis he calls himself a=0A = great doctor (or at least appears to be one). Same thing are=0A = scientists, they are recognized as great after they have=0A = learned on how to tramp down opposition as the first step in=0A t= heir life as scientists, then they have to defend their=0A researc= h to grant-organization, and fill up the applications=0A with "why= this is so important for the future and society".=0A Still in a n= ear pseudo-darwinistic behavior, the scientist=0A figh= ts through the hierarchy of late nights and hard work, and=0A at t= he age of 70 reaches the Emeritious stage. To many this is=0A "lif= e at its best", and many are also good examples of nice=0A events,= but at the end of the day, the way scientist DO=0A science is bui= ld on that everything has to be bullet and water=0A proof before h= e even discusses the theory with others,=0A otherwise the classica= l debates begin. I have also heard from=0A previous Senior Scienti= sts passing the age of 50 of witnessing=0A and ENJOYING debates wh= ere scientist where verbally=0A annihilating each other, and I rec= all particularly what this=0A professor said in the context with t= he debate he saw "it was=0A blood on the dance floor". At the end = of the day it is a=0A litigious procedure that scientists have to = "survive" through,=0A and it creates FRICTION. This friction is my= whole point of=0A the discussion: It is energy and can be used to= do great=0A science (pr other positive things), and not wasted on= =0A discussions and debates. Those are just for entertaining the= =0A competitive nature in people. Competition, debate and=0A = discussion requires energy, again, that energy can be used for=0A = other things and is valuable.
=0A Therefore, the quite and = contemplating scientist who doesn't=0A bother about debating or sh= owing his results before reaching a=0A full final format, and perh= aps not even showing them then but=0A wait till people are not so = interested in debating him, is a=0A calm and relaxing scientist, t= hat cares about the object of=0A science, not the subject behind i= t or those around it.
=0A
=0A
=0A Ser= gio
=0A
=0A

=0A
=0A
--= ---=0A=0A Original Message -----
=0A =
From:=0A=0A j j= robinson jameschums^^^yahoo.com
=0A
Sent:=0A=0A 08/17/12 09:48 PM<= /span>
=0A
To:=0A=0A = Manzetti, Sergio
=0A
Subject:=0A=0A CCL: On "defending"= and "opposing" science
=0A
=0A =
=0A
=0A
= Dear CCLers,
=0A

=0A =
might I suggest the original correspondent=0A = watches the film "Insignificance". We all have=0A = knowledge... but I prefer insight, understanding..I=0A = suspect I am simply too stupid to find the truth..=0A = Experiment, observation, hypothesis. The debates are=0A = not battles of gladiators, nor personal=0A feuds..scienc= e and/or natural philosophy - is=0A patient observation,= measurement, correlation,=0A verification of experiment= al facts, comparison,=0A perspective, understanding..we = debate with others to=0A make sure we are not simply del= uding ourselves or=0A that other are not deluded. We can= agree to differ,=0A review papers, admit mistakes..we a= re human too.=0A Results and conclusion do not simply re= sult from=0A pressing the return key and waiting to see = how many=0A "hartree's" come out at the end. =0A

=0A
J J Robinso= n - personal email - opinions are=0A personal only.
= =0A
=0A
=0A =

=0A
=0A =
=0A
=0A
=0A =
=0A
=0A

=0A
=0A
= =0A
=0A
-- =0AProf. Dr. Andreas Klamt=0ACEO / Ge= sch=E4ftsf=FChrer=0ACOSMOlogic GmbH & Co. KG=0ABurscheider Strasse 515= =0AD-51381 Leverkusen, Germany=0A=0Aphone =09+49-2171-731681=0Afax =09+49-2171-731= 689=0Ae-mail =09klamt##cosm= ologic.de=0Aweb =09www.cosmologic.de=0A=0A[University address: = Inst. of Physical and=0ATheoretical Chemistry, University of Regensburg]= =0A=0AJoin us at the 4th-COSMO-RS-Symposium April 2013=0ADetails at www.cosmologic.de/symposium2013 =0A=0AHRA 20653 Amtsgericht Koeln,= GF: Prof. Dr. Andreas Klamt=0AKomplementaer: COSMOlogic Verwaltungs GmbH= =0AHRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt=0A=0A=0A
= =0A
=0A=0A

=0A

---15486822-32061779-1345326515=:40977-- From owner-chemistry@ccl.net Sat Aug 18 23:07:00 2012 From: "Fatima Mons Fatima.mons]~[yahoo.com" To: CCL Subject: CCL: On "defending" and "opposing" science Message-Id: <-47398-120818180324-5525-LaJ3Ien0VqEj/dqtbKbz8g%server.ccl.net> X-Original-From: "Fatima Mons" Date: Sat, 18 Aug 2012 18:03:15 -0400 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 Sat Aug 18 23:42:00 2012 From: "Fatima Mons Fatima.mons^^yahoo.com" To: CCL Subject: CCL:G: .chk from log Message-Id: <-47399-120818183122-19695-i6hblAIUo/8LHVSr8Jwh5Q%a%server.ccl.net> X-Original-From: "Fatima Mons" Date: Sat, 18 Aug 2012 18:31:21 -0400 Sent to CCL by: "Fatima Mons" [Fatima.mons\a/yahoo.com] Checkpoint files are written in a binary format which Gaussian can directly read. If you want to transfer the file to a different machine, especially a different platform then you need to use the FORMCHK utility that converts the binary file into a formatted ascii file. The conversion should be done on the machine that created it. If you want to use the file in a Windows environment, then you'll need to run UNIX2DOS command (it replaces the Line Feed (LF) ascii code with Carriage Return (CR) Line Feed (LF) used by Windows), before FTPing it to the Wondows machine. There is Unix2dos utility for Windows called Tofrodos (http://www.thefreecountry.com/tofrodos/) if you wish to do the Unix-DOS conversion under Windows/DOS. For more info see: http://www.gaussian.com/g_tech/g_ur/u_formchk.htm Fatima.