From owner-chemistry@ccl.net Tue Aug 21 03:01:00 2012 From: "Karol M. Langner karol.langner-$-gmail.com" To: CCL Subject: CCL: Dipole Moment Question Message-Id: <-47434-120820170105-25560-Zv9rANGh3iGFFqKRrWpOxQ]=[server.ccl.net> X-Original-From: "Karol M. Langner" Date: Mon, 20 Aug 2012 17:01:03 -0400 Sent to CCL by: "Karol M. Langner" [karol.langner++gmail.com] What molecule and method are you look at? > "Mark Zottola mzottola~!~gmail.com" wrote: > > Sent to CCL by: Mark Zottola [mzottola(0)gmail.com] > --e89a8f83ac518b18c504c76bc1d7 > Content-Type: text/plain; charset=ISO-8859-1 > > I recently encountered a phenomenon that has me a bit baffled. > > For fun, I was plotting the dipole moment of a molecule as a function of > the bond length (compression and expansion). I obtained this data from a > set of relaxed potential energy scans. It turned out for a range of > approximately 1.1 Angstroms of deformation the dipole moment varied as a > cubic function of the deformed bond length. The interesting part of that > correlation was the goodness of fit was exactly 1. In other words for a 12 > point data set, the fit of the cubic to the data was perfect. > > I am not overfitting the data and redoing the calculations at a different > level of theory and different basis set gave another perfectly fitting > cubic function. I have reread the basic physics of dipole moment and see > no reason why I should see a such a perfect fit. > > If I am missing something obvious - can I get a pointer to the appropriate > information? Thanks. From owner-chemistry@ccl.net Tue Aug 21 07:43:01 2012 From: "Pierre Archirel pierre.archirel!=!u-psud.fr" To: CCL Subject: CCL: dielectric constant of a binary mixture Message-Id: <-47435-120821073854-30079-7W38XYwnDiOJaDtfvz063w{:}server.ccl.net> X-Original-From: "Pierre Archirel" Date: Tue, 21 Aug 2012 07:38:53 -0400 Sent to CCL by: "Pierre Archirel" [pierre.archirel.:.u-psud.fr] This is an answer to Jean-Pierre Djukic. Dear colleague, Your system is a difficult one for PCM methods, because it can be expected that in the vicinity of your solute the composition of the solvent is not that of the bulk. Consequently the dielectric constant to be used is simply unknown. This statement is actually true for any pure solvent: in the vicinity of a solute the (pure) solvent is more rigid than in the bulk, and its dielectric constant is smaller. This is called 'electrostriction' in textbooks. In most PCM methods this is globally taken into account via the famous alpha=1.2 factor: you give the bulk value of epsilon in your data and the program multiplies all the atomic radii by alpha. The error due to this simplification is corrected (along with several other errors !) by the optimisation of the atomic radii. I once performed PCM calculation of anionic solutes in water/alcohol mixtures. Obviously I got the better results with the epsilon of PURE WATER. This is due to the fact that - due to its larger dipole moment - water is more present in the vicinity of the solutes than in the bulk solvent. In summary, any formula giving the epsilon of a mixture may be poorly suited to the PCM calculation of a solvation DG in this mixture. If you expect that some component of the mixture concentrates in the vicinity of the solute, then take the epsilon of this pure component. Pierre Archirel, LCP Orsay France From owner-chemistry@ccl.net Tue Aug 21 08:31:00 2012 From: "James Womack 5inowsy1maiq : gmail.com" To: CCL Subject: CCL: On "defending" and "opposing" science Message-Id: <-47436-120821050601-16945-K8wgSODFPx0usDUPH/zwoQ]~[server.ccl.net> X-Original-From: James Womack <5inowsy1maiq,gmail.com> Content-Type: multipart/alternative; boundary=e89a8f64790bf4606d04c7c2eede Date: Tue, 21 Aug 2012 10:05:53 +0100 MIME-Version: 1.0 Sent to CCL by: James Womack [5inowsy1maiq[#]gmail.com] --e89a8f64790bf4606d04c7c2eede Content-Type: text/plain; charset=ISO-8859-1 I suggest the creation of a CCL-OT (CCL-off topic) list, hosted somewhere like Google Groups so as not to burden CCL servers, where off topic discussions can be shifted to. If someone posts an off-topic, but nevertheless interesting, message, members could request the author repost to the OT list and if people are interested in the topic, they can subscribe to the CCL-OT list and continue the discussion there. On 20 August 2012 20:22, Pedro Silva pedros*ufp.edu.pt < owner-chemistry###ccl.net> wrote: > > Sent to CCL by: Pedro Silva [pedros(-)ufp.edu.pt] > On Mon, Aug 20, 2012 at 5:45 PM, Sergio Manzetti > sergio.manzetti++gmx.com wrote: > > Laurence and Sebastian, if it was solely "junk" it wouldn't generate so > many > > postings and reactions. > > The point is not whether or not it is junk, but whether or not it > belongs on CCL, rather than on a more general science mailing list. I > I guess most people do not subscribe to CCL to read a discussion on > peer review, the shoprtcomings of some traditional ways of teaching > the L Chatelier principle, and/or the politicization of science ( no > matter how interesting those might be), but rather to discuss > computational chemistry topics. > > >Evidently it is a part of the CCL ring as well, > > otherwise the admin would just block it. > > > > The fact that a message is posted does not mean it has been "approved" > in any way by the "powers that be". > FYI, Dr. Labanowski does NOT perform any moderation of the CCL list, > as that would take him too much time and possibly legal responsibility > as well. > > -- > Pedro J. Silva > Associate Professor > Universidade Fernando Pessoa > Porto - Portugal > http://homepage.ufp.pt/pedros/science/science.htm > http://biochemicalmatters.blogspot.com> > > --e89a8f64790bf4606d04c7c2eede Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I suggest the creation of a CCL-OT (CCL-off topic) list, hosted somewhere l= ike Google Groups so as not to burden CCL servers, where off topic discussi= ons can be shifted to. If someone posts an off-topic, but nevertheless inte= resting, message, members could request the author repost to the OT list an= d if people are interested in the topic, they can subscribe to the CCL-OT l= ist and continue the discussion there.

On 20 August 2012 20:22, Pedro Silva pedros*= ufp.edu.pt <owner-chemistry###ccl.n= et> wrote:

Sent to CCL by: Pedro Silva [pedros(-)ufp.edu.pt]
On Mon, Aug 20, 2012 at 5:45 PM, Sergio Manzetti
sergio.manzetti++gmx.com &= lt;owner-chemistry|,|ccl.net> wrote:
> Laurence and Sebastian, if it was solely "junk" it wouldn= 9;t generate so many
> postings and reactions.

The point is not whether or not it is junk, but whether or not it
belongs on CCL, rather than on a more general science mailing list. I
I guess most people do not subscribe to =A0CCL to read a discussion on
peer review, the shoprtcomings of some traditional ways of teaching
the L Chatelier principle, and/or the politicization of science ( no
matter how interesting those might be), but rather to discuss
computational chemistry topics.

>Evidently it is a part of the CCL ring as well,
> otherwise the admin would just block it.
>

The fact that a message is posted does not mean it has been "app= roved"
in any way by the "powers that be".
FYI, Dr. Labanowski does NOT perform any moderation of the CCL list,
as that would take him too much time and possibly legal responsibility
as well.

--
Pedro J. Silva
Associate Professor
Universidade Fernando Pessoa
Porto - Portugal
http://homepage.ufp.pt/pedros/science/science.htm
http:/= /biochemicalmatters.blogspot.com



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--e89a8f64790bf4606d04c7c2eede-- From owner-chemistry@ccl.net Tue Aug 21 11:52:00 2012 From: "John McKelvey jmmckel^gmail.com" To: CCL Subject: CCL: dielectric constant of a binary mixture Message-Id: <-47437-120821110347-664-dVnRW+CHROUXSqjyGFt9/w]|[server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 21 Aug 2012 11:03:40 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel(!)gmail.com] I would comment that I believe that Klamt's "D-COSMO-RS" handles mixed solvents correctly, properly taking into account "hot-spot" interactions" between solute and solvent in solvent mixtures. John McKelvey On Tue, Aug 21, 2012 at 7:38 AM, Pierre Archirel pierre.archirel!=!u-psud.fr wrote: > > Sent to CCL by: "Pierre Archirel" [pierre.archirel.:.u-psud.fr] > This is an answer to Jean-Pierre Djukic. > Dear colleague, > Your system is a difficult one for PCM methods, because it can be expected that in the vicinity of your solute the composition of the solvent is not that of the bulk. Consequently the dielectric constant to be used is simply unknown. > This statement is actually true for any pure solvent: in the vicinity of a solute the (pure) solvent is more rigid than in the bulk, and its dielectric constant is smaller. This is called 'electrostriction' in textbooks. In most PCM methods this is globally taken into account via the famous alpha=1.2 factor: you give the bulk value of epsilon in your data and the program multiplies all the atomic radii by alpha. The error due to this simplification is corrected (along with several other errors !) by the optimisation of the atomic radii. > I once performed PCM calculation of anionic solutes in water/alcohol mixtures. Obviously I got the better results with the epsilon of PURE WATER. This is due to the fact that - due to its larger dipole moment - water is more present in the vicinity of the solutes than in the bulk solvent. > > In summary, any formula giving the epsilon of a mixture may be poorly suited to the PCM calculation of a solvation DG in this mixture. If you expect that some component of the mixture concentrates in the vicinity of the solute, then take the epsilon of this pure component. > > Pierre Archirel, LCP > Orsay France> > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel _ gmail.com From owner-chemistry@ccl.net Tue Aug 21 17:56:00 2012 From: "David A Mannock dmannock[-]ualberta.ca" To: CCL Subject: CCL: Suggestion Message-Id: <-47438-120821142314-1888-MgYm9BVfelGV4bJrYj6S0g===server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=f46d040714cf8ebc4b04c7cab746 Date: Tue, 21 Aug 2012 12:23:03 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock]^[ualberta.ca] --f46d040714cf8ebc4b04c7cab746 Content-Type: text/plain; charset=ISO-8859-1 No, it's real. However, I should point out that governments, local and national, fund all kinds of stupid ideas based on reviews by committees that are not up to date in every area. I could tell you some real howlers in that direction. You also have to deal with the incest, nepotism issue. For others, good ideas can be shot down because of the "not invented here" philosophy, people protecting their own technology, enemies the PI may have made, the list is endless. The only real solution is to have people on the committees make full academic and commercial disclosure and for the referees to do the same. We need to get some honesty back into science and the scientific funding process. On Mon, Aug 20, 2012 at 9:44 AM, Sergio Manzetti sergio.manzetti%x%gmx.com < owner-chemistry_+_ccl.net> wrote: > Dear Sukumar, I agree on that, it should be through study-loans and own > financing that they should be able to pursue their own goals, not on the > institutes economical fate. However, that type of research on SETI and Cold > Fusion I have never even heard of in science or read of, I thought it was a > movie with Keanu Reeves... > > Maybe it should remain a movie with Keanu Reeves? > > Best wishes > > Sergio > > ----- Original Message ----- > > From: N. Sukumar nagams**rpi.edu > Sent: 08/20/12 01:24 PM > To: Manzetti, Sergio > Subject: CCL: Suggestion > > Sent to CCL by: "N. Sukumar" [nagams[a]rpi.edu] > let students and young > newcomers test their "stupid" theories > not matter how stupid they sound. > They need to try. > Sergio With their own money, of course! Scientists have > raised private funds to pursue cold fusion and SETI research. There are > even those (using the term "scientist" loosely) who pursue "research" on > creationism/intelligent design. There is no law against it. But if you > expect to do it with MY (taxpayer) money or on company time, I expect to > have a say in determining how my money should be spent. N. Sukumar > Rensselaer Exploratory Center for Cheminformatics Research Professor of > Chemistry Shiv Nadar University, India ---------------------------- > "Equations are the devil's sentences." -- Stephen Colberthttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--========GMXBoundary7327134547745674015 > Content-Type: > text/html; charset="utf-8" > Content-Transfer-Encoding: quoted-printable > > Dear > Suk= > umar, I agree on that, it should be through study-loans and own financing > t= > hat they should be able to pursue their own goals, not on the institutes > ec= > onomical fate. However, that type of research on SETI and Cold Fusion I > hav= > e never even heard of in science or read of, I thought it was a movie with > = > Keanu Reeves...
=20 >
=20 > Maybe it should remain a movie with Keanu Reeves?
=20 >
=20 > Best wishes
=20 >
=20 > Sergio
=20 >
=20 >

=20 > =C2=A0

=20 >
margin= > -left: 5px; margin-bottom: 0px; margin-top: 0px; margin-right: 0px;" type= > =3D"cite">=20 >

=20 > style=3D"font-size:12px">----- = > Original Message -----

=20 >

=20 > style=3D"font-size:12px">From: = > N. Sukumar nagams**rpi.edu

=20 >

=20 > style=3D"font-size:12px">Sent: = > 08/20/12 01:24 PM

=20 >

=20 > style=3D"font-size:12px">To: Ma= > nzetti, Sergio

=20 >

=20 > style=3D"font-size:12px">Subjec= > t: CCL: Suggestion

=20 >
=20 >
=20 >
=20 > 
 break-word; font-size:11=
> ;pre">=20
> Sent to CCL by: "N. Sukumar" [nagams[a]rpi.edu]=20
> > let students and young newcomers test their "stupid" theories=20
> > not matter how stupid they sound. They need to try.=20
>
> > Sergio=20
>
> With their own money, of course!=20
>
> Scientists have raised private funds to pursue cold fusion and SETI=20
> research. There are even those (using the term "scientist" loosely) who=20
> pursue "research" on creationism/intelligent design. There is no law=20
> against it.=20
>
> But if you expect to do it with MY (taxpayer) money or on company time, I=
> =20
> expect to have a say in determining how my money should be spent.=20
>
> N. Sukumar=20
> Rensselaer Exploratory Center for Cheminformatics Research=20
> Professor of Chemistry=20
> Shiv Nadar University, India=20
> ----------------------------=20
> "Equations are the devil's sentences." -- Stephen Colbert=20
>
>
>
> -=3D This is automatically added to each message by the mailing script
> =3D-=
> =20=20=20=20=20=20=20=20
>
> Subscribe/Unsubscribe:=20=20=20
>
> Job: http://www.ccl.net/jobs=20=20=20=20=20
=20 >
=20 >
=20 >
=20 >

=20 > =C2=A0

=20 >
=20 > > --f46d040714cf8ebc4b04c7cab746 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable No, it's real. However, I should point out that governments, local and = national, fund all kinds of stupid ideas based on reviews by committees tha= t are not up to date in every area. I could tell you some real howlers in t= hat direction. You also have to deal with the incest, nepotism issue. For o= thers, good ideas can be shot down because of the "not invented here&q= uot; philosophy, people protecting their own technology, enemies the PI may= have made, the list is endless. The only real solution is to have people o= n the committees make full academic and commercial disclosure and for the r= eferees to do the same. We need to get some honesty back into science and t= he scientific funding process.

On Mon, Aug 20, 2012 at 9:44 AM, Sergio Manz= etti sergio.manzetti%x%gmx.com <owner= -chemistry_+_ccl.net> wrote:
Dear Sukumar, I agree on that, it should be = through study-loans and own financing that they should be able to pursue th= eir own goals, not on the institutes economical fate. However, that type of= research on SETI and Cold Fusion I have never even heard of in science or = read of, I thought it was a movie with Keanu Reeves...

=A0Maybe it should remain a movie with Keanu Reeves?

=A0Best wishes

=A0Sergio

----- Original Message -----
> From: N. Sukumar nagams**= rpi.edu
Sent: 08/20/12 01:24 PM
To: Manzetti, Sergio
Subject: CCL: Suggestion

=A0Sent to CCL by: "N. Sukumar" [nagams[a]rpi.edu] > let students and young newcomers te= st their "stupid" theories > not matter how stupid they sound.= They need to try. > Sergio With their own money, of course! Scientists = have raised private funds to pursue cold fusion and SETI research. There ar= e even those (using the term "scientist" loosely) who pursue &quo= t;research" on creationism/intelligent design. There is no law against= it. But if you expect to do it with MY (taxpayer) money or on company time= , I expect to have a say in determining how my money should be spent. N. Su= kumar Rensselaer Exploratory Center for Cheminformatics Research Professor = of Chemistry Shiv Nadar University, India ---------------------------- &quo= t;Equations are the devil's sentences." -- Stephen Colberthttp://<= a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net= /chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=3D=3D=3D=3D=3D= =3D=3D=3DGMXBoundary7327134547745674015%0AContent-Type" target=3D"_blank">w= ww.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_uns= ub.shtmlhttp://www.ccl.net/spammers.txt--=3D=3D=3D=3D=3D=3D=3D=3DGMXBoundar= y7327134547745674015
Content-Type: text/html; charset=3D"utf-8"
Content-Transfer-Encoding: quoted-printable

<span style=3D3D'font-family:Verdana'><span style=3D3D'= ;font-size:12px'>Dear Suk=3D
umar, I agree on that, it should be through study-loans and own financing t= =3D
hat they should be able to pursue their own goals, not on the institutes ec= =3D
onomical fate. However, that type of research on SETI and Cold Fusion I hav= =3D
e never even heard of in science or read of, I thought it was a movie with = =3D
Keanu Reeves...<br />=3D20
<br />=3D20
Maybe it should remain a movie with Keanu Reeves?<br />=3D20
<br />=3D20
Best wishes<br />=3D20
<br />=3D20
Sergio<br />=3D20
<br />=3D20
<p style=3D3D"margin:0px; padding:0px;" >=3D20
=A0 =A0 =A0 =A0 =3DC2=3DA0</p>=3D20
<blockquote style=3D3D"border-left: 1px solid #CCC; padding-left: 5= px; margin=3D
-left: 5px; margin-bottom: 0px; margin-top: 0px; margin-right: 0px;" t= ype=3D
=3D3D"cite">=3D20
=A0 =A0 =A0 =A0 <p style=3D3D"margin:0px; padding:0px;" >= =3D20
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 <span style=3D3D"font-family:Verdan= a"><span style=3D3D"font-size:12px">----- =3D
Original Message -----</span></span></p>=3D20
=A0 =A0 =A0 =A0 <p style=3D3D"margin:0px; padding:0px;" >= =3D20
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 <span style=3D3D"font-family:Verdan= a"><span style=3D3D"font-size:12px">From: =3D
N. Sukumar nagams**rpi.edu= </span></span></p>=3D20
=A0 =A0 =A0 =A0 <p style=3D3D"margin:0px; padding:0px;" >= =3D20
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 <span style=3D3D"font-family:Verdan= a"><span style=3D3D"font-size:12px">Sent: =3D
08/20/12 01:24 PM</span></span></p>=3D20
=A0 =A0 =A0 =A0 <p style=3D3D"margin:0px; padding:0px;" >= =3D20
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 <span style=3D3D"font-family:Verdan= a"><span style=3D3D"font-size:12px">To: Ma=3D
nzetti, Sergio </span></span></p>=3D20
=A0 =A0 =A0 =A0 <p style=3D3D"margin:0px; padding:0px;" >= =3D20
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 <span style=3D3D"font-family:Verdan= a"><span style=3D3D"font-size:12px">Subjec=3D
t: CCL: Suggestion</span></span></p>=3D20
=A0 =A0 =A0 =A0 <br />=3D20
=A0 =A0 =A0 =A0 <div>=3D20
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 <div>=3D20
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 <pre style=3D3D"whi= te-space: pre-wrap; word-wrap: break-word; font-size:11=3D
;pre">=3D20
Sent to CCL by: "N. Sukumar" [nagams[a]rpi.edu]=3D20
&gt; let students and young newcomers test their "stupid" the= ories=3D20
&gt; not matter how stupid they sound. They need to try.=3D20

&gt; Sergio=3D20

With their own money, of course!=3D20

Scientists have raised private funds to pursue cold fusion and SETI=3D20 research. There are even those (using the term "scientist" loosel= y) who=3D20
pursue "research" on creationism/intelligent design. There is no = law=3D20
against it.=3D20

But if you expect to do it with MY (taxpayer) money or on company time, I= =3D
=3D20
expect to have a say in determining how my money should be spent.=3D20

N. Sukumar=3D20
Rensselaer Exploratory Center for Cheminformatics Research=3D20
Professor of Chemistry=3D20
Shiv Nadar University, India=3D20
----------------------------=3D20
"Equations are the devil's sentences." -- Stephen Colbert=3D2= 0



-=3D3D This is automatically added to each message by the mailing script = =3D3D-=3D
=3D20=3D20=3D20=3D20=3D20=3D20=3D20=3D20

Subscribe/Unsubscribe:=3D20=3D20=3D20

Job: http://www.ccl.net/jobs=3D20=3D20=3D20=3D20=3D20</pre>= =3D20
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 </div>=3D20
=A0 =A0 =A0 =A0 </div>=3D20
</blockquote>=3D20
<p style=3D3D"margin:0px; padding:0px;" >=3D20
=A0 =A0 =A0 =A0 =3DC2=3DA0</p>=3D20
<br />=3D20
</span></span>

--f46d040714cf8ebc4b04c7cab746-- From owner-chemistry@ccl.net Tue Aug 21 18:31:00 2012 From: "David A Mannock dmannock_-_ualberta.ca" To: CCL Subject: CCL: Suggestion Message-Id: <-47439-120821142922-2268-jW4mtityKirPmvh88S6b9A]^[server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=f46d04088c7597689604c7cacd59 Date: Tue, 21 Aug 2012 12:29:13 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock^^^ualberta.ca] --f46d04088c7597689604c7cacd59 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Oh, boy! You may have heard of urban myths, well there are scientific myths as well. Things that people already know? Every generation has to reinvent the wheel. Papers lost in the mill are now coming back into circulation because of their availability online. I am now citing stuff from the 20s thru to the 60s. Most people are lazy by nature and want credit for everything they do, farts and all! In the lab that I have spent 30 years working in, we have knocked down so many myths assumed by the great, supposedly intelligent scientific community, it is mind boggling. On Mon, Aug 20, 2012 at 10:43 AM, Van Dam, Hubertus J HubertusJJ.vanDam[] pnnl.gov wrote: > Hi James,**** > > ** ** > > I think there is merit in your suggestion. If handled well it should be > able to capture most of the aspects of the current publishing model. I ha= ve > three comments on your suggestion. **** > > **1. **Reviewers often make valuable comments on aspects of a work > that weren=92t clear in the submitted manuscript. This feedback gives the > authors the opportunity to improve the work and make it more valuable > before it goes out in the final version. Your suggestion seems to lose th= is > extra polishing loop which would reduce the quality of work published.***= * > > **2. **On social media hot items get commented on a lot! An item > can have several hundred comments and the casual reader has little hope o= f > doing justice to all these comments. In science of course one can hope th= at > if several hundred scientists bothered spending time on commenting on > something it might be worth reading simply from the fact the publication > seems to be influential (for right or wrong reasons). **** > > **3. **I don=92t know Stack Exchange or Reddit but in social media > the comments are usually named. On the one hand this is important for > accountability reasons (although extensive aliasing interferes with that)= , > on the other hand it opens the door to reviewers being treated unfairly b= y > authors in influential positions as has been pointed to before. Your > suggestion that people should achieve a certain status before being able = to > comment might alleviate this to some extent (the commentator would no > longer be that junior). However, one would have to be careful how status = is > accrued not to stifle innovation. (What if someone publishes in a variety > of places, how does he accrue enough status anywhere? Do people get force= d > to publish things that everyone essentially already knows so that they ge= t > enough positive comments to up their status rather than going after reall= y > new and potentially controversial things)? **** > > I don=92t think that any of these are show stoppers, and there are ways t= o > fix them but maybe this is something to keep in mind.**** > > ** ** > > Best wishes,**** > > ** ** > > Huub**** > > ** ** > > *From:* owner-chemistry+hubertus.vandam=3D=3Dpnnl.gov*o*ccl.net [mailto: > owner-chemistry+hubertus.vandam=3D=3Dpnnl.gov*o*ccl.net] *On Behalf Of *J= ames > Womack 5inowsy1maiq|,|gmail.com > *Sent:* Monday, August 20, 2012 2:04 AM > *To:* Van Dam, Hubertus J > *Subject:* CCL: Suggestion**** > > ** ** > > ** ** > > 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 whi= ch > 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 reviewe= r > 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 the= ir > status. If we see the bickering and petty quarrels between some of the > greatest minds of science, such as Newton and Hooke, it's no surprise tha= t > these things go on now. Being a scientist is not a guard against the vice= s > of human nature... :-)**** > > > Not necessarily a better model, but a different one: publish ALL articles > online in an open access model and then extend peer-review to the entire > community of readers. Let readers comment on and vote up or down articles > online. Articles with negative score and poor comments will be considered > poor or unreliable, while those with a high positive score and good > comments will be considered good and reliable. This system would rely upo= n > the assumptions that (i) the majority of people voting/commenting will be > honest and reasonable, with enough knowledge to make a good judgement, (i= i) > enough people read the articles and interact with the system that the > scores are meaningful. The key here is that comments can also be voted > upon, so comments that are widely regarded as unreasonable would be > designated as such. This would be the "Stack Exchange/Reddit" model of > scientific publishing. > > To ensure that the commenters are honest and reasonable, one could assign > "reputation" to voters/commenters. Obviously the system could easily be > gamed if anyone with an account could vote/comment. On Stack Exchange sit= es > this problem is mitigated by the fact that new users need to gain a certa= in > reputation score before being able to vote/comment, and this score is > earned through posting a question or providing an answer which other > members consider useful or interesting and vote upon to reflect this. > Perhaps on a scientific publication site using this system, new users wou= ld > earn sufficient reputation points to vote by publishing their own article= s > and having this "voted up" or by providing comments which other users "vo= te > up".**** > --f46d04088c7597689604c7cacd59 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Oh, boy! You may have heard of urban myths, well there are scientific myths= as well. Things that people already know? Every generation has to reinvent= the wheel. Papers lost in the mill are now coming back into circulation be= cause of their availability online. I am now citing stuff from the 20s thru= to the 60s. Most people are lazy by nature and want credit for everything = they do, farts and all! In the lab that I have spent 30 years working in, w= e have knocked down so many myths assumed by the great, supposedly intellig= ent scientific community, it is mind boggling.

On Mon, Aug 20, 2012 at 10:43 AM, Van Dam, H= ubertus J HubertusJJ.vanDam[]pnnl.gov <owner-chemistry!^!ccl.net> wrote:

Hi=A0 James,<= u>

=A0<= /p>

I think there is merit= in your suggestion. If handled well it should be able to capture most of t= he aspects of the current publishing model. I have three comments on your s= uggestion.

1.=A0=A0=A0=A0=A0=A0 Reviewers often make valuable comments on aspects o= f a work that weren=92t clear in the submitted manuscript. This feedback gi= ves the authors the opportunity to improve the work and make it more valuab= le before it goes out in the final version. Your suggestion seems to lose t= his extra polishing loop which would reduce the quality of work published.<= u>

2.=A0=A0=A0=A0=A0=A0 On social media hot items get commented on a lot! A= n item can have several hundred comments and the casual reader has little h= ope of doing justice to all these comments. In science of course one can ho= pe that if several hundred scientists bothered spending time on commenting = on something it might be worth reading simply from the fact the publication= seems to be influential (for right or wrong reasons).

3.=A0=A0=A0=A0=A0=A0 I don=92t know Stack Exchange or Reddit but in soci= al media the comments are usually named. On the one hand this is important = for accountability reasons (although extensive aliasing interferes with tha= t), on the other hand it opens the door to reviewers being treated unfairly= by authors in influential positions as has been pointed to before. Your su= ggestion that people should achieve a certain status before being able to c= omment might alleviate this to some extent (the commentator would no longer= be that junior). However, one would have to be careful how status is accru= ed not to stifle innovation. (What if someone publishes in a variety of pla= ces, how does he accrue enough status anywhere? Do people get forced to pub= lish things that everyone essentially already knows so that they get enough= positive comments to up their status rather than going after really new an= d potentially controversial things)?

I don=92t think that any = of these are show stoppers, and there are ways to fix them but maybe this i= s something to keep in mind.

=A0<= /p>

Best wishes,=

=A0<= /p>

=A0=A0=A0=A0 Huub

=A0<= /p>

From: owner-ch= emistry+hubertus.vandam=3D=3D= pnnl.gov*o*ccl.net [ma= ilto:owner-chemistry+hubertus.vandam=3D=3Dpnnl.gov*o*cc= l.net] On Behalf Of James Womack 5inowsy1maiq|,|gmail.com
Sent: Monday, August 20, 2012 2:04 AM
To: Van Dam, Hubertu= s J
Subject: CCL: Suggestion

=A0

=A0<= /u>

The peer review system does at times become adversarial, which is unfo= rtunate, but can anyone suggest a working model that would do things differ= ently and better? Of course, the peer review system can be improved and ref= ormed, 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 sy= stem 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 p= restigious institution who is perhaps chair of a national granting committe= e? 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, it's no surprise that these things go on now= . Being a scientist is not a guard against the vices of human nature... :-)=


Not necessarily a better model= , but a different one: publish ALL articles online in an open access model = and then extend peer-review to the entire community of readers. Let readers= comment on and vote up or down articles online. Articles with negative sco= re and poor comments will be considered poor or unreliable, while those wit= h a high positive score and good comments will be considered good and relia= ble. This system would rely upon the assumptions that (i) the majority of p= eople voting/commenting will be honest and reasonable, with enough knowledg= e to make a good judgement, (ii) enough people read the articles and intera= ct with the system that the scores are meaningful. The key here is that com= ments can also be voted upon, so comments that are widely regarded as unrea= sonable would be designated as such. This would be the "Stack Exchange= /Reddit" model of scientific publishing.

To ensure that the commenters are honest and reasonable, one could assi= gn "reputation" to voters/commenters. Obviously the system could = easily be gamed if anyone with an account could vote/comment. On Stack Exch= ange sites this problem is mitigated by the fact that new users need to gai= n a certain reputation score before being able to vote/comment, and this sc= ore is earned through posting a question or providing an answer which other= members consider useful or interesting and vote upon to reflect this. Perh= aps on a scientific publication site using this system, new users would ear= n sufficient reputation points to vote by publishing their own articles and= having this "voted up" or by providing comments which other user= s "vote up".


--f46d04088c7597689604c7cacd59-- From owner-chemistry@ccl.net Tue Aug 21 19:05:00 2012 From: "Salter-Duke, Brian James - brian.james.duke^gmail.com" To: CCL Subject: CCL: On "defending" and "opposing" science Message-Id: <-47440-120821180634-31077-myU4G5rXK4vyv5KOuFcYBA ~~ server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 22 Aug 2012 08:06:21 +1000 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke]=[gmail.com] On Mon, Aug 20, 2012 at 03:16:27AM -0700, Sebastian Kozuch kozuchs(0)yahoo.com wrote: > Indeed very interesting discussions came on the "defending" and > "opposing" science issue. My question is: Is CCL the right forum for > this debate? If the answer is yes, then we'll have to be aware that > there are thousands of other different debates about general science > awaiting, and that may fill our mail accounts  (I can easily propose a > list of topics). If the answer is no, then we should stick to > computational chemistry, the real raison d'etre of the list. I am not > answering my question; just making an objective observation. I would like to defend this discussion, at least if it focuses down a bit. Readers of CCL publish, and in a realtively small list of journals. Discussion about refereeing might improve refereeing in the journals that our readers publish in and review for. This is not the place to try to improve refereeing in general, but it could lead to modest improvements in the journals in computional chemistry. For example, if readers here agree with my earlier suggestion that authors be not allowed to nominate referees (but are allowed to black-list referees), then a consensus here on that might pursuade the editors of computational chemistry journals, who may even read CCL, to end that practice. Brian Duke. > > Best, > Sebastian -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke[A]monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia From owner-chemistry@ccl.net Tue Aug 21 20:38:00 2012 From: "Chirag Vora chirag740=-=gmail.com" To: CCL Subject: CCL: Bioinformatics and Computational Biology on Linux Message-Id: <-47441-120821203607-30206-5dsmcS9Ycgl/xCm0IsNF1w]*[server.ccl.net> X-Original-From: "Chirag Vora" Date: Tue, 21 Aug 2012 20:36:05 -0400 Sent to CCL by: "Chirag Vora" [chirag740 : gmail.com] A recent post at Molecular Modelling Blog discussing various flavours of linux for bioinformatics and computational biology related work: http://eventheodd.blogspot.in/2012/08/bioinformatics-and-computational.html Topics covered: DNALinux Bioknoppix Vigyaan VLinux BioSLAX Bio-Linux 6.0 CentOS Ubuntu From owner-chemistry@ccl.net Tue Aug 21 21:13:00 2012 From: "Chirag Vora chirag740_-_gmail.com" To: CCL Subject: CCL: PyMOL on the iPad Message-Id: <-47442-120821202738-29405-yeXRdZLk+w8gM4mBJTUTLw(~)server.ccl.net> X-Original-From: Chirag Vora Content-Type: multipart/alternative; boundary=bcaec54d495cee739a04c7cfcebf Date: Wed, 22 Aug 2012 05:57:30 +0530 MIME-Version: 1.0 Sent to CCL by: Chirag Vora [chirag740##gmail.com] --bcaec54d495cee739a04c7cfcebf Content-Type: text/plain; charset=ISO-8859-1 Thanks for sharing. A highly awaited app. You might want to comment on this post about it: http://eventheodd.blogspot.in/2012/07/smartphone-apps-to-improve-your.html On Mon, Aug 20, 2012 at 5:22 PM, Jason Vertrees jason.vertrees]|[ schrodinger.com wrote: > > Sent to CCL by: "Jason Vertrees" [jason.vertrees]-[schrodinger.com] > Greetings, > > Schrodinger is delighted to announce the release of PyMOL on the iPad. It > is a free download from the > App Store. Please visit http://pymol.org/mobile to learn more. > > Cheers, > > -- Jason > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrdinger, LLC > > (e) Jason.Vertrees{}schrodinger.com > (o) +1 (603) 374-7120> > > --bcaec54d495cee739a04c7cfcebf Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks for sharing. A highly awaited app. You might want to comment on this= post about it: http://eventheodd.blogspot.in/2012/07/smartphon= e-apps-to-improve-your.html

On Mon, Aug 20, 2012 at 5:22 PM, Jason Vertr= ees jason.vertrees]|[schrodinger.com= <owner-chemistry,+,ccl.net> wrote:

Sent to CCL by: "Jason =A0Vertrees" [jason.vertrees]-[schrodinger.com]
Greetings,

Schrodinger is delighted to announce the release of PyMOL on the iPad. It i= s a free download from the
App Store. Please visit http://pymol.org/mobile to learn more.

Cheers,

-- Jason

--
Jason Vertrees, PhD
PyMOL Product Manager
Schrdinger, LLC

(e) Jason.Vertrees{}sc= hrodinger.com
(o) +1 (= 603) 374-7120



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