Sanctity of the scientific record

I have not read the chemical blogosphere for some time (other than Blue Obelisk) and have been catching up with some of this in the plane. This is ChemBark from January and some my specific comments may be out of date, but the general questions remain. Scholars of scientific accuracy/fraud may wish to pursue the posts (which are IMO a valuable addition to the formal review process).
=== ChemBark ==

Posted by Paul on January 11th, 2007

I missed this since I read JACS by the ASAP alerts and every single addition/correction from Sames has been allowed to bypass the system. A tip of my hat to the kind person who e-mailed it.Edit: I don’t have the time right now to investigate the e-mail’s note that the original supporting information file has been altered so that you cannot compare the new SI with the old, but I wouldn’t be surprised. I’ll get to it tonight, but feel free to investigate this lead on your own. On the surface, it doesn’t look good.Edited again: The supporting information files from 2005 and 2007 appear to be identical. They are also many many pages long, and I’m busy, so you probably won’t get a post from me today. Sorry.=======
I haven’t read this in detail so have no idea whether the question of scientific fraud has been resolved. My concern is about the scholarly record. On pursuing the links I find the correction/retraction:
Direct Palladium-Catalyzed C-2 and C-3 Arylation of Indoles: A Mechanistic Rationale for Regioselectivity [J. Am. Chem. Soc. 2005, 127, 8050-8057].
Benjamin S. Lane, Meghann A. Brown, and Dalibor Sames*
For comparison purposes, this article refers to a palladium-catalyzed arylation of free azoles in the presence of magnesium oxide, published previously in a separate communication. Although the magnesium oxide procedure has recently been found irreproducible (J. Am. Chem. Soc. 2006, 128, 8364), this fact does not affect the conclusions of this paper. Consequently, the magnesium oxide protocol has been removed from the Supporting Information. Also, Figures S5 and S8 have been replaced with corrected versions.

Supporting Information Available

Experimental procedures, spectral data, and base optimization data (corrected). This material is available free of charge via the Internet at
I make now comment on the question of misconduct, but am concerned with the sanctity of the scientific record. The publishers’ statement could be interpreted as implying that the record has been amended, rather than that an amended piece of information has been added to the scientific record. The blogosphere certainly queried this – I don’t know whether it has been resolved.
However the ACS policy on journals is then worrying:

“Socialized Science” (ACS[*] commentary on NIH)

RUDY M. BAUM, Editor-in-Chief, C&E News,
September 20 2004 Volume 82, Number 38 p. 7
I find it incredible that a Republican Administration would institute a policy that will have the long-term effect of shifting responsibility for communicating scientific research and maintaining the archive of STM [1] literature from the private sector to the federal government.

What is important to realize is that a subscription to an STM journal is no longer […] a subscription; in fact, it is an access fee to a database maintained by the publisher.

[…] one important consequence of electronic publishing is to shift primary responsibility for maintaining the archive of STM literature from libraries to publishers. I know that publishers like the American Chemical Society are committed to maintaining the archive of material they publish. Maintaining an archive, however, costs money.
(PM-R’s emphasis and ellipses)
[*] American Chemical Society
The scientific record is thus not a paper or even epaper journal – it is a set of database records. With paper journals the record was very clearly preseved – mutliple copies were distributed and could never be recalled. Here there is effectively only one record and it is controlled by the publisher. (I know that certain depositing libraries have electronic copies, but it is unrealistic for the average scientist to pursue this).
I don’t doubt that Rudy Baum has a sincere commitment to preserving the scientific record. But I can imagine cases – with less reputable publishers – where it was embarassing to the publisher for the record to be visible and it was convenient for the database to be amended.
There is another point which the chemical community should take seriously if it cares about the accuracy of scientific publications – and certainly the blogosphere does. ChemBark says that it is impossible to check by eye whether the copies are identical or what has been changed. I gather that there might be PDF diff tools but I don’t have one. OTOH if the supporting information were in CML then it would be possible to compare not only the text but also the spectra, compounds, etc.
So I’d like to be sure that the complete record is available. And encourage chemical cows rather than chemical hamburgers

— function createCookie(name,value,days) { if (days) { var date = new Date(); date.setTime(date.getTime()+(days*24*60*60*1000)); var expires = “; expires=”+date.toGMTString(); } else var expires = “”; var ck = name+”=”+value+expires+”; path=/”; document.cookie = ck; } function readCookie(name) { var nameEQ = name + “=”; var ca = document.cookie.split(‘;’); for(var i=0;i<ca.length;i++) { var c = ca[i]; while (c.charAt(0)==' ') c = c.substring(1,c.length); if (c.indexOf(nameEQ) == 0) return c.substring(nameEQ.length,c.length); } return null; } function URLEncode(plaintext) { // The Javascript escape and unescape functions do not correspond // with what browsers actually do… var SAFECHARS = "0123456789abcdefghijklmnopqrstuvwxyz-_.!~*'()"; var HEX = "0123456789ABCDEF"; var encoded = ""; for (var i = 0; i 255) { alert( “Unicode Character ‘” + ch + “‘ cannot be encoded using standard URL encoding.\n” + “(URL encoding only supports 8-bit characters.)\n” + “A space (+) will be substituted.” ); encoded += “+”; } else { encoded += “%”; encoded += HEX.charAt((charCode >> 4) & 0xF); encoded += HEX.charAt(charCode & 0xF); } } } // for return encoded; }; function getWLHost() { var hostdev=””; var hosttest=””; var hostprod=””; var localhost=window.location.toString(); if (localhost!=null) localhost=localhost.toUpperCase(); if (localhost.indexOf(“DEV.”)!=-1) { return hostdev; } else if (localhost.indexOf(“TEST.”)!=-1) { return hosttest; } else { return hostprod; } } function openURLRedirect(query) { var myframe=window.document.getElementById? window.document.getElementById(‘openURLFrame’): window.document.frames[‘openURLFrame’]; var myform=myframe.contentDocument? myframe.contentDocument.openURLForm: window.document.frames[‘openURLFrame’].openURLForm; //var subscriberId=myform.subscriberId.value; var subscriberId=readCookie(“OpenURL_Saved_SubscriberId”); var url=”http://”+getWLHost()+”/wls/ACSOpenURLWeb/servlet/OpenURLRedirectorServlet?subscriberId=”+subscriberId+”&”+query; // document.location=url; // new window,”openurl”,”toolbar=yes,menubar=yes,location=yes,scrollbars=yes,resizable=yes”); } var history_len1; var history_len2; function openURLSubmit() { // works with IE // window.document.frames[‘openURLFrame’].openURLForm.submit(); // this works with both IE and netscape history_len1=history.length; var myframe=window.document.getElementById? window.document.getElementById(‘openURLFrame’): window.document.frames[‘openURLFrame’]; if (myframe==null) { window.setTimeout(‘openURLSubmit()’,100); return; } var myform=myframe.contentDocument? myframe.contentDocument.openURLForm: window.document.frames[‘openURLFrame’].openURLForm; if (myform==null) { window.setTimeout(‘openURLSubmit()’,100); return; } myform.action=”http://”+getWLHost()+”/wls/ACSOpenURLWeb/servlet/OpenURLServlet”; myform.submit(); openURLProcess(); } function openURLProcess() { var myframe=window.document.getElementById? window.document.getElementById(‘openURLFrame’): window.document.frames[‘openURLFrame’]; var mydoc=myframe.contentDocument? myframe.contentDocument:window.document.frames[‘openURLFrame’].document; var myform=myframe.contentDocument? myframe.contentDocument.openURLForm: window.document.frames[‘openURLFrame’].openURLForm; var isOpenURL=myform.isOpenURL.value; var imageLocation=myform.imageLocation.value; if (isOpenURL==null || isOpenURL==” || isOpenURL==’unknown’ || imageLocation==null || imageLocation==” || imageLocation==’unknown’) { window.setTimeout(‘openURLProcess()’,100); return; } if (isOpenURL==’true’) { var i; for (i=0;i<999;i++) { if (window.document.images==null) break; if (window.document.images[i]==null) break; var image_name=window.document.images[i].id; if (image_name.indexOf('openURL_img')!=-1) { window.document.images[i].style.visibility=""; window.document.images[i].src=imageLocation; } } } // 12/14/2005 // go back to previous page so users don't have to click twice history_len2=history.length; var subscriberId=myform.subscriberId.value; createCookie("OpenURL_Saved_SubscriberId",subscriberId); var agt=navigator.userAgent.toLowerCase(); var version=parseInt(navigator.appVersion); if (history_len2-history_len1==1 || history_len1-history_len2==1) { // 4/17/2005 safari fix if (agt.indexOf('safari') == -1 ) { history.back(); } } }
–var SA_ID=”acspix;acspix”; (I have quoted this without permission and argue fair use).
The publisher states that figures in the supporting information have been replaced. There is some doubt in the blogosphere as to whether an amended copy of the supporting information was added to the scientific record or whether the record itself was changed. If it is the latter then it is very serious. The ACS policy is:
This entry was posted in Uncategorized. Bookmark the permalink.