LETTERS CHEMICAL & ENGINEERING NEWS 1155—16th St., N.W., Washington, DC 20036 1202) 872-4600 or (800) 227-5558 EDITOR-IN-CHIEF: Rudy M. Baum MANAGING EDITOR: Pamela S. Zurer ART DIRECTORS: Nathan Becker, Robin L. Braverman ASSOCIATE DESIGNER: Yang H. Ku STAFF ARTIST: Linda Mattingly SENIOR CORRESPONDENT: Lois R. Ember NEWS EDITOR: William G. Schulz EDITOR-AT-LARGE: Michael Heylin SENIOR ADMINISTRATIVE OFFICER: Marvel A. Wills ADMINISTRATIVE ASSISTANT: Marilyn Caracciolo BUSINESS Michael McCoy, Assistant Managing Editor NORTHEAST: (732) 906-8300. Vivien Marx (Associate Editor), Rick Mullin (Senior Editor), Marc S. Reisch (Senior Correspondent), William J. Storck (Senior Correspondent), Alexander H. Tullo (Associate Editor). Rachel Eskenazi (Administrative Assistant). HONG KONG: 852 2984 9072. Jean-Francois Tremblay (Bureau Head). LONDON: 44 20 8870 6884. Patricia L. Short (Senior Correspondent) GOVERNMENT & POLICY David J. Hanson, Assistant Managing Editor WASHINGTON: (202) 872-4495. Glenn Hess (Contributing Editor), Bette Hileman (Senior Editor), Cheryl Hogue (Senior Editor), Jeffrey W. Johnson (Senior Editor), Susan R. Morrissey (Associate Editor) SCIENCE/TECHNOLOGY/EDUCATION Doron Dagani, Assistant Managing Editor A. Maureen Rouhi, Deputy Assistant Managing Editor WASHINGTON: (202) 872-6216. Stuart A. Borman (Senior Correspondent), Bethany Halford (Assistant Editor), Cetia M. Henry (Senior Editor), Stephen K. Ritter (Senior Editor), Sophie L Rovner (Senior Editor). BOSTON: (617) 395-4163. Amanda T. Yarnell (Associate Editor). CHICAGO: (847) 679-1156. Mitch Jacoby (Senior Editor). HOUSTON: (281) 486-3900. Ann M. Thayer (Senior Correspondent). WEST COAST: (510) 849-0575. Elizabeth K. Wilson (Senior Editor). LONDON: 44 1256 811052. Michael Freemantle (Senior Correspondent) ACS NEWS & SPECIAL FEATURES Linda Raber, Assistant Managing Editor Corinne A. Marasco (Associate Editor), Aalok Mehta (Associate Editor), Rachel A. Petkewich (Assistant Editor) EDITING & PRODUCTION Robin M. Giroux. Assistant Managing Editor Janet S. Dodd (Senior Editor), Arlene Goldberg-Gist (Senior Editor), Melissa A. Kuhnell (Assistant Editor). Deanna Milter (Associate Editor), Stephen M. Trzaska (Associate Editor), Linda Wang (Assistant Editor) C&EN ONLINE Melody Voith, Editor Luis A. Carrillo (Production Manager). Wesley M. Lindamood (Production Associate), William B. Shepherd (Manager, Chemjobs), Rachel Sheremeta Pepling (Associate Editor) PRODUCTION & IMAGING Krystat E. King (Senior Digital Production Associate) SALES & MARKETING Etise Swinehart, Manager Elaine Facciolli Jarrett (Marketing Associate) ADVISORY BOARD Stephanie A. Burns, Joe Carleone, Terry Collins, F. Fleming Crim, Marijn E. Dekkers, Michael P. Doyle, Richard M. Gross, Rudolf Hanko, L. Louis Hegedus, Nancy B. Jackson. Sunil Kumar. Robert L. Lichter. Charles M. Lieber. Joseph A. Loo, Eli Pearce, Peter Pollak, Patrick Prevost, Marquita M. Quails, Paul J. Reider, Gregory H. Robinson, Alan Shaw. Wilhelm Stahl. JoelTickner. Guy Villax Published by the AMERICAN CHEMICAL SOCIETY
Madeleine Jacobs, Executive Director & CEO Robert D. Bovenschutte, President, Publications Division EDITORIAL BOARD Grace Baysinger (Chair); ACS Board of Directors Chair: James D. Burke; ACS President: William F. Carroll; Ned D. Heindet, Madeleine M. Joullie. Peter C. Jurs, Peter J. Stang Copyright 2005, American Chemical Society Canadian GST Reg. No. R127571347
WWW.CEN-0NLINE.ORG
NIH on PubChem C&EN recently receiveda letter byJeremy M. Berg director of the National Institutes of Healths National Institute of General Medical Sciences. Berg responds to an open letter by American Chemical Society President William F. Carroll posted on chemistry.org Carroll's letter, published on Aug. 23, can be found at acswebcontent.acs.org/pdf/pub chem_openJetter2.pdf and is printed below in its entirety and without alteration. Berg's letter follows.
I
WANT TO UPDATE YOU ON THE STATUS OF
our work toward a resolution of the NIH "PubChem" database issue, which was the subject of my June 20 letter to members (http://acswebcontent.acs.org/pdf/ pubchern_openJetter.pdf). According to NIH, PubChem has two purposes: to disseminate data from the molecular libraries screening center network and to create a comprehensive database of chemical structures with biological activities. While the first has drawn wide support, the second puts PubChem on course to fully duplicate a widely available database offered by ACS: the CAS Registry. ACS has invested heavily over decades to build and maintain the CAS Registry, which already includes the kind of data N I H is assembling in PubChem. We believe N I H should take advantage of and not replicate the CAS Registry to advance its molecular libraries initiative (http://nihroadmap.nih.gov). ACS has been striving to work with N I H to arrive at a mutually beneficial solution. We have initiated more than a dozen good faith meetings, letters, e-mails, and phone calls with NIH, and I personally have had several face-to-face and telephone communications with N I H Director Elias Zerhouni. Despite assurances from N I H that PubChem will focus only on a limited set of "biomedically relevant" compounds, PubChem was recently expanded from 600,000 to more than 3 million compounds, most of which have no particular biomedical focus or affiliated data. We believe there is a better way to serve science, and we have proposed a truly collaborative approach to NIH. ACS has offered to build, manage, and make ava&ableforfreea database for N I H of data created both by its screening centers and all other compounds with associated bioassay data. ACS would contribute up to 15 staff and costs worth $10 million over 5 years. Because ACS already analyzes and manages data on virtually all compounds, this approach would save money I
and guarantee the high-quality data verification and standardization scientists expect. ACS and N I H would work together to disseminate any additional compound data in away that utilizes, and avoids competition with, existing databases. Unfortunately, N I H has just rejected our offer, but we are studying their newly proposed alternative structure for resolving this issue. In the end, by taking advantage of the CAS Registry, we believe N I H can: • Avoid unnecessary duplication and gain cost savings that can be used for research grants. • Satisfy federal policies that direct agencies to rely on substantially similar private services that can meet agency missions and avoid unfair government competition. • Accelerate its molecular libraries initiative by utilizing a well-established, comprehensive, and high-quality tool for disseminating data on chemical compounds. The issue is not whether to advance the N I H Molecular Libraries Initiative but how. Both the House and Senate appropriations committees have urged N I H to focus PubChem to avoid unnecessary duplication and competition with private sector databases. We arefirmlycommitted to working toward a resolution that advances NIH's Roadmap, respects long-standing private efforts, and best serves science. I genuinely hope we can achieve this soon. Sincerely, WILLIAM F CARROLL
President, American Chemical Society
I
AM WRITING IN REGARD TO THE AUG. 23
open letter by American Chemical Society President William F. Carroll about discussions between ACS leadership and N I H staff regarding PubChem. PubChem is intended to be "a new and comprehensive database ofchemical structures and their biological activities ... that will house both compound information from the scientific literature as well as screening and probe data from the {NIH Roadmap for Medical Research's] Molecular Libraries Screening Center Network," according to N I H Roadmap documents. Each PubChem record includes only a chemical structure, available bioassay data, names provided by the depositor, properties such as molecular weight calculated from the structure, and links to the depositor and to other information within the suite ofbiomedical databases developed by the National Center for Biomedical Information (NCBI) at NIH. PubChem records do not systematically include experimentally derived properties, information about suppliers, information about synthesis and C&EN / SEPTEMBER
19, 2005
3
LETTERS reactions, links to patents, or links to much of the chemical literature. Both ACS leadership and NIH staffled by NIH Director Elias A. Zerhouni have worked hard to find ways to avoid unnecessary duplication between PubChem and private-sector databases such as those provided by Chemical Abstracts Service. As a chemist and the director of an institute that supports a large amount of chemical research, I have personally participated in essentially all of these meetings. Unfortunately, Carroll's letter misrepresents several important aspects of these discussions. First, while PubChem is focused on biomedically relevant compounds, neither ACS nor NIH has been able to develop a suitable definition of biomedical relevance that would accurately guide what compounds should or should not be included in PubChem. And contrary to a statement in Carroll's letter, no assurances about the number of compounds to be housed in PubChem have been given. Second, the expansion of PubChem from 600,000 compounds to more than 3 million compounds noted in the open letter is due largely to the inclusion of the ZINC database (C&EN, Feb. 14, page 8). This database was developed with support fromagrantfromNIH(R01GM071896) for the explicit purpose of making publicly available a large and diverse set of compounds for computational screening against biomedical targets. The NIH Roadmap Molecular Libraries Initiative explicitly includes support for developing and testing "new algorithms for computational chemistry and virtual screening."Thus, Carroll's statement that "most {of the newly posted compounds} have no particular biomedical focus" is inaccurate and misleading. Third, while we appreciate the offer from ACS to build a PubChem-like database forfree,the statement that this would result in significant cost savings to NIH is
inaccurate. The great majority of the expense related to the development of PubChem involves the thorough integration of information regarding chemical entities with the biomedical literature in PubMed, protein structural information, biological activities, and other data housed at NCBI. This integration is where the great value of PubChem for biomedical research lies. NIH continues to work with public-sector chemical information suppliers to advance the NIH Roadmap Molecular Libraries initiative and other research at the interface between chemistry and biomedical research. From our first discussions with ACS, NIH has offered to provide links from records in PubChem to records in CAS databases. This would allow researchers to navigate easilyfromthe biomedically oriented information in PubChem to the extremely valuable chemically oriented data developed and maintained by CAS.Tbgether, these and other databases will serve the research community as we apply chemical tools to understand biological systems and to improve human health. JEREMY M. BERG
Director, National Institute of General Medical Sciences National Institutes of Health Bethesda, Md.
Chemical naming controversy
A
FTER CAREFULLY READING "CHEM-
ical 'Naming' Method Unveiled," I believe I must comment, because the article unnecessarily inflates a derivative work that is far from revolutionary in chemical structure description (C&EN, Aug. 22, page 39). C&EN readers deserve to understand that International Chemical Identifiers (InChls) are merely another chemical structure exchange format, just like SMILES
Small-Scale Reaction Calorimeter for Early Process Development and Process Safety Screening The benchmark reaction microcalorimeter used by 80% of the top chemical and pharma companies worldwide
SuperCRC ™ A calorimetric device for tt^^^ browsing reaction conditions, kinetic profile and max energy release Pl^^^^
OmniCal Technologies Inc. Houston TX USA e-mail:
[email protected] www.omnicaltech.com
(Simplified Molecular Input Line Entry Specification), Molfile, and the Chemical Abstracts Service Connection Table. It is not a naming method, and it is not a registry system that must identify both well-defined and ill-defined chemical structures and ensure that they are uniquely identified. InChI is simply a Molfile derivative workit is a representation ofand solely based on theMDLMolfile. The term "dream team," which the article uses to refer to the InChI development team, would be more accurately applied to the scientists who perfected the connection table concept, which is at the heart of the CAS Registry System. For example, CAS's Harry Morgan, building on the efforts ofDonald GluckfromDuPont, perfected an algorithm that converted a structure into a connection table, which became the basis for the CAS Registry System in 1965. If this perspective had been given, the reader would have been able to easily see how InChI builds on the works of those named above and others. As the article says: "The string for naphthalene, for instance, is InChI=l/C10H8/cl-2-6-10-8-43-7-9(10)5-l/hl-8H. ThefirstT refers to the version of the InChI software. The next segment of the string, C10H8, provides the molecular formula. The third segment is the connection table, which indicates how the atoms are connected." This so-called third segment, as I have already noted, is not in the least novel; it is a derivative of connection table work. The comparison of CAS Registry Numbers and Beilstein Numbers to InChls reflects a lack of understanding regarding what lies behind these numbers. The CAS Registry Number is a concise identifier and provides the link between chemical nomenclature, the CAS Connection Table that describes the atom bond linkages of a chemical structure, and the molecular formula. It was never intended to be a structure exchange format that could be "decoded" to understand the chemical structure. It is true that InChI is an open format, while the CAS Connection Table is a proprietary format. However, the CAS Connection Table must describe all types of chemical substances, because it is at the heart of the CAS Registry System, which encounters all possible substances described by scientists (or chemists, biochemists, molecular biologists, and so on); it is a unique identification of chemical substances. The developers of InChI acknowledge that InChI is just away for computers to ex-
Request more at AdlnfoNow.org 4
C&EN
/ SEPTEMBER
19,
2005
www.CEN-ONLINE.ORG
Your Responsive Partner in Surfactants, Wherever You A r e We consistently invest in new application knowledge, sustainable products, process technologies and state-of-the-art production facilities, to meet your needs.
AKZO NOBEL Creating the right chemistry WWW.SUrface.akzonobeI.com
Request more at AdlnfoNow.org
J-KEM HOW TO REACH US CHEMICAL & ENGINEERING NEWS LETTERS TO THE EDITOR • Our e-mail address is
[email protected]. • Our fax number is (202) 872-8727. • Or you can send your letter to: C&EN Editor-in-Chief 1155—16th St.. N.W. Washington, DC 20036 • Letters should generally be 400 words or fewer and should include the writer's full name, address, and home telephone; letters may be edited for purposes of clarity and space. SUBSCRIPTIONS • Send all new and renewal subscriptions and requests for subscription rates to ACS, Dept. L-0011, Columbus, OH 43268-0011. • Changes of address, claims for missing issues, subscription orders, status of records, and accounts should be directed to Manager, Member & Subscriber Services, ACS, P.O. Box 3337, Columbus, OH 43210; telephone (800) 333-9511 or (614) 447-3776; or send an e-mail to
[email protected]. REPRINTS AND PERMISSIONS • Information on obtaining permission for copying articles is available at pubs.acs.org/cen/copyright.html. • For quotes and information on ordering bulk reprints, call CJS Reprint Services at (888) 257-2134 or (410) 819-3995, e-mail:
[email protected]. ADVERTISING • For advertising rates and our editorial calendar, contact Centcom Ltd., 676 East Swedesford Rd., Suite 202, Wayne, PA, 19807-1612; telephone (610) 9648061; or fax(610)964-8071. ACS INFORMATION • For more information about American Chemical Society activities and departments, call (800) 227-5558. When prompted, ask for operator assistance. Or visit the ACS website, chemistry.org.
change information about chemical structures. EILEEN SHANBROM
Manager, Online Services, SciFinder and Web Chemical Abstracts Service Columbus, Ohio
Confusing caption
T
HE PHOTO CAPTION IN THE STORY
'Arsenic in Rice" that reads "HIDD E N T O X I N Rice grown in the U.S. contains arsenic" is very misleading (C&EN,Aug.8,pagel7). There is nothing extraordinary about the fact that arsenic is in rice. Arsenic is in every grain on the planet—regardless of
national origin. It is a naturally occurring element found in nearly all soils. Keep in mind that approximately 15 to 25 ug of arsenic appears to be a requirement in human nutrition, according to many chemistry textbooks and scientific papers. This should dispel the alarmist notion carried recently in mass media stories that the mere presence of arsenic in rice or any food is a cause for alarm, as was implied in the photo caption.
Scientific
Custom Robotics Eclipse Solid Phase Synthesis Static
I
I
DAVID COIA
Arlington, Va.
Redefining 'ACS'
T
HE AMERICAN PHYSICAL SOCIETY HAS
voted overwhelmingly (76% in favor) to change its name to the American Physics Society Now it is time for ACS to get on board. Either 'American Chemist Society" or 'American Chemistry Society" would be acceptable. Let the American chemicals get their own society DANA D. DLOTT
Urbana, 111.
Technicians and training
E
RNEST LEE RECTOR III IS TO BECOM-
mended for his education and experience in the field of chemistry (C&EN, Aug. 8, page 11). It is true that many of us with Ph.D.s or B.S. degrees in chemistry rely on chemical technicians to get the job done, and in my experience, chemical technicians are appreciated for their contributions throughout the industry And I agree that including associate's degrees as a category in ACS publications is reasonable. I take issue, however, with Rector's implied suggestion that the difference between his associate's degree and a B.S. degree boils down to "art appreciation" courses and that his education provided "as much, and in some cases more" chemistry-related education as for those with B.S. degrees. That's hogwash. Anyone with a B.S. in chemistry has at least two years of 300and 400-level courses beyond what a twoyear associate's holder gets, including a year of physical chemistry, inorganic chemistry, and other advanced courses with laboratories. B.S.-degree holders have also taken at least a year of calculus and calculus-based physics. In fact, many B.S.-degree holders finish the "breadth courses" in their secContinuedonpage 43
Robotics For: * * * * *
Synthesis & Dissolutic Crystallization studies Cherry picking SPS&SPE Reformatting
User Programmable Original Windows code supplied with every workstation
Eclipse-WS Weighing Station - $23J 00 * 0.01 ingMettler balance * Excel input/output * Multiple vial sizes
Temperature Control Precision Simplicity *
Safety
J-KEM Scientific, Inc. (800)827-4849 http://\vv\ wjkcm.com Request more at AdlnfoNow.org
6
C&EN / SEPTEMBER
1 9 . 2C
WWW.CEN-0NLINE.ORG
Antoine Lavoisier wasn't the only 18thcentury chemist on the trail of oxygen. Five-time Pulitzer Prize nominee Joe Jackson explores whether Lavoisier or the English scientist Joseph Priestley can claim credit for the discovery in "A World on Fire: A Heretic, an Aristocrat, and the Race to Discover Oxygen," Viking, 2005, 432 pages, $27.95 (ISBN 0-670-03434-7).
Lavoisier was also different because he was wealthy Born into a bourgeois family, he rose to an essentially aristocratic status through his influential roles in the French government's tax authority and gunpowder administration. These associations were, of course, ultimately to precipitate Lavoisier's downfall during the French Revolution's Reign of Terror, but before that they enabled him to finance an elaborate laboratory which gave him an advantage over his chemical competitors such as Joseph Priestley and Carl Wilhelm Scheele, both also on the trail of oxygen. Even back then, funding made all the difference. But that was not the only reason for Lavoisier's success. His acute mind was coupled to a driving ambition, which saw him constantly scribbling semicoherent notes to the French Academy of Sciences to lay claim to his discoveries. Bell softpedals the common charge that Lavoisier was both arrogant and ruthless, but he artfully comments that the French chemist "took steps to protect the priority of his discoveries, somewhat in advance of actually making them." Bell does a good job of showing just how difficult those discoveries were. The oxygen theory looks obvious now; but faced, for example, with the fact that wood, metals, and nitre behave so utterly differently when heated in air, it was hard to see how any single idea could make sense of it all. Phlogiston had its problems, but it was not without its virtues, and Bell illustrates that Lavoisier's path toward a better idea was tortuous and confused. That he got there in the end is a wonder, and a testament to a genius who unquestionably earned a place alongside Einstein and Darwin. He was no angel, but Lavoisier's untimely end among the shabby anarchy of the French Revolution is a reminder that science can still be noble in ignoble times.
LETTERS continued frompage 6
gan-based company said that they had never hired a chemical technician and could see no reason why that practice would not continue. A few years later, they hired three-quarters of my class, and the next year they hired 100% of my A.A.S. graduates. The A.A.S. chemical technician has come a long way, because they are needed by the chemical industry Look at John Engelman, chair of CTA; he holds an A.A.S. degree. There are many places for the A.A.S. chemical technician in ACS, and those opportunities continue to expand. I, too, hope that starting salaries of the A.A.S. chemical technician will soon be published in the pages of C&EN.
ond year, even while taking all the chemistry courses an associate takes; they then spend their final two years taking only chemistry and other science courses. Add another two years for a master's degree or at least four for a Ph.D. While the associate's degree in chemical technology provides a student with sufficient background to assist in the laboratory, there is simply no way the education compares to that of a B.S. or advanced degree in chemistry Is this grounds for snobbery on the part of B.S. or advanced-degree holders? No. But if Rector ever wants others to think that his chemical education is as complete as it is for NORMAN G. PETERSON a B.S. degree, all he has to do is enroll for a Big Rapids, Mich. couple more years ofschool, study hard, and get his own B.S. degree in hand.
Where are the jobs?
SCOTT A. HEIDECKE
Eugene, Ore.
I
JUST RECEIVED THE ISSUE CONTAINING
the annual salary and employment survey (C&EN, Aug. 1, page 41). The quescles and polls dealing with levels of tion in my mind is, where are the jobs? education." He says his degree level There are a plethora of articles detailing is omitted or relegated to "undergraduate how we do not graduate enough scientists, student" or "less than bachelor's degree." how other countries are turning out more He says he has a difficult time participat- doctorates than the U.S., and how we need ing in these polls; yet he is a member of to relax immigration laws to allow more ACS and has an A.A.S. (associate in applied foreign-born scientists into the U.S. science) degree. It has been two years since I graduated I am glad Rector is amember ofACS and with my doctorate in chemistry In those has the desired A.A.S. degree; congratula- two years, I have sent out thousands of retions that he became a technician by design, sumes and made countless phone calls, and not by default. But he did not say whether yet I am still waiting for my first employhe is a member of ACS's Committee on ment as a chemist at the doctoral level. The Technician Activities (CTA). Practicing closest employment that I have had using chemical technicians should not only be my skills was teaching one semester offreshmembers of ACS, but also members ofCTA man chemistry at a local community colI hope that I will see Rector's name among lege. However, this was only apart-time job. new members ofour division in the next isI went deeply into debt to obtain my sue of CTAs quarterly publication. doctorate, but in the two years since gradWho am I to talk? In 1957,1 was hired uation, I have been working in call centers to lead an A.A.S. program at Ferris State as a customer service representative. My College, a program that trains chemical salary has ranged from $5.00 to $11.50 per technicians academically. At that time, hour. If I had not had the help of my wife's there was no place in ACS for those who salary as a nurse and the help of relatives, graduated from my program. Today, grad- I would be bankrupt. As it is, I have used uates of the program, which I led for 30 all of my retirement funds to help payback years, are welcome to join ACS. During school debts. I do not have the resources my first year of teaching, one large Michi- to travel to exotic cities and stay in expensive hotels to attend ACS meetings to hand out resumes. I have to be content CORRECTION with using either the mail or the Internet. I noticed that the median salary for a • Aug. 29, page 16: Vical's vaccine for doctorate in my regionis $90,000 peryear, melanoma has completed Phase II clinPhilip Ball is a science writer and a consult- ical trials, and its cytomegalovirus treatI would be willing to work at one-third of ing editor for Nature. His next book is "The ment for bone marrow transplants has that just to get back into the laboratory Devil's Doctor: Paracelsus and the World of Re-completed Phase I trials. Subsequent Again I ask, where are the jobs? naissance Magic and Science" to be publishedtrials have not begun. F. WILLIAM WEAVER in spring 2006. 1empe,Ariz. WWW.CEN-0NLINE.ORG
R
ECTOR'S LETTER WAS ABOUT "ARTI-
C&EN / SEPTEMBER
19, 2005
43
