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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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May 23, 2007

Exalted Paper

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Posted by Derek

It might not always be obvious from the blog, but I've been rather literature-deprived lately. I'm not talking literature-literature, naturally - my favorites are all over here on the shelf to my left (For anyone who's interested, those would include Nabokov's wonderful Pale Fire, Brad Leithauser's underappreciated Hence, Martin Amis's best, which is Money, his father Kingsley's immortal Lucky Jim, Chesterton's The Man Who Was Thursday, and Evelyn Waugh's Decline and Fall). No, what I'm beginning to starve a bit for is full-text scientific literature, which is understandable, given that (a) I've been unemployed since the beginning of February, and (b) full-text subscriptions to all the major journals would cost me cash that I'd rather hose away on frivolities like my mortgage.

I do have some recourse to the local universities, where I've gone, uh, periodically to catch up on things. The same processes I saw at work in the Wonder Drug Factory's library are at work in these, too, of course: dwindling shelf space for paper journals and increasing numbers of flat screen displays in their place. It's a bit of a shame for a person like me, who grew up in the era of dead tree journals, because I still like to pick them up in my hands (and because the experience of reading them online still isn't as pleasant as it no doubt will be eventually).

What I've noticed is that the most widely read ones remain in paper as well as digital subscriptions. It's becoming a clear sign of respect for a journal's influence. That means Science, Nature and the like are always still to be had physically. Chemistry libraries always seem to have JACS, Angewandte Chemie and, interestingly, Organic Letters in hard copy, which is probably a good sign for the latter.

So I've been making due with the open-access journals, few of which have strong chemistry ties as yet, and with abstracts and individual free-access articles from the others. Which reminds me - does the ACS ever make anything from its journals open access? Fly-by-night rags like the NEJM or PNAS will open up the most-discussed papers in each of their issues to give them wider exposure, but I've never heard of that happening with, say, JACS. Maybe they figure that the most-discussed articles there are going to be read largely by people that they can get to pay for them, anyway, so why bother?

Comments (31) + TrackBacks (0) | Category: The Scientific Literature


COMMENTS

1. Still Scared of Dinosaurs on May 23, 2007 9:51 AM writes...

One thing Science and Nature have going for them is that they are visually interesting publications, which can't be said for most of the scientific journals. Even worse are the Math and Stats journals I often read. Believe me, beautiful equations do exist but they are few and far between.
For most journals, though, you open the pdf and print (double-sided, please!) and you lose nothing except the weight of the pages you don't want to read anyway.

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2. RKN on May 23, 2007 9:59 AM writes...

I'm a bit surprised; doesn't Duke provide their PhD alumni access to online journals? Or at least at a reduced cost?

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3. RKN on May 23, 2007 10:02 AM writes...

I'm a bit surprised; doesn't Duke provide their PhD alumni access to online journals? Or at least at a reduced cost?

...

Btw, if you enjoy Waugh you might like his short stories. I've got a copy of a collection of his stories. If you don't, and you're interested, send me an email with your address and I'd be happy to send you mine.

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4. Still Scared of Dinosaurs on May 23, 2007 10:25 AM writes...

re: Lucky Jim, I still can't read the words, "He felt bad" without cracking up after reading that book.

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5. Jonathan on May 23, 2007 10:32 AM writes...

Any work that was funded by the NIH, and possibly by the NSF, ought to be open access within 12 months of its inital publication date these days, so the situation is getting better.

Regarding the ACS, they probably get most of their revenue from the journal, and society journals remain the most opposed to the spread of open access publishing.

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6. Laura on May 23, 2007 10:50 AM writes...

Yeah--Derek, as a Duke alumna I know I'll always have library access. Maybe this isn't the case for your year, but if you had a login and password to the Duke system, it's very likely still valid. I've also been told it will never be removed. It's what I used for research in graduate school and sometimes now on the job as well--the OIT website will tell you how to either download the VPN (which never wants to work for me) or to set your server proxy.

Aerosol related articles can be hard--AAAR is narrower than many other publications and thus pricier by some logic.

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7. Brian on May 23, 2007 11:33 AM writes...

You don't have any professor friends that would be willing to give you their proxy server login info so that you can read them on-line from the comforts of your living room?

P.S. I sent someone your way (but he's got his e-mail public, so you might want to be proactive):
http://www.linkedin.com/answers/technology/biotech/TCH_BIO/48148-9847577

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8. david on May 23, 2007 11:39 AM writes...

Given the trend towards online publishing and the lack of a new ink and paper journal in almost a decade, I think the days of ink and paper are numbered. Sure, for some journals it may take a while before they give up ink and paper, but the reality is that ink and paper is doomed. It's that simple.

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9. Wavefunction on May 23, 2007 12:08 PM writes...

I have the same question about Duke. My cousin (lucky dog) who graduated from John Hopkins now has lifelong access to all journals that Hopkins subscribes to.

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10. Derek Lowe on May 23, 2007 12:53 PM writes...

I should check into the Duke connection - but it's not like I have any sort of password there. When I was there, there was no such thing as an electronic version of a journal, and there was no Web access because there was no Web. Ah, the mid-1980s.

It's terrifying for me to recall that when Apple's "1984" commercial came out, I was already doing graduate research.

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11. Anonymous on May 23, 2007 1:40 PM writes...

And these were as old then:
1. I Fall To Pieces, Patsy Cline
2. Tossin' And Turnin', Bobby Lewis
3. Michael, Highwaymen
4. Cryin', Roy Orbison
5. Runaway, Del Shannon
6. My True Story, Jive Five
7. Running Scared, Roy Orbison
8. Wheels, String-a-longs
9. Raindrops, Dee Clark
10. Wooden Heart (Muss I Denn), Joe Dowell

As these are now:
1. When Doves Cry, Prince
2. What's Love Got To Do With It, Tina Turner
3. Say Say Say, Paul McCartney and Michael Jackson
4. Footloose, Kenny Loggins
5. Against All Odds (Take A Look At Me Now), Phil Collins
6. Jump, Van Halen
7. Hello, Lionel Richie
8. Owner Of A Lonely Heart, Yes
9. Ghostbusters, Ray Parker Jr.
10. Karma Chameleon, Culture Club

I thought I was reasonably well versed in pop-rock history, but the String-a-longs? On the other hand, I do remember Mr. T on The A Team saying, "Everybody loves Culture Club!"

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12. Laura on May 23, 2007 1:56 PM writes...

As an alumnus you might be able to request a DukeID. The revamped FAQ on the OIT website (http://www.oit.duke.edu/netid-security/netid/faq.html) describes how to go about getting one, and it's not entirely clear that they wouldn't just give you one for being an alumnus, which I think we would all coconsider a formal affiliation with the university. You just need someone onsite to email the specified information to the email address listed there and see if they'll give you one--trying couldn't hurt, and then you'd have the online library.

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13. molecularArchitect on May 23, 2007 2:02 PM writes...

Derek, I share your pain on this one. My unemployment has now stretched to 14 months. I still scan the abstracts for J Med Chem, Org Lett, etc but am frustrated that I cannot access the full papers. It bothers me because I feel like I'm losing my edgy by not staying current. Maybe it's time to mount a grass-roots ACS members campaign to allow free access to older papers, at least for ACS members.

I too make the occassional trip to the local university but the general public cannot download pdf copies of papers. The library printing costs are too expensive for my strained financial resources unless I have a real need for the information.

Is life-long access for graduates common at schools today? Any recent or current Purdue grads here who could tell me if PU offers this? Like Derek, I had no need of a password in the early 80s because dead tree copies were the only copies available.

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14. LNT on May 23, 2007 3:28 PM writes...

I'm a duke PhD alumni too. As of a few years ago, the Duke library would not grant alumni access to online journals. You do have access to every other aspect of the library (ie, you can check out books, use it's search services, etc.) but online journals are off limit, unless they have recently changed thier policies.

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15. Brooks Moses on May 23, 2007 4:35 PM writes...

Jonathan @5: I think that's somewhat of an overbroad statement, regarding society journals. The APS (American Physical Society) seems to be at least tentatively in support of open-access; for instance, they have a program where for a reasonable fee one can make any article in one of their journals open to the public. A reasonable fee in this case being something like $1600, if I'm remembering correctly, which seems reasonably in line with the per-page costs that many journals charge when they're doing the "author pays" rather than "reader pays" revenue model.

molecularArchitect @13: I don't know about schools in general, but for a counter-datapoint I am quite certain that Stanford doesn't offer such a thing.

As for public access to online journals -- one of the things that I particularly like about the University of California system libraries is that, as a branch of the state government, they consider it their obligation to be open to the public, including allowing public access to all of their online journals. There've been a few times that I've made use of this for journals Stanford doesn't subscribe to. (The computers with access have very limited functionality, including no USB ports, but one function that they do have is "email this file somewhere", which is how I downloaded the papers I wanted to print a copy of at home.)

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16. bad wolf on May 23, 2007 4:47 PM writes...

mA: you might be best served to take a flash-drive (available in all sizes, pretty cheap) with you to the local edu, download interesting pdfs onto it, and take home to peruse/printout at your leisure.

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17. molecularArchitect on May 23, 2007 5:34 PM writes...

Bad Wolf @ 17: no accessible USB ports on the library computers at Univ. California libraries (at least not at UCSF, UCB).

Brooks @ 16: Thanks for the tip about "email this file somewhere". I hadn't noticed it. I'll check next time I am there. I like to get pdf files because I can link the file to my personal EndNote databases. Also, recently found a really nice new program for organizing pdf files. It's call "Papers". Still a work in progress but a neat aid for organizing personal references. If interested: see mekentosj.com

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18. Anne on May 23, 2007 6:16 PM writes...

It's too bad you're not in astronomy, the arxiv.org preprint server is extremely useful. No, it's not a journal, yes you get both extremely sketchy articles and good articles which are never updated to their final version. But I would bet that papers that appear on arxiv.org get read by many more people than ones that don't. Combine this with the vast amount of X-ray data that's public-access and with the free availability of not just the tools to manipulate it but HEASARC's Hera system - a public-access machine you can use to analyse HEASARC data - and amateur astronomy takes on a whole new meaning.

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19. Brooks Moses on May 23, 2007 7:22 PM writes...

molecularArchitect @17: The "email this file somewhere" command is, if I'm remembering correctly, added to the "file" menu in whatever application is displaying the PDF files (I can't remember if it uses a plugin in the web browser, or calls up Acrobat separately), sort of where you'd expect the "print" command to be.

When I was doing it, I used the fact that they do allow connections to .edu sites (it's firewalled to only .edu sites and a whitelist of journal sites) to check my Stanford webmail to make sure the files went through.

Thanks for the "Papers" recommendation -- I'll look into it!

(Also, thanks to Derek for promptly deleting my accidental double-post. Sorry about that.)

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20. Joel on May 23, 2007 7:47 PM writes...

I have to chime in and strongly recommend "Papers" too. I particularly like how it allows you to keep notes (via a clipboard) while reading the PDF. It is only for Mac however.

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21. wcw on May 23, 2007 7:58 PM writes...

Way off-topic, but one of your authors (imo) does not belong. He can, to his credit, string together a gorgeous sentence, his novels wrap up nicely, his plots twist like a knife -- but he has absolutely nothing to say. Lots of smart people I know love him, so I kept reading his stuff for years until I decided that something was wrong, and I stopped.

Let's just say I see him as the nepotism hire.

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22. Rosie Redfield on May 23, 2007 11:22 PM writes...

It's not journals that decide to make high-interest articles open access, but authors who decide to spend their hard-won grant money on what is basically a point of principle.

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23. KinasePro on May 23, 2007 11:25 PM writes...

Umm, Just read KinasePro?

Free Stuff @

ARKIVOC
Blood
JBC

I don't understand why ARKIVOC or at least the ARKIVOC model hasn't caught on. There's also a bunch of free podcasts worth keeping up with too.

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24. Petros on May 24, 2007 1:24 AM writes...

Yes it's galling not to be able to access the primary literature when you want to.

From using the web for the past 10 years things have improved in that many journals now have full text freely available, at least for all bar the most recent couple of years.

I can't think of any significant chemistry journal that offers this facility. The ACS, RSC and Elsevier all offer nothing more than access to abstracts. Chem Pharma Bull is probably the most signifcant Med Chem journal that is freely available.

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25. Bryan Vickery on May 24, 2007 4:25 AM writes...

Dear Derek,

I wanted to write to you, as I too was unemployed for 6 months (after leaving Elsevier) and also had no access to the chemistry literature. It was a real worry not be able to keep up with changes in something I had been so involved with for years.

I am now at Chemistry Central [www.chemistrycentral.com] as Editorial Director, part of BioMed Central - the open access publisher. We have launched Chemistry Central Journal [journal.chemistrycentral.com] as a home for those who desire the benefits that open access brings. We're just starting out, but we're getting there.

Open access is not just about free access to the manuscript you want to read. For authors it means that they automatically retain copyright to their own work, and do not face page restrictions and unnecessary calls to reduce the length of their article. For readers is means they can download, use and redistribute the article as well as the associated data files.

We (BioMed Central) make our entire corpus available for download, mirroring and datamining.

We also enforce the same stringent forms of peer review as traditional journals. We allow readers to comment on articles and are about to add blog trackbacks too. Both are valuable forms of post-review.

After we announced the launch of Chemistry Central Journal both the RSC and ACS added open access publishing options.

We are working with out current "member institutions" to encourage their chemists to make use of our publishing services, and are working with non-members to bring them on board. Full-members opt to cover the cost of publishing in our open access journals centrally, and therefore Rosie wouldn't need to spend her funding directly. I would encourage chemists reading this to lobby their institutions to take out membership of BioMed Central, so that they can publish with Chemistry Central Journal.

Other journals published by, or in cooperation with us, in the field of chemistry include:

Beilstein Journal of Organic Chemistry
BMC Biochemistry
BMC Chemical Biology
Carbon Balance and Management
Geochemical Transactions

Chris Swain is our Medicinal Chemistry Section Editor

I wish you good luck in you search for employment.

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26. yagwara on May 25, 2007 2:58 AM writes...

Re #18: I'm curious about what forces prevent the existence of an arXiv for chemistry. I would guess that about 80% of theoretical physics and 40% of mathematics papers are posted there in preprint form.

If I had to guess, I would say that arXiv survived by being a fait accompli. If it didn't already exist and was invented today, Elsevier and Springer would be introducing draconian measures against authors who posted papers there. But the arXiv had been chugging along for many years before big publishers noticed, and now, any publisher churlish enough to restrict posting to the arXiv gets a bad reputation. They do restrict posting of the "final version", but often this differs only in having the journal name at the top of the pages.

Probably not coincidentally, mathematicians and physicists are also generally able to post their work on their personal webpages.

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27. Bryan Vickery on May 25, 2007 5:26 AM writes...

Re #26. I don't think it's fair to use Elsevier as an example each time you want to have a go at commercial publishers yagwara. I was previously Director at ChemWeb.com, an Elsevier owned portal for chemists, and in about 2000 we launched the Chemistry Preprint Server as an experiement in communication for chemists. We did this with the full backing and technical support of Elsevier and cooperated totally with OAI. The CPS *was* arXiv for chemistry. Many major publishers allowed posting of articles to this preprint server - be they works in progress or author copies of final articles. Elsevier allowed the posting of final versions. The most vocal against such a service was the American Chemical Society.

When Elsevier sold ChemWeb (a shortsighted decision given today's web 2.0 community vision, and online ad revenues) the CPS was closed down. The articles posted there can still be searched and viewed on ScienceDirect, you need to register, but this is free.

http://preprint.chemweb.com

will still get you there.

A PDF of a presentation my colleague (at the time), James Weeks, gave can be found here: http://eprints.rclis.org/archive/00000897/02/weeks.pdf

James and I were very proud of the work we put into the CPS, and were equally sad when ChemWeb was sold and the service closed down. But remember, Elsevier didn't try to ban it - it built it!

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28. Chris Swain on May 28, 2007 2:36 AM writes...

Dear Derek,

I also add that whilst open access to the journal articles will be an important step forward perhaps equally important is open access to the experimental data behind the publication.
The ability to refine, combine or explore SAR models using new techniques, particularly for off target toxicities will become invaluable.

Regards,

Chris

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29. The Strider on May 28, 2007 7:19 AM writes...

Google scholar (http://scholar.google.com) is very useful as it points occasionally to the personal homepage reprint of a journal article.

Many publishers, such as the ACS, rely on the copyright form and prohibit people from posting their work on preprint servers.

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30. DocLightning on June 3, 2007 8:25 AM writes...

What I like about paper journals is that they never crash, deny you access, or ask for a password that you can't remember.

I read online and I love reading online, but for journal articles, it needs to be on paper.

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31. Edward on June 14, 2007 12:24 PM writes...

I wanted to respond to comment #6, which stated that as a Duke alum she would always have access to library material. This is not an accurate statement. Duke alumna do not have permanent access to library material since their Duke NETIDs are either purged from the system or disabled for login to certain services. Furthermore, there are efforts to address this issue in more detail to make sure services are restricted based on alumni status, or other affiliated status, so that Duke NETIDs may be retained by alumni for access to alumni only services, but not licensed databases.

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