Corante

About this Author
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

Chemistry and Drug Data: Drugbank
Emolecules
ChemSpider
Chempedia Lab
Synthetic Pages
Organic Chemistry Portal
PubChem
Not Voodoo
DailyMed
Druglib
Clinicaltrials.gov

Chemistry and Pharma Blogs:
Org Prep Daily
The Haystack
Kilomentor
A New Merck, Reviewed
Liberal Arts Chemistry
Electron Pusher
All Things Metathesis
C&E News Blogs
Chemiotics II
Chemical Space
Noel O'Blog
In Vivo Blog
Terra Sigilatta
BBSRC/Douglas Kell
ChemBark
Realizations in Biostatistics
Chemjobber
Pharmalot
ChemSpider Blog
Pharmagossip
Med-Chemist
Organic Chem - Education & Industry
Pharma Strategy Blog
No Name No Slogan
Practical Fragments
SimBioSys
The Curious Wavefunction
Natural Product Man
Fragment Literature
Chemistry World Blog
Synthetic Nature
Chemistry Blog
Synthesizing Ideas
Business|Bytes|Genes|Molecules
Eye on FDA
Chemical Forums
Depth-First
Symyx Blog
Sceptical Chymist
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa


Science Blogs and News:
Bad Science
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Nobel Intent
SciTech Daily
Science Blog
FuturePundit
Aetiology
Gene Expression (I)
Gene Expression (II)
Sciencebase
Pharyngula
Adventures in Ethics and Science
Transterrestrial Musings
Slashdot Science
Cosmic Variance
Biology News Net


Medical Blogs
DB's Medical Rants
Science-Based Medicine
GruntDoc
Respectful Insolence
Diabetes Mine


Economics and Business
Marginal Revolution
The Volokh Conspiracy
Knowledge Problem


Politics / Current Events
Virginia Postrel
Instapundit
Belmont Club
Mickey Kaus


Belles Lettres
Uncouth Reflections
Arts and Letters Daily
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

In the Pipeline

« Chinese Pharma: No Shortage of Ambition, Anyway | Main | China's Pharma Ambitions: Hua Pharmaceuticals Responds »

August 30, 2011

Why Isn't There an ArXiv For Chemistry?

Email This Entry

Posted by Derek

Nature has an article on the 20th anniversary of the ArXiv preprint server by its founder Paul Ginsparg. That's gradually worked its way through many parts of physics and mathematics to become a major route for releasing scientific results. (They're now getting about 7,000 submissions a month, with a million downloads a week). But many areas of science remain untouched:

Physicists were quick to adopt widespread sharing of electronic preprints, but other researchers remain reluctant to do so. Fields vary widely in their attitudes to data and ideas before formal review, and in choosing to share electronic preprints, each community will have to develop policies and protocols best suited to their users. A talk I gave in 1997 to a group of biologists helped catalyse the resource now known as PubMedCentral — run by the US National Institutes of Health. I served on the initial advisory board, which soon decided not to host any unrefereed materials, even carefully quarantined, in part for fear of losing essential publisher participation. There remain many legitimate reasons for individual researchers to prefer to delay dissemination, from uncertainty over correctness, to retaining extra time for follow-ups, to sociological differences in the way publication is regarded — in certain fields, the research somehow doesn't count until peer reviewed.

No community that has adopted arXiv usage has renounced it, however, so the growth has been inexorable. . .

But back in its early days, it looked like it would be even more inexorable than that:

The idea that print journals had outlived their usefulness was already in the air in the early 1990s. David Mermin memorably wrote in Physics Today in 1991: “The time is overdue to abolish journals and reorganize the way we do business.”1 By the mid 1990s, it seemed unthinkable that free and unfettered access to non-refereed papers on arXiv would continue to coexist indefinitely with quality-controlled but subscription-based publications. Fifteen years on, researchers continue to access both, successfully compartmentalizing their different roles in scholarly communication and reward structures.

The transition to article formats and features better suited to modern technology than to print on paper has also been surprisingly slow. Page markup formats, such as PDF, have only grudgingly given way to XML-based ones that support features such as manipulable graphics, dynamic views, linked annotations and semantic markup. . .

Well, in chemistry, that transition has been even slower. Our field is still very much dominated by the societies (ACS, RSC, etc.) and the commercial publishers like Elsevier, Nature, Wiley, etc. When's the last time - when's the first time - you heard of a significant organic chemistry paper appearing anywhere else? There's absolutely no equivalent of the ArXiv system, and although I know that the question has been asked before, I'll ask it again: why not? If someone had started such a thing back in the early 1990s, would it (could it) have taken off? Or are there other factors that would have kept it from doing so (the same ones as now?)

Comments (51) + TrackBacks (0) | Category: The Scientific Literature


COMMENTS

1. Curious Wavefunction on August 30, 2011 7:42 AM writes...

I too have been saying this for some time. Compared to the chemistry community the physics community is much more open about its results. Not only is there ArXiv, but the APS journals like Phys. Rev. also allow you to see the number of citations for all their articles.

I never understood why the ACS or Angew. Chem. website cannot display the number of citations for their papers. Are chemists much more secretive and obsessed with results and citations compared to physicists?

Permalink to Comment

2. bill on August 30, 2011 8:33 AM writes...

Alan Katritzky has had Arkivoc going for some time online. I have found some very good chemistry published there - I think ACS (oops, that should be CAS - when will ACS cure its addiction) is abstracting it.

Maybe the big names are just too close to the big name journals - I mean those free trips to Miami in February are nice and this would mean the end...

I predict RSC leads the way and ACS follows 5 years later

Permalink to Comment

3. Mat Todd on August 30, 2011 8:36 AM writes...

Very good question. I don't know. I feel it may be based on this assumption that research pre-peer review is dodgy, and that a journal's peer review process anoints the work with respectability. Having seen the review process up close over the years, that's obviously not true. But that perception makes it difficult for preprints to be taken seriously.

How to provide a preprint with respectability? Or believability? A partial solution would be to insist on the highest standards of data deposition. Every compound would come with raw and PDF'd NMR spectra, for example, so we can see if a compound has been made, and how clean it is.

(I don't want to distract from your question, Derek, but if people are interested in raw data and journal policies, I ask some questions here: http://intermolecular.wordpress.com/2011/08/07/raw-data-in-organic-chemistry-papersopen-science/)

Permalink to Comment

4. Nate on August 30, 2011 8:51 AM writes...

What a completely different world it would be if we could all share our successes AND failures over on a single site. It would be great if the world could decide what was important or not and not three peer reviewers and and editor....

Permalink to Comment

5. myma on August 30, 2011 8:53 AM writes...

Impact factor.

Permalink to Comment

6. gyges on August 30, 2011 8:53 AM writes...

I'm surprised that the current system hasn't been challenged by anyone. I've most probably said it before in the comments on this blog but I think that the transfer of property from taxpayers to publishing houses by Universities is most probably illegal. The property belongs to the taxpayers - they paid for it.

As for charities who publish in closed source journal; again, it is highly likely that they are putting at risk their charitable status, at least in the UK.

However, don't hold your breath; the UK Charity Commission is extraordinarily poor at doing what they're supposed to do. An example of their incompetence was highlighted by a group of artists called the Stuckists.

"In 2006 the Charity Commission ruled that the Tate's 2005 purchase of its trustee Chris Ofili's work The Upper Room for £705,000 was illegal and that the Tate had been acting illegally for 50 years in this way. This followed considerable press coverage of the matter, initiated by Charles Thomson, Co-founder of the Stuckists, who obtained Tate Trustee minutes and forced the Tate to reveal the price of the work under the Freedom of Information Act, as detailed below."

If it wasn't for the group of artists - the Stuckists - this illegality would never have come to light and may have continued for another fifty years.

I see a parallel in scientific publishing. Until challenged the business model will continue.

Permalink to Comment

7. Quintus on August 30, 2011 8:57 AM writes...

@4 Impact factor + Money!
Chemists are a secretive lot, the biggest concern is IP. There may not be such a need for extensive IP in physics, I'm not sure.

Permalink to Comment

8. Deepak on August 30, 2011 8:57 AM writes...

And Chemistry also has fewer open source applications and open data repositories than other fields. For some reason there is a tradition in the chemistry community to keep things closed. I don't know why, but perhaps the traditional role of chemistry in pharma and the materials science industry has something to do with it.

Permalink to Comment

9. johnnyboy on August 30, 2011 9:19 AM writes...

I don't think it's just chemistry though. I work in a more medical-oriented field, and i'd never even heard of such a thing as pre-print - and I think it's a brilliant idea. It seems to me the perfect medium for putting out there interesting research results which are not sufficient in themselves to warrant the hassle and uncertainty of official publication, but which help others to not have to reinvent the wheel. But competitiveness is probably the main obstacle to this system - people in academic (or industry) labs often see themselves mainly in a competition against other labs, rather than working towards a common goal, which is a damn shame.

Permalink to Comment

10. andrewD on August 30, 2011 9:31 AM writes...

Derek
You might find this interesting
http://www.guardian.co.uk/commentisfree/2011/aug/29/academic-publishers-murdoch-socialist

It is written by George Monbiot, and raises some interesting questions

Permalink to Comment

11. Frank Adrian on August 30, 2011 9:43 AM writes...

A lot of this does have to do with IP issues. Physicists and mathematician's papers tend to have information that won't be monetized for years (if ever). Work in the chemistry and medical fields seems as if it has a shorter timeline before practical use and the findings can easily be tweaked to get around patent issues. On the other hand, most of the engineering fields are even more quickly monetized and easily copied and most of their stuff is published online. Go figure...

Permalink to Comment

12. Will on August 30, 2011 10:15 AM writes...

I don't think IP has anything to do with it. It doesn't matter if you publish in a trad. journal or online, it's still in the public domain. you shouldn't be submitting anything to any type of publisher (free or otherwise) until your patent ducks are in a row

Permalink to Comment

13. Quintus on August 30, 2011 10:25 AM writes...

@12,
My company refused the permission to publish some of my work, in spite of complete IP coverage. Their argumentation made no sense to me. But no publication or open source or anything except NO.

Permalink to Comment

14. CR on August 30, 2011 11:38 AM writes...

@Quintos, #13/14:

Even though you had "complete IP coverage" (which, by the way, I don't think exists), companies are still concerned about giving anything away - including just the thought they might be working in an area. Their argument doesn't need to make sense to you or to them for that matter. Many companies will only publish on compounds in the clinic, which sort of cuts out the medicinal chemist because very few will actually go back and publish several years after the fact.

Other companies take the route of patenting and then publishing to expand the prior art around their patents without having to file additional patent (Merck). Although I'm not sure how much of this happens anymore.

It is the companies prerogative to not publish "your work" because, well, "your work" is "their work".

Permalink to Comment

15. leftscienceawhileago on August 30, 2011 12:22 PM writes...

Pfft. "IP" coverage? Really?
What could possibly be so valuable from an industry with failure rates like pharma?

I will put forth a more controversial hypothesis:

Chemists are less intellectually curious than people in mathematics and physics, they need to spend more time with their "hands" rather than abstracting.

Have you opened up an issue of JACS lately? Someone clicking this and that together, GFP tagged to a quantum dot, crystal structure of a useless mutant, some dumb combinatorial screen revealing some pathway that no one will ever verify...

The institution of chemistry publishing relies on being able to shovel out a high volume of tripe that is all justified by a single catch phrase: "..this may lead to a new drug one day...", and 99.9% of the time it never does.

The sad thing is that once in a while you do see a new cool fundamental discovery, but I can't remember the last time I've seen one lead to a cure to a disease. RNAi anyone?

Not that physics, computer science and astronomy are changing our lives everyday, but the peoples in those fields are seem to be driven to use very sophisticated methods mathematical methods and understand them very deeply. I don't see a lot of that in chemistry, outside of comp chem groups (who are really just physicists in disguise anyway!). Not that it is the chemist's fault, it isn't as if by using Bayesian statistics we'll somehow solve all of our problems and discover magical new cures.

I think what's really sad is that there isn't a
"arXiv + comments". Running a comment system isn't easy (and there is a lot of noise), but it would be useful to be able to call out some high profile shenanigans in a central location. Derek's review of a Schriber DoS paper was a good example of the type of review I am thinking of. No one really wants to rick the boat though, AFAICT.

Permalink to Comment

16. leftscienceawhileago on August 30, 2011 12:50 PM writes...

I realized I didn't really get to the point in my post, and just went rambling on...

Well my point was that people like mathematicians are depeer thinkers, happy just to exchange papers for free and let the really good papers rise to the top by informal consensus.

Chemists are less secure, they have to pay for a lot of hands, equipment etc. and need some sort of product to justify the investments in them. The product is a published paper in a journal that has some sort of barrier to entry (not just merit based either), thus imbuing your product with some value.

Chemists also don't want a central place where someone can publicly call out a terrible paper (or question the very premise of an idea), after all, look at bag of money was dumped into it! Who is going to pay for that?

Permalink to Comment

17. Chris on August 30, 2011 1:00 PM writes...

http://www.chemistrycentral.com/

A number of open access chemistry publications

Permalink to Comment

18. CVL on August 30, 2011 1:00 PM writes...

It sounds like ChemWeb once tried to organize a chemistry preprint server but that ended up failing. I think the primary reason why chemists are hesitant to upload preprints is simply because of this simple line on the ACS website:

"The use of preprint servers will vary from discipline to discipline and is highly dependent upon the culture and traditions of individual disciplines. Chemisty has strong tradition or rigorous, formal peer review."

Followed by

"A preprint will be considered as an electronic publication and, according to positions taken by most editors of ACS journals, will not be considered for publication. If a submitted paper is later found to have been posted on a preprint server, it will be withdrawn from consideration by the journal."

RSC has commented against preprints. Simply put, if the societies control the avenues towards publishing, ArXiv will never exist.

Permalink to Comment

19. Uncertain on August 30, 2011 1:16 PM writes...

Probably for the same reason why the community has not embraced LaTeX for typesetting articles, whatever that reason may be.

Permalink to Comment

20. Uncertain on August 30, 2011 1:19 PM writes...

Probably for the same reason why the community has not embraced LaTeX for typesetting articles, whatever that reason may be.

Permalink to Comment

21. johnnyboy on August 30, 2011 1:23 PM writes...

@16: well, if ACS charges sizeable subscription fees for its journals and access fees per article, then the use of pre-print would be a direct threat to a fairly large revenue stream, so no wonder they would do everything to censor it.

Permalink to Comment

22. Anonymous on August 30, 2011 1:24 PM writes...

It is general corporate paranoia, not IP per say, that drives the traditional inhibitions on industrial publication. What corporate manager in his right mind wants to be the one who signed the OK to publish anything that gives away some key scientific insight to competitors that is subsequently turned into a valuable competitive product? It is potentially career suicide to sign such an OK unless there is a corporate culture that demands rapid publication and bureaucratic SOP to give everyone cover.

However that does not explain why academics cannot publish all their taxpayer funded research in a government sponsored web journal that is fee to access by us who paid for the research with our taxes. Poor libraries would save a bundle of their very limited resources for other things and some of that library funding could be diverted to subsidize the free web journals. Scientists working in poor countries would gain access to important studies. The general public would benefit by having free access to the research results it was taxed to generate. The cost of delivering those results would collapse to the betterment of society and the tax payer who pays to fund libraries. None of us would have to pay outrages tolls to publishers like the ACS to the access our own work product.

Peer review exists because of real world limits on paper publishing. For me, just put it all out there and I can decide what is important and what is crap. I do not need a censor to filter this stuff. Plus some really significant work that is really out there would not be blocked from our view by reviewers who prefilter it away because it does not fit their view of the world.

Support government funded open access publishing and statutory probitions on copyright transfer to publishers of all government sponsored research results.

Permalink to Comment

23. Marty on August 30, 2011 2:17 PM writes...

It's not the same thing as arXiv, but there is a new open-source crystallography journal:

http://www.mdpi.com/2073-4352/1/1/1/

mdpi is starting (or has started) various open-access journals.

Permalink to Comment

24. quintus on August 30, 2011 2:37 PM writes...

@13,
Publishing papers in reputable scientific journals was a part of my job description, thus the company prevented me from doing a part of my job for which one can be penalized. So they had their cake and ate it too.

Permalink to Comment

25. RD on August 30, 2011 3:21 PM writes...

I recently asked some ACS reps these very questions at a local meeting of unemployed chemists in May. If you're trying to keep up with the literature, you have to shell out $30/paper if you don't have a subscription. And who has a subscription to all of the journals? At the beginning of a project, I sift through a dozen or so from multiple journals. If you're on your own, there's just no way and $30 is best spent on groceries or prescription co-pays or the water bill.
So, I asked the ACS guys why they don't just switch to an iTunes model for journals. Charge $1-$5 per paper and that way, they would be picking up business from the thousands of us who are unemployed because right now, we have to just pass and the ACS is *losing* money.
They looked both patronizing and bewildered. I'm not sure if it was because they didn't like the question or whether they didn't know what iTunes was.
Probably both.
A friend of mine who develops software for education for a major hardware company approached the ACS with a proposal for an app for chemistry. He said the conversation went nowhere.
Arrogant or oblivious? Does it matter? Chemists are screwed either way. The ACS let us down. They should have been more proactive on our behalf.
Oh, well. It's only an entire generation of chemists.

Permalink to Comment

26. petros on August 30, 2011 4:00 PM writes...

RD's comments ring a bell. Many years ago MDL developed an interface for CAS that could provide substructure searching (in the days when searching used terminals or pre-Windows PC with terminal emulation).

CAS pulled the plug on the interface!

Permalink to Comment

27. Sili on August 30, 2011 4:10 PM writes...

Money and IP, yes.

We even have to pay to get at the structures in the CCDC despite depositing them there ourselves for free.

To be fair, though, the CCDC does do hella work to make that database far more easy to search and to interrogate the aggregate data.

Presumably the commercial publishers were stronger in chemistry than in physics as well. I too hope that the RSC will do something to kill them off.

Permalink to Comment

28. Anonymous on August 30, 2011 4:38 PM writes...

Not because I necessarily believe this is always the case, but just as a possibility...is it possible that peer-review is more important in chemistry? Math and physics equations don't always take a huge investment of time/equiptment to double check, and so the quality papers will bear the test of time relatively quickly (I am not dismissing the time or effort that goes into diriving those equations.) As has been said here before, synthetic chemistry can take much longer to double check, so having a peer-review by someone familiar with the field should (in theory...sometimes in practice too) prevent the dissemination of garbage. I am reminded of the University of Utah cold fusion press release, which wasted the time/money of a lot of people, and which a reviewer would have shut down in a second by simply telling them to go back and run a few controls.

Permalink to Comment

29. leftscienceawhileago on August 30, 2011 4:43 PM writes...

28,
It isn't as if reviewers go and actually perform experiments. Just a bunch of people with some knowledge and no conflicts of interest (ah, there is the rub) taking a look over the paper.

It isn't obvious that it is more costly to review chemistry papers rather than math papers. If anything, I'll bet math papers take longer...

As to relative amounts of 'garbage' in the respective fields, I would probably guess 'about the same'.

Permalink to Comment

30. Healthy on August 30, 2011 5:14 PM writes...

Certainly arXiv is a great initiative that should be borrowed by other science fields.
Relating final paper sharing you can take a look at laywers conclusions from Mendeley. It basically says that as long as it is for non-profit porpouses it is completly legal. So it seems that it is mostly an issue of non-sharing capability from researchers that a real legal issue.

To find research lines and funding please check the non-profit aging portfolio.

Permalink to Comment

31. Pete on August 30, 2011 6:45 PM writes...

Taking another look at that rather intemperate rant about bloggers that Analytical Chemistry published as an editorial will go some way to answering the question.<