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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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December 17, 2009

Why Don't Chemists Communicate? (Or Do We?)

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Posted by Derek

There's a commentary in the December issue of Nature Chemistry asking why our field has been comparatively slow to adopt web-based technologies like arXiv and GenBank:

"New web-based models of scholarly communication have made a significant impact in some scientific disciplines, but chemistry is not one of them. . .why do similar initiatives in chemistry fail to gain critical mass and widespread usage?"

The article considers several possibilities - among others, that (a) other fields aren't actually quite as techno-webby as we think they are, or (b) there might be a mismatch between chemistry as a discipline and the current tools, one that isn't found in some other fields of science, or (c) that there could be just a few defined issues that need to be addressed, then things will take off, or (d) that chemists already have the communication tools that they need, anyway.

The authors point out that technical hurdles can probably be ruled out as an explanation, and in many cases they can also rule out "because no one's ever tried". Elsevier, for example, tried to get an arXiv-type preprint server going a few years ago, but that bombed pretty thoroughly (not least, I think, because people were naturally a bit suspicious of such an effort being launched under Elsevier's banner, and because the ACS journals refused to take manuscripts that had appeared there). Nature has been trying something similar in the last couple of years with Nature Precedings, but I'm not sure if it's taking off or not. I've never really used it myself, if that's a data point worth mentioning.

One key point that the authors make is that totally new means of communication don't just pop into existence in a scientific discipline. The ones that catch on tend to build on things that the scientists are already doing. I think that physicists, for example, were already more used to sharing preprints of articles, and that the arXiv server just helped them do that more easily. Chemists, on the other hand Just Don't Do That, so announcing to them that Now They Can! isn't enough to bring in participants.

On the same chemistry-is-different front, the commentary also notes that our field has always had an emphasis on making stuff, although they don't put it quite that way. The computer is not usually the machine that produces our results; it's just the means by which we keep track of them. And we don't generate the piles of (sometimes) reusable data that physicists do, so much as we generate new substances and new ways of making and using them. The data are there to show that we did, in fact, make what we said we made. Those piles of data also tend to hold their value much longer than in other fields, too - after all, a compound is a compound, and its NMR spectrum doesn't change. If you want to know how some class of compounds behave, a paper from fifty years ago (or more) can be a perfectly good place to look.

Also in contrast to the physics community, chemistry is broken up into many smaller units. You'll never see a chemistry paper with as many co-authors as a high-energy physics paper, because we don't have to run our experiments on the One Big Machine In the Whole World. It may be that parts of the physics world have basically been forced to collaborate more widely, because that's the only way to get anything done. We also have a wide range of sub-disciplines, what with physics on one side of us and biology on another, and these all have their own idiosyncracies. (And, of course, many of us work in areas where we basically can't share some information until we're good and ready to).

One thing that the whole article doesn't quite address though, is: what would these wonderful new communication modes be, actually? And how would they improve my research life? Electronic literature searching certainly has, as has the availability of journals online. Electronic notebooks definitely have. What else would? I'm sure that there must be a few things, but I find that some of the Web 2.0 info-heaven visions that people outside the field talk about don't do much to excite me. It's like seeing some scientific abstract online, and then noting the little row of social-media icons below it, inviting me to submit the thing to Digg, Reddit, or what have you. Or to go visit the journal's page on Facebook, of all things. Why I'd do that is something I haven't quite figured out yet.

But hey, I'm not as much of a Luddite as that makes me sound. I also note this passage from the article (emphasis mine):

An increasing number of scientists have adopted blogging as a means of informal communication. Typicall, the writing style of blogs is conversational, and humorous content gets mixed with posts of a more serious tone. Some blogs are dedicated to educating lay audiences, others aim at an academic discussion, and many are like personal diaries. At this point in time, many science bloggers are assumed to be less than 30 years old, and are primarily journalists, teachers, graduate students, or young researcher. Hardly any established scientists maintain a blog - after all, blogging regularly is very time-consuming. The question remains open whether these will remain fringe phenomena or become part of the mainstream communication in science.

Comments (44) + TrackBacks (0) | Category: The Scientific Literature


COMMENTS

1. Cloud on December 17, 2009 10:28 AM writes...

I've always put the difference down to money. As in back when the databases were first getting created, the chemists had money and the biologists didn't.

Chemistry does have some decent databases and literature services- they are just for profit, not free. A lot of chemistry got done at companies that could afford to pay for database access, so private companies had an incentive to create and sell the databases. There were heaps of compounds, so the scientists could see the value of paying for access to a database. In those early days, no one was going to pay for access to a database of gene sequences and there weren't that many available, anyway, so the biology databases ended up being government run free things.

But I have no hard data to back that up. Its just how I've rationalized the difference in culture over the years. I can get all sorts of decent bioinformatics tools and databases for free, whereas I pay through the nose for the chemistry tools we use.

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2. Sili on December 17, 2009 10:34 AM writes...

To be fair, you're the only chemist I follow online. I've learned far more from professional biologists and physicists online.

But that claim does seem to indicate some lack of research, yes.

Are there any (good?) open access chemistry journals? I think I'd be ideologically inclined to use those if given the chance.

I'm way out of the loop, but while decades old spectra are indeed still not only usable, but excellent resources, they seem to me to be pretty hard to get at. Crystallographic data are collated (but proprietarily, unfortunately), but where do I go to find NMR and IR in a standardised, easily accessible format?

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3. gyges on December 17, 2009 10:40 AM writes...

"...why our field has been comparatively slow to adopt web-based technologies..."

Simply, this is because it doesn't matter whether or not we get read.

That is, it doesn't matter whether or not the whole world and his dog can get access to what we write.

Our audience isn't the whole world but a relatively small clique (sic). And our audience has someone to pony-up access to massively expensive journals. Try doing a literature search by paying for it out of your own pocket and what I'm saying will become clear.

One of the reasons for this is that what we do is incredibly esoteric. Another reason is that it doesn't matter that the whole world and his dog cannot read what we write. We can still get our funding / reputation / etc ; it simply doesn't matter to those who are information haves, that in the chemistry world there are information have-nots. Afterall, information is the lifeblood of this profession, those that don't have it will simply wither and die and, along with them any chance of changing the system from within.

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4. CMCguy on December 17, 2009 10:58 AM writes...

Derek I for one am very appreciative that you break the stereotype of bloggers and do take time to provide thought-provoking and frequently entertaining material on a regular basis.

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5. MTK on December 17, 2009 11:02 AM writes...

One reason why chemists have not used web-based technologies as much is that the largest chemical society in the world, ACS, has actively opposed it.

ACS lobbied against PubChem. They have lobbied against open access. ACS sued Google over Google Scholar.

ACS has done everything it can to protect it's own interests without regard to the interests of it's members or in the interests of science.

Shocking.

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6. Chris on December 17, 2009 11:15 AM writes...

A few thoughts, much of the biology published 50 years ago is now known to be incorrect, in contrast chemistry from the 1900's is still useful, so chemists have needed ways to search historical information.
For some subjects text-based searching is fine, in chemistry there is the need for specialist structure-based searching and tools for actually displaying the structural information. The institutions that developed the technology now jealously guard the results. Describing biology of physics results on a web page and hoping people can read it is easy. Putting intelligent chemical structures (not an image) into a web page and hoping all readers will be able to view them is much more difficult.

I do know of a research group in a major company who spent considerable effort trying to get a reaction to work, after many months a publication appeared in the literature that gave critical insight, the authors of the paper were from another site working for the same company.

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7. anon the II on December 17, 2009 12:00 PM writes...

Derek posed the question of why chemists don't communicate. The question is really why don't chemist communicate electronically. I think that most of the post have hit the real reason pretty good. Chemistry communication is more complicated but it's about money, mostly.

Proprietary systems and software have been the norm in chemistry. Money from the pharmaceutical industry has provided most of the incentive. Who are the villains? Well, the ACS has certainly not done anything to open up access for the have-nots. Ditto for Elsevier and all the other article publishers. But there are a lot of others. The parallels to Microsoft's tricks are pretty obvious.

MDL vigorously protected the copyrights on their file formats for a long time. Just long enough to lead to the Babel-like mess we have with electronic formats for structural information. One could talk for a long time about how MDL stymied development of computer technology for chemistry while squeezing the last drop of profit out of it. Thankfully, MDL (now in Symx) is slowly becoming irrelevant but the damage is done.

The analytical file format mess has existed because all the instrument makers want to get lock-in. There was a pretty good attempt with JCAMP, but not enough people jumped on board. Bruker and Varian embraced JCAMP by tweaking the formats so that they were different. Any parser would have to figure out which instrument made the file. And chromatography was never part of JCAMP. Later attempts at developing an XML format for analytical data (ANIML) were squashed by the very companies claiming to be interested in making it happen. ACD sent their man (now an open source advocate) in to stymie the efforts. Waters bought and buried two companies that were close to figuring it out. Thermo bought and destroyed the other two. ANIML still exists but the momentum is gone. Thanks guys.

The good news is that the pharmaceutical industry, which had all the money to provide the incentives for all the hanky-panky with proprietary formats, is no longer willing to spend that kind of money. After they get rid of all the scientists, the money they are paying for the subscriptions will start to look really high and need will drive us to do things like the biologists and physicists have been doing for a while. The modeling program, Avogadro, might be an example to that. The bad news is that the money going into biology will cause it to close up if they're not vigilant.

Having watched the use of computers in chemistry pretty closely my whole career, there is one other thing that has gotten us here. Many chemists, especially organic chemist, just don't care. All of the efforts to apply computer technology to chemistry have been done or pushed by a small minority, maybe 5% or less. The rest are just along for the ride. It may be, as Derek alluded, that it's just the nature of chemists.

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8. RB Woodweird on December 17, 2009 12:24 PM writes...

MTK and anon the II hit it square: it is the ACS, which is dedicated to protecting its little profitable fiefdom, not the the best interests of the chemist.

Someday I will be able to input into some piece of software, a browser window probably, a structural transformation I am interested in. A goes to B. And I will hit enter and be able to see all the chemical information available: A to B, analogs of A to B, various reagents which made B from A, etc. All the data I need in one place from every source.

Alas, that day will be far in the future

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9. Sili on December 17, 2009 12:26 PM writes...

Thanks, anon the II,

It's a pity you're anonymous, because it sounds like you really have this stuff down.

This is Derek's blog, but I for one would not complain should he ask you to do a guest post on this subject.

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10. David P on December 17, 2009 12:32 PM writes...

I would think ChemSpider (http://www.chemspider.com) would be a good example of something the chemistry community has built up. Not a complete list of everything but a lot of chemicals in there, searchable, with features added. That the Royal Society of Chemistry adopted it is a good sign for its future as well.

I also recall reading that Symyx were going to coordinate/collaborate with chemspider as well.

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11. MonkeyNinja on December 17, 2009 12:54 PM writes...

Look at us chemists communicating on the web.

Anon II, you got my attention as well. I've been in analytical R&D for ten years and I still don't get what's up with JCAMP and ANIML history despite being a software guy. I'd love some references or more detail.

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12. SoulSearcher on December 17, 2009 12:59 PM writes...

I think it is entirely cultural. People like Woodward and Corey who have essentially defined the field and collaboration had never been part of it.

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13. lynn on December 17, 2009 1:09 PM writes...

It does seem to be about the money [as noted by #1 & 7]. I'm a biologist, retired from Big Pharma but still consulting and writing reviews. And I am sorely in need of free access to chemical [largely ACS, but there are others] publications and databases. Chem Spider is handy but incomplete [as #10 said]. I solve the publication problem by writing to authors and requesting reprints - thankfully done pretty easily nowadays with email and pdfs. I wish chemical stuff was more accessible.

To Chris at #6, there is a lot of old biology that doesn't get accessed enough, nor referenced enough. As a reviewer, I've seen papers repeating experiments done 30-40 years ago - re-inventing the wheel. It's useful and educational to see experimental details in old papers - especially those that have been proven wrong.

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14. Anne on December 17, 2009 2:09 PM writes...

Perhaps we lack the communication skills to use apostrophes in titles correctly? ;) Kidding, kidding.

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15. TJ on December 17, 2009 2:13 PM writes...

there was plenty of hardcore chemistry discussion and conversation at the now defunct rhodium.ws ... so perhaps it's not the chemists, but the conversation that is key.

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16. Derek Lowe on December 17, 2009 2:30 PM writes...

Can't believe I did that, Anne. Fortunately, it's a low-traffic day around here, what with the holidays coming on. . .

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17. RM on December 17, 2009 3:53 PM writes...

Why don't chemists communicate? Because the successful ones are conniving, backstabbing a**h***s who would sell out their own mother to get a Nature article or a JACS communication, and have no qualms about stealing your work and passing it off as their own.

I exaggerate, of course, but there's a real reticence to share any information, lest your competitors get even the slightest advantage over you. Add to that the institutional/legal framework which encourages minimal disclosure (e.g. the trade secrecy practically mandated by patent rules), and you're left with a culture that's not quite a "kumbaya", "what's mine is yours" one.

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18. David on December 17, 2009 4:59 PM writes...

#2: Same here, this blog is the only scientific blog I follow, but it is also the only one updated daily with interesting content.

I thought about starting one in my field (proteomics), but I decided that if I were to attempt one that I would do it right or not at all. This meant posting regularly with plenty of pertinent material to the field, as well as interesting science and lab culture topics from time to time. There are blogs that were started in this attempt, but have fizzled out after a short period of time or only post every 3 months.

As a grad student I'm not sure I can muster the time (I have thought of co-hosting with a colleague).

Any advice, Derek?

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19. RTW on December 17, 2009 5:25 PM writes...

#5 MTK - You are correct. I have a REALLY big problem with ACS Journal access policy. I have been a member for 25 years mostly for Journal access. And for 3 years before that as a student member. I never had the companies I worked for pick up my dues or my journals costs. I pay for them myself. I can at any time look at articles in JOC and JMed Chem for 28 years without charge from my print editions.

Recent ACS policy states that next year there will no longer be individual print additions. I have to access them on line. I am not at all happy about that as it limits my access to journals that I pay for. If by chance I can't afford to be an ACS member any longer - I can't access journals I have paid for, as I can with my print additions. This really ticks me off! Its also not clear, if in the future I will have online access for all the years I subscribe to the journal on line, or just the current year. Would I have to pay again to access an article referenced in the previous year for instance? I wouldn't have to if I had them in print.

I have subscribed to JOC and JMed Chem for 28 years. If forced to go electronic then I should as long as I live have access to those I subscribed to, member or not. What if after I retire I can't afford to be a member any longer? Do I loose access to what I paid for? This was just an ill conceived policy IMHO.

I have always had issues with ACS where it concerns access to Journal Articles and particular CAS. Our dues helped to develop and market CAS and only institutions can afford access now. It was nice when I worked for a big company and had access to resources like that but now I don't as they are hidiously expensive. I can't even go back to pre electronic methods of searching literature using paper CAS indexes in Libraries I am not aware if any library that still have them. So what exactly has the electronic revolution done for me lately?

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20. Sili on December 17, 2009 6:08 PM writes...

This meant posting regularly with plenty of pertinent material to the field, as well as interesting science and lab culture topics from time to time.
Regular updates really aren't important now that we have aggregators; once I have your feed, it doesn't matter how often you post, as long as it's good.

So once a week or once a month is plenty often.

But group blogging is good as well - it's good for both bloggers and readers to bounce ideas off eachother.

And honestly, I'm really impressed that Derek can post each and every day. And don't get me started on PeeZed and his non-stop blogging.

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21. barry on December 17, 2009 6:10 PM writes...

consider that chemistry had Gmelin, Beilstein and CA decades before other fields could do any systematic searching of their literature. The need wasn't as great to invent new modes of communication in chemistry. Heck, biologists still can't seem to agree to any standardized nomenclature for the systems and proteins they study.

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22. Anon on December 17, 2009 6:22 PM writes...

Chemists also communicate via blackmail:
Cf: http://www.sciencemag.org/cgi/content/summary/326/5960/1610

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23. dearieme on December 17, 2009 6:31 PM writes...

"Why don't chemists communicate? Because the successful ones ....have no qualms about stealing your work and passing it off as their own." Twice in my career I was warned against collaborating with someone on just those grounds -once with a chemist, once a physicist. By coincidence or not, both were FRSs, both had received honours from the Queen and both had held an Oxbridge chair.

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24. cliffintokyo on December 17, 2009 7:35 PM writes...

Its mainly about the specialized tools we need (structures and equations) for chemical communiciation is it not?
You can't write a chemical equation in proper format (let alone a structure) using e-mail, and not easily using Word (please correct me if I am wrong...)
I wonder if mathematicians blog? They have a similar problem with their equations. I often suspect that they cannot communicate in English, and may have a worse problem than chemists.
Some chemists have clearly learned how to write, though, as evidenced, and surely partly influenced by, this blog.

Seasons Greetings and Salutations, Derek!

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25. Rich Apodaca on December 17, 2009 7:43 PM writes...

"One thing that the whole article doesn't quite address though, is: what would these wonderful new communication modes be, actually? And how would they improve my research life?"

Very good questions. My company started Chempedia Lab to find some answers:

http://lab.chempedia.com

The idea is simple. You hit a problem in the lab - none of your colleagues have an answer. Post your question to Chempedia Lab and get fast, peer-reviewed answers.

Many commenters on this post point to money and power as the reasons why open, Web-based, peer-to-peer communication hasn't flourished in chemistry. That every information need a chemist has is already being met by an expensive, closed system.

Chempedia Lab is your chance to prove this hypothesis wrong.

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26. Cloud on December 17, 2009 7:51 PM writes...

barry- in defense of biologists, nomenclature on the things that are easy to uniquely identify usually is pretty well standardized these days. But biology is complicated. In chemistry, you can always default back to the structure for uniqueness. That's not the case in biology. If you have a 100% accurate algorithm for determining when two sequences are the "same" protein, I'd live to see it. I've seen cases where splice variants of the same protein and related (but different) proteins have the same percent identity. I've never found a way to sort out these questionable cases without involving a real live scientist.

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