Nature Has a Graphical Abstracts Problem

Or I should say, it had a problem. The most annoying thing about Nature journals, not including Nature Chemistry, is they do not have a graphical abstract associated with their rss feed or even in their Table of Contents. However, I made a hack to view Nature with an associated graphical abstract over at ChemFeeds.

link: Nature via ChemFeeds

I also went ahead and made it for all the other Nature journals.

• Nature
• Nature Chemistry (actually already had this one, but including it for completeness.)
• Nature Physics
• Nature Neuroscience
• Nature Nanotechnology
• Nature Cell Biology
• Nature Medicine
• Nature Methods
• Nature Biotechnology
• Nature Immunology
• Nature Materials
• Nature Chemical Biology
• Nature Genetics

If you happen to be a Nature lover you can see them all with this link: All Nature.

If some of the feeds don’t have many abstracts within them it is because they are very new and more abstracts will be added automatically as Nature updates their AOP feeds.

Update: PNAS ADDED!

Update 2: Science Added.

Mitch

Subscribe to the comments for this post

How Can Science Embrace Web 2.0: A Response to Rudy Baum

(This post is in response to the May 10 editorial in C&E News.  For the response to the April 19 editorial, click here)

First, I want to thank Rudy Baum, editor-in-chief of C&E News, for taking the time to respond to my commentary.  I know he probably has other issues he’d rather talk about on his editorial page, and I appreciate the engagement in this dialogue.

I’d like to continue the dialogue here and I hope to keep this conversation going – at least informally – for a long time.

Mr. Baum and I seem to agree that Web 2.0 is a part of science now; however, we may disagree on the merits of SciW2.0.  If you don’t believe SciW2.0 has arrived, consider that the fact that you are even privy to this conversation.  Not only do I have a W2.0 platform upon which I can comment on C&E News editorials, but within days the comments were populated with a who’s who of SciW2.0 leaders offering their opinions and helping shape the conversation.  And the conversation became so loud that it prompted an editor-in-chief to write an entire editorial in response to, essentially, a nobody in the chemistry world (let’s face it.  I certainly don’t count myself in the elite of chemistry, blind or not).  That all of these things can happen within a month – and without any face-to-face meetings between any of the players – proves the establishment of SciW2.0 as a communication tool.

Now, before we continue, I want to re-link to this blog post on Nature‘s Nascent blog.  In my opinion, this post is a must read for anyone who wants to engage this discussion.  It is a nice overview of SciW2.0, its strengths and especially its weaknesses.  Why there’s resistance to SciW2.0, why academic and industry leaders aren’t all buying in, and why he’s committed to making SciW2.0 successful.  It really is mandatory, and I’ll wait for you to click over and read it now.

(lounge music break)

While severely cautioning people about SciW2.0 (but not denouncing), Baum seems to want to walk a fine line.  It’s dangerous, it’s not a panacea, he reads blogs, he’s not an opponent of all W2.0, he agrees with author Jaron Lanier when he warns scientists not to adopt W2.0 ideals, and he finds proponents of W2.0 overenthusiastic.  Perhaps he is just cautioning scientists against ‘irrational exuberance’ when it comes to buying in to SciW2.0.  And those warnings would be well heeded (although I doubt we’re anywhere near the irrationally exuberant days of SciW2.0).  My question for Baum is: if he doesn’t think SciW2.0 is a panacea, does he think the current model for scientific communication (peer-reviewed journals) is a utopia?  And if not, what would he suggest happen differently?

As to his comment about the panacea of W2.0 and how it ‘changes everything’ as he says W2.0 proponents adamantly claim, I suspect he’s referring to Don Tapscott’s and Anthony Williams’ book Wikinomic: How Mass Collaboration Changes Everything.  I haven’t read it, so I can’t comment on it.  But I would imagine, as is true in other areas of life, when people mention ‘everything,’ they rarely mean things like cutting edge academic and scientific research.  Rather, I imagine people mean ‘everyday things,’ usually for everyday people.  I’ll link here to notes by Will Richardson on W2.0 and how it’s changing politics, government, journalism, and business, and how it is starting to change education.  So while it seems to be changing certain industries, I’ll admit that it’s not changing everything.  In fact, I don’t think any of the commenters on the other post thought so, either.  Pop science is not the same as pop culture and does not think the same way.  Comments made in one arena are not necessarily transferable to the other arena.

But rather than getting into a hair-splitting contest over who used what words and who meant what, I propose to move the conversation forward in a different direction.  My open question: What should SciW2.0 look like, and how will we know it’s successful?

W2.0 is ultimately a communication tool.  It harnesses the power and dexterity of the internet and allows people to communicate with each other in ways never before possible and on timescales never before possible.  In certain circles (politics, pop culture), if you’re not actively following the W2.0 scene, you’re way behind and have nothing to bring to the table.  Not so in SciW2.0.  If you’re following SciW2.0, you’re reading about and reacting to people’s analysis of things that happened in the past.  Missing a week or two won’t put you behind, because by and large you’ve already read the same papers and seen the same announcements.

I doubt that SciW2.0 will become an instant data/paper communicating tool for hard science anytime soon the way it has in other aspects of life.  I agree with the reasoning by Timo Hannay in the Nascent link:

[E]ven if the direct financial cost of sharing this information is low, the cost in terms of scooped findings, rejected papers and grant applications, and perhaps even diminished reputation could be very high. … It’s sad, but most scientists don’t publish in order to share results with their peers, they do so in order to secure grant funding and promotions. We know this because when we provide ways of sharing information that do not affect their likelihood of getting funding or promotions – such as preprint servers for biologists – most don’t use them.

There will always be a place for reactionary SciW2.0.  Communities of people talking about science and sharing ideas and information cannot hurt anyone.  But because there’s rarely breaking news coverage on SciW2.0 (see Totally Synthetic’s sodium hydride oxidation post for an example of breaking news coverage), the majority of chemists don’t seem to find the need to tune in regularly.

Before we’ll get large numbers of people on board, in my opinion, might we need to make SciW2.0 less reactionary and more innovative?   I think we’ve started seeing bits and pieces of that scattered throughout, and that might be how we make it more appealing to the science community at large.  I mentioned in the comments previously that ACS had their NanoTube contest, which asked users to upload original videos explaining ‘What is Nano’ in an clear and entertaining way.  Perhaps this is the way science utilizes W2.0 in a productive manner.  Demystifying aspects of science to make it accessible to anyone curious about science, but perhaps without the training.

But, as the Nascent link alludes to, other types of crowd sourcing have not been as successful.  Nature‘s open peer-review system posted a small number of ‘opt in’ papers online and asked the crowd to review and comment on them before being accepted to the journal.  The open peer-review process happened concurrently with the ‘typical’ closed, anonymous peer-review process.  As noted if you listen to the audio version of the talk, it added no apparent value, but a lot more work for the Nature folks, so they abandoned the experiment.  I suspect it was just ahead of its time.

We may look to the results of a current crowd sourcing experiment to see if the time is right yet.  The Haystack, one of CENtral Science’s child blogs, reports on the expansion of the Pool for Open Innovation against Neglected Tropical Diseases.  In this experiment, scientists dump patented information into an open pool, and different users around the world are able to access the data to try to make progress on treatments for neglected diseases.  It will be interesting to watch that story unfold over the next few years.

I guess I don’t really know what SciW2.0 needs to look like to be successful. … But I bet I know a way to get some of the brightest minds in the field together to think about it communally!   I’d love to hear from people what their ideas are for the future of SciW2.0 and how to make it more commonplace in the field.

Finally, I’d like to say to Baum (and everyone else reading), if you haven’t read Who Moved My Cheese?, then pick it up from the library on the way home tonight and read it.  It will take maybe an hour, and it can be read in the easy chair after dinner while watching 24 if you’d like.  The cheese is moving, Rudy, I just don’t know where to, yet.

Subscribe to the comments for this post

Most Popular Chemistry Papers 2010 (1/3)

There are finally enough people visiting ChemFeeds (~150/day) that metrics like most accessed chemistry paper might actually be statistically significant information. So below I present the top two most clicked on abstracts from ChemFeeds for the first third of 2010.

First Place: Emil Knoevenagel and the Roots of Aminocatalysis
by Benjamin List in Angewandte Chemie International Edition
(DOI: 10.1002/anie.200906900)

2nd Place: Total Synthesis of the N,C-Coupled Naphthylisoquinoline Alkaloids Ancistrocladinium A and B and Related Analogues
by Gerhard Bringmann, Tanja Gulder†, Barbara Hertlein, Yasmin Hemberger and Frank Meyer in Journal of American Chemical Society
(DOI: 10.1021/ja9097687)

Some Notes on the metrics. This information probably says more about the people visiting ChemFeeds than the quality of the papers. It would appear ChemFeeds visitors skewer heavily towards the organic synthetics. Perhaps with the recent addition of being able to click on category feeds like all materials and all physical feeds it’ll balance out.

Mitch

Subscribe to the comments for this post

Is Chemistry Incompatible with Web 2.0?

(This post is in response to the April 19 editorial in C&E News.  For the response to the May 10 editorial, click here)

A recent ChemJobber post notes that C&E News Editor-in-Chief Rudy Baum‘s editorials sometimes have a tendency to approach the controversial – and sometimes the purely political.  I wanted to discuss this weeks editorial which threatens to call into question much of my online existence (sorry, Mitch.  If Rudy’s right, I think you’re about to spontaneously e-implode).

In this week’s editorial, “The Limits of Web 2.0,” Baum decries the cliché “information wants to be free” for both its out-of-context usage (the full quote says information wants to be expensive because it is valuable and free because the cost of information dissemination is shrinking almost hourly – thus a struggle) and for its lunacy (information can’t wish for anything – it’s inanimate).  Rather, Baum says that it’s people who wish that information would be free.  I’d amend Baum’s correction slightly.  People really want information to be free and readily accessible.  I’d argue public libraries have long made most information “free,” if you were willing to do the legwork to get it.

But the bulk of Baum’s editorial promotes Jaron Lanier’s book You are Not a Gadget: A Manefesto, and summarizes Lanier’s main points, namely that the wisdom of crowds can be dangerous and science should be loath to adopt web 2.0 ideals.  Lanier points out that around the turn of century, a “torrent (a word hijacked by the web 2.0 crowd -ed.) of petty designs sometimes called web 2.0″ flooded the web.  And through the use of web 2.0, we apparently are losing sight of the trees for the forest, er, the taggers for the cloud.

Baum writes in his editorial (cross-posted for free on the web 2.0 CENtral Science blog, natch), “The essence of what Lanier is saying is that individuals are important and that we’re losing sight of that at our own peril in elevating the wisdom of the crowd to a higher plane than the creativity of a single person.”  That is, we are valuing the cloud more than the individuals, when the cloud can’t exist – and has no meaning - without the existence of the individuals.  Lanier notes that collective intelligence can be used well, but only when guided by individuals who can direct the course of the hive mind and help steer clear of common groupthink pitfalls.

But the most interesting quote comes near then end, when Baum quotes Lanier as saying that scientific communities “achieve quality through a cooperative process that includes checks and balances, and ultimately rests on a foundation of goodwill and ‘blind’ elitism.”  I’m not really sure what that means…

But to Lanier’s thesis that science ought to be wary of embracing web 2.0 and its ideals, I find it interesting that Baum writes his editorial at C&E News, the magazine of the ACS, whose flagship publication, the Journal of the American Chemical Society, has featured a JACSβ page for some time now.  The same C&E News whose blog has become so popular that it had to split off into several child blogs.  Where each post for each ACS article has links to share the article on one of several social networking sites.  Where scientists can now browse their favorite article on their iphones with ACSMobile.  While perhaps late to the party in some areas, the American Chemical Society has certainly ‘logged on’ to web 2.0 as a way to export content to the web-savvy scientist.

Plus, we have our own Mitch, a one man walking encapsulation of web 2.0.  His most successful application is, in my opinion, the chemical forums, which typically sees between 8,000 and 11,000 visitors per day.  This blog seems to be a big hit, and his ChemFeeds is a one-stop source for your aggregated list of your favorite journals’ graphical abstracts.  All this innovation on Mitch’s part earned him an interview with David Bradley (of ScienceBase) in his chemistry WebMagazine, Reactive Reports.

There’s also the Chemistry Reddit as another outlet of chemistry news and notes.

In the inaugural issue of Nature Chemistry, the Nature Publishing Group recounted how they have completely bought into web 2.0 as a means of science communication – each issue of Nature Chemistry even features a roundup of their favorite posts from the chemical blogosphere (which reminds me, to the left, Mitch has also created an aggregated rss feed of several popular chemistry blogs).

And, of course, web 2.0 in the sciences has been discussed in the blogs several times over the years.  We have over 3 pages of posts categorized Web 2.0, mostly Mitch’s posts on new web 2.0 platforms he’s developed.  Jean-Claude Bradley writes about web 2.0 in response to a very interesting post at Nascent, a blog from the folks at Nature.

So, all of these prove that web 2.0 has been talked about many times in the context of science.  Has it worked?  With the exception of blogs, sadly I’m inclined to say no.  At least not yet.  And even with blogs (with the possible exception of All Things Metathesis, and In the Pipeline, though Derek isn’t allowed to talk about his work b/c of intellectual property issues), not a lot of academic or industry leaders are prone to blogging.  It’s not like we’re reading Phil Baran’s blog and getting inside his head on a daily basis.

Sure, there is a subculture of people who are active on the web 2.0 scene, but it surely hasn’t taken off as a medium for all chemists to enjoy.  It theoretically should.  Chemists are always benefited from communal sharing of results and information.  But there are still (and probably always will be) people who seem reluctant to join the new technological paradigm.  I like the way Timo Hannay words it in his post on Nascent,

“But it’s not up to the doubters to ‘get it’, it is up to those of us who support these developments to demonstrate their value. And if we can’t then they don’t deserve to be adopted and we don’t deserve to be heard.”

Especially if there are people at the position of Editor-in-Chief for arguably the top chemistry magazine denouncing the web 2.0 movement, clearly it has a ways to go before it will be appreciated by all to the point where web 2.0 is ‘taken for granted,’ where we don’t even realize what we’re doing when we post results and opinions via web 2.0 technologies.

Let’s get moving!

Subscribe to the comments for this post

ACS – Day 4: Peer-Review Reviewed

Wendy Warr

Wendy Warr gave a bleak and blistering critique on the current state of chemical peer-review at the recent ACS National Meeting in San Francisco. Her points are even more poignant as she is an associate editor for ACS. The salient features of her critique are listed below.

Problems with Peer-Review:

• It can delay publications for months.
• An editor can make or break a paper by sending it to the author’s friends or competitors.
• Historically biased against women, single authors, etc…
• It costs reviewers’ time (she gave a statistic that 41% of reviewers would like to be paid).
• Reviewers tend to favor conservative science and not far-out new ideas.
• Difficult finding qualified reviewers for multidisciplinary work.
• Basing the quality of a paper on 2 reviewers, basically just 2-data points, is statistically insignificant.
• As more papers are being submitted the burden for reviewers is increasing.

Warr did not give many solutions to these problems. However, she did point to resources addressing peer-review.

• Peer-to-Peer – Nature’s blog specifically focusing on peer-review.
• Naboj – A website where you can comment on arxiv papers and pubmed papers.
• Faculty of 1000 – A website that tracks what authoritative people in the field think are the good current papers.

Unfortunately, Naboj and Faculty of 1000 do not really address the problems of peer-review. The former is just a comments hub, and the latter is just an aggregator. At the end of her talk George Purvis asked, why the government simply doesn’t setup a system for peer-review like ebay. Where submitters can have a trust scale associated with them, and people could thumb through the history of a reviewer. The idea of a peer-review ebay is seductive, but I doubt it would be greatly used; I could live without seeing “A+++++ paper will read again!!!!”

Bluntly speaking, you can not expect to have a vibrant peer-review community without a vibrant post-review community, and the chemical community seems decidedly averse to putting their name on-the-line.

Mitch

Post Script: Before Dr. Warr began she made explicit that she was not speaking on behalf of the ACS-Pubs machine but as an independent scientist.

Subscribe to the comments for this post

ACS Mobile

Credit: Linda Wang/C&EN

ACS has released an app that streams new ACS graphical abstracts to your iphone. Unfortunately you have to pay $2.99 for the app. A free alternative I wrote can be found at the mobile site for ChemFeeds.

The nice thing about my version is it works for any mobile device that gets internet and not just iphones. It also covers RSC and Elsevier journals in addition to ACS. You can email article links to yourself for later reading and even leave comments on the abstracts. Admittedly the ACS version looks sleek, but iphones only apps are worthless for us Android users.

Link to C&EN’s ACS Mobile coverage: ACS Publications Go Mobile

Link to ChemFeeds Mobile: http://m.chemfeeds.com/

Note: If you are not a member of the smart phone community yet, you can still get your graphical abstracts fix at the regular ChemFeeds website: http://www.chemfeeds.com/

Mitch

Subscribe to the comments for this post

Online Textbooks: ChemWiki Part 1

I remember buying my first O-chem books back when I was attending DVC (Diablo Valley College), a not-so-little community college here in the Bay Area. At first I checked the bookstore and lost my lunch when I saw the price of the new books. The text was $215, the lab manual was another $70, and the solutions manual was $100. Unfortunately, a new edition had been released that year, so even though the professor said that we could use older editions, many of the problem sets wouldn’t match up, so we’d have to get the problems from our classmates. In the end, the cheapest and most convenient route was to go online and buy the international editions. Even after extending the method to all my other classes, I still paid almost $500 for books that semester. Now I attended DVC before California went belly-up, so my classes were still a great bargain at $18 a unit. Since I usually took ~19 units, my total tuition cost was around $350 a semester. The cost of the books were actually greater than my cost of tuition. The sad thing is, this wasn’t an unusual case. Luckily this wasn’t too much of a hardship for me; I had a job on campus and money saved up. However, I knew a lot of students for whom the beginning of the semester meant not eating lunch in order to save up gas money.

Now students have probably been complaining about textbooks since time immemorial. Aristotle probably complained that his scribe made spelling mistakes in his copy of The Republic. Most of the time our bellyaching is justified. Not only do textbooks cost a lot, but there is often a gross amount of errors in them. Everyone knows that the first time you find a caption or answer wrong, it makes the rest of the book suspect. Also, these errors give the publishers a reason to release a next edition…that never seems to fix even half of the errors. However, they do switch around problem numbers, add a few pages of new content, and possibly even rearrange chapters. So now the professors lesson and homework plan, that goes by chapter numbers, page numbers, and problem numbers, is moot. And the student is effectively forced to buy the new edition (price “adjusted for inflation”) or suffer some inconveniences. Most choose to simply buy the new edition since tracking down the old one can be difficult and you have to be quick. Also, sometimes bookstores won’t buy back the old edition so if you had it, and an edition switch occurred before you finished your course track, you are up the creek.

Some of these issues can be addressed with online textbooks. The idea of supplementing physical texts with online modules has been around and implemented by publishers for many years. However, I’ve yet to see a good entirely online chemistry textbook. The advantages of online texts are of many: accessible anywhere you get 3G or Wi-Fi and have your mobile device, interactive learning capabilities, easy distribution, instant update/revision, and low cost publishing (server fees). Of course this won’t necessarily result the publisher make more money, but at 4 billion (yea, you read that correctly, billion) dollars a year, the industry doesn’t really need much help.

The student, however, does. We need these online textbooks, not just to save our wallet, but also to help prevent being stuck with an expensive and lousy text for a year that does a poor job of explaining the material. That expensive O-Chem book I bought really was terrible and it forced my professor to do a lot of extra work in teaching us not to follow the book’s direction of simply memorizing 500 reactions, but to see the patterns and the underlying physical explanations. In the end, we learned from his powerpoints and I paid $215 for a glorified reference book.

Well, some people are pioneering an effort to create an “Open Access Textbook”. In a perfect example of “chem 2.0″, UC Davis Professor Delmar Larsen is the project director of the ChemWiki, a truly free online textbook written by everyone, for everyone. In an absolutely Herculean effort, the developers and Larsen (Mary Obrien, Ron Rusay, Brent Krueger, Michelle McCombs) are trying to create a free and complete, as in covering all branches, chemistry textbook using a community of students, faculty, and outside experts from around the world. Of course they aren’t there yet, and there is still a long way to go but hey, their text literally gets better everyday.

Now I know you probably have a lot of questions: what about correctness and plagiarism? Could such a thing ever be considered an Authority? What do the publishers say? Does anyone actually use the thing? Well, it just so happened that a couple of weeks ago, I was at Davis for the Borge fellowship visitation and I had a chance to talk with professor Larsen who agreed to answer some of these questions for me. In a couple of days, I’ll post the interview here. For now, I suggest you go and check out http://chemwiki.ucdavis.edu/ and browse not just through the core, but the wikitexts and community as well.

Subscribe to the comments for this post

Smart companies do smart things: Materia has a blog

So it’s not like anyone NEEDS encouragement to think about using olefin metathesis in their chemistry, but in case you wanted to talk to real experts, Materia (the company founded by Grubbs et al. to commercialize metathesis) has recently opened a blog called All Things Metathesis.

It’s got some literature reviews and stuff, but most helpful for chemists is the best practices category, where they explore how to plan your metathesis reactions and how best to purify them. So very 2003 to say this, but blogging is a great medium for businesses to communicate with their customers. This is a really nice example. They have comments, so you can even talk to metathesis experts!

So how long before there’s an Ask Dr. Metathesis column, where frustrated grad students write in with their late-night isomerization angst?

Subscribe to the comments for this post

Web 2.0: In the Classroom?

I went to a workshop a while ago under the title of Teaching During Budgetary Crises.  Among the topics covered were alternative teaching methods and free or inexpensive methods of interacting with your students other than traditional the 50 minute lecture.

We were given a list of a variety of web 2.0 platforms and suggested ways to use them in a classroom setting.  The workshop participants spanned a variety of departments across the university, so as I glance through the list, I can see how some platforms would lend themselves to use in certain departments, while others might make more sense for the physical sciences.

Here’s the list we were given, with links to information about the site.  Have any of you seen any of these technologies used in a classroom or seminar setting?  If so, how were they implemented?  Were they successful?  Would you have done it differently?

I think I could see myself using Jing as a resource to walk through out-of-class examples of more complex or complicated synthesis problems and mechanisms.  Jing is a screen-capture technology that allows you to upload video of your onscreen actions.  I could propose a synthesis problem, jump to my slides covering the needed concepts, and jump to ChemDraw to illustrate my thought process and the correct answer.

Times and technology are certainly changing before our eyes.  Are educators going to stick with the traditional lecture model, or are we going to move with the trends to bring content to students in new and exciting ways?  Or, if we do move with the trends, are we going to end up sacrificing quality to increase curb appeal?

Tools for Interactive Questioning

• Audience Response Clickers (more)
• Surveys/Discussion boards w/i the universities course management system (like Blackboard)
• Google Forms
• Harvard’s Berkman Center’s Live Question Tool

Strategic Recording

• Broadcasting classroom lectures for students taking the course online
• iMovie or Windows Movie Maker
• Jing
• CamStudio (open source screen capture)
• VoiceThread
• iTunes U
• Vimeo
• Ning (create your own social network) (more)
• Facebook

Collaborative Learning

• XMind Concept Mapping
• Google Docs/Google Sites
• PBWorks (formerly PB Wiki)
• Zoho Writer
• WordPress/Blogger.com course blog
• Skype
• Elluminate/Adobe Connect/DimDim and other e-conferencing platforms

Subscribe to the comments for this post