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

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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.

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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!

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NanoPropulsion

Stephen J. Ebbens

Jonathan Howse

The current state of the art in nanopropulsion devices was recently reviewed by Ebbens and Howse in an article last Friday.^[SoftMatter] A short summary of the nano- systems is presented below with video action shots when I could find them.

The Whitesides

Catalyst: Pt
Fuel: H₂O₂
Propulsion: Bubble propulsion
Terrain: Aqueous meniscus
Max Speed: 2 cm/s
Mitch’s Name: The Karl Benz (since it was the first)
Article: Autonomous Movement and Self-Assembly

The Sen-Mallouk-Crespi

Catalyst: Pt
Fuel: H₂O₂
Propulsion: Self electrophoresis/Interfacial tension
Terrain: Settled near boundary in aqueous solution
Max Speed: 6.6 um/s
Mitch’s Names: The Ford Mustang of nanopropulsion. (It is a hot rod, get it?)
Article: Catalytic Nanomotors: Autonomous Movement of Striped Nanorods

The Jones-Golestanian

Catalyst: Pt
Fuel: H₂O₂
Propulsion: Pure self diffusiophoresis
Terrain: Free aqueous solution
Max Speed: 3um/s
Mitch’s Name: The Volkswagen Beetle
Article: Self-Motile Colloidal Particles: From Directed Propulsion to Random Walk

The Mano-Heller

Catalyst: Glucose oxidase and Biliruben oxidase
Fuel: Glucose
Propulsion: Self electrophoresis
Terrain: Aqueous meniscus
Max Speed: 1 cm/s
Mitch’s Name: The Komatsu Truck (because it is huge)
Article: Bioelectrochemical Propulsion

The Feringa

Catalyst: Synthetic catalse
Fuel: H₂O₂
Propulsion: Bubble/interfacial
Terrain: Acetonitrile solution
Max Speed: 35 um/s
Mitch’s Name: The F150 (has some exhaust issues)
Article: Catalytic molecular motors: fuelling autonomous movement by a surface bound synthetic manganese catalase

The Sen-Mallouk

Catalyst: Pt (CNT) (+cathodic reactions at Au)
Fuel: H2O2/N2H4
Propulsion: Self electrophoresis
Terrain: Settled near boundary in aqueous solution
Max Speed: 200 um/s
Mitch’s Names: The Ford Mustang GT (has more kick than the regular version)
Article: Bipolar Electrochemical Mechanism for the Propulsion of Catalytic Nanomotors in Hydrogen Peroxide Solutions

The Feringa v2

Catalyst: Glucose oxidase and catalse
Fuel: Glucose
Propulsion: Local oxygen bubble formation
Terrain: Free aqueous buffer solution
Max Speed: 0.2–0.8 um/s
Mitch’s Name: The Chevrolet Nova (more hot rod action)
Article: Autonomous propulsion of carbon nanotubes powered by a multienzyme ensemble

The Gibbs-Zhao

Catalyst: Pt
Fuel: H₂O₂
Propulsion: Bubble release mechanism
Terrain: Aqueous solution
Max Speed: 6 um/s
Mitch’s Name: The Rover
Article: Autonomously motile catalytic nanomotors by bubble propulsion

The Bibette

Engine: External magnetic field
Propulsion: Flagella
Terrain: Aqueous solution
Max Speed: unknown
Mitch’s name: The BMW Mini E (because there is no such thing as a magnetic car)
Article: Microscopic artificial swimmers

The Sagués

Engine: External magnetic field
Propulsion: Doublet rotation coupling with boundary interactions
Terrain: Settled near boundary in aqueous solution
Max Speed: 3.2 um/s
Mitch’s Name: The Smart ED
Article: Magnetically Actuated Colloidal Microswimmers

The Fischer

Engine: External magnetic field
Propulsion: Propeller drive
Terrain: Aqueous solution
Max Speed: 40 um/s
Mitch’s Name:
Article: Controlled Propulsion of Artificial Magnetic Nanostructured Propellers

The Najafi-Golestanian

Engine: Conformation changes in linking units
Propulsion: Time irreversible translations
Terrain: Free solution
Max Speed: ?
Mitch’s Name: The Eternal Concept Car
Article: Propulsion at low Reynolds number

Some devices that were not included by the authors of the review article, but should definitely be included in any list like this are below:

The Gracias

Engine: External magnetic field
Propulsion: Brute Force
Terrain: Aqueous solution
Max Speed: ?
Mitch’s Name: The Truck Cranes
Article: Tetherless thermobiochemically actuated microgrippers

Tetherless Microgrippers Grabs Tissue Sample – Watch today’s top amazing videos here

The Nelson

Engine: External electromagnetic fields
Propulsion: Flagella
Terrain: ?
Max Speed: 18 um/s
Mitch’s Name: The Tesla Roadster (simply awesome)
Article: Characterizing the Swimming Properties of Artificial Bacterial Flagella

Artificial Sperm – Watch more funny videos here

Link to Review Article: In pursuit of propulsion at the nanoscale

Mitch

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Long-term Experiments

I recently read this Nature article, where is described what is probably one of the longest experiments ever to be conducted. A population of E. coli was kept for 20 years (!) in a nutrient solution (low on glucose), and samples were taken and deep-frozen after 2000, 5000, 10000, 15000, 20000 and 40000 generations. The authors sequenced the genome of the sample bacteria to investigate the rate of mutations.

Up to generation 20K, the number of mutations grew steadily to a total of 45. The adaptation to the environment, however, only increased strongly in the beginning. It was concluded that the most beneficial mutations were the first to occur. After generation 20K, a change in the mutT gene caused a rapid increase in the mutation rate to result in 653 mutation at generation 40K, but with a neutral signature, i.e. no further adaptation.

What I find most fascinating about this extreme long-term experiment is the confidence of the researchers that it would be possible to analyze the genes at a later point; this was not at all self-evident in the late ’80s! In addition, some work had to be done each day, for twenty years. What if the power had failed for a week or so? Of course, this unique opportunity to watch evolution as it happens is very intriguing.

An experiment that took even longer was awarded this year’s Ig Nobel Prize in medicine: Donald L. Unger of Thousand Oaks, CA, cracked the knuckles of his left hand, but not his right hand, every day for 50 years to see if knuckle-cracking leads to arthritis. After this time, both hands were fine, so he concluded: “While a larger group would be necessary to confirm this result, this preliminary investigation suggests a lack of correlation between knuckle cracking and the development of arthritis of the fingers.” Apparently, the experiment must be repeated.

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Joking in a Nature journal?

Was reading this earlier this evening on the hobby science forum Sciencemadness.org –it’s amusing.

Read the letter carefully.

Well, let’s hope this is a joke.

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Condensed Print Format

My boss has pointed out this piece of news covered by C&EN. Apparently, starting from July, all ACS journals will be printed in a “rotated and condensed” format, that is two pages on one printed page in landscape format. This is an effort to reduce printing and distribution costs.

In my opinion, this change is just one further step towards purely electronic journals that are not printed at all. I think this will deeply affect the way we present our data and how we look at formatting. Preparing a manuscript in a way meant for printing is different from one which will never appear in print. Some may welcome this change because it saves paper, others will probably miss the possibility of flicking through a new issue of JACS. Although I rarely go to the library to pick up a printed journal, I admit to reading printouts very often (see this post).

Update: Apparently, in 2010 the print versions will stop completely, with the exception of JACS, Acc. Chem. Res. and Chem. Rev. See also Nature News.

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Scientific Misconduct

This nature article discusses the results of a survey about scientific misconduct, while an editorial makes some comments.

Quote: “The 2,212 researchers we surveyed observed 201 instances of likely misconduct over a threeyear period. That’s 3 incidents per 100 researchers per year. A conservative extrapolation from our findings to all DHHS-funded researchers predicts that more than 2,300 observations of potential misconduct are made every year.” Almost 9% of the respondents had witnessed some sort of misconduct, and 37% of those incidents went unreported.

The authors conclude that, besides protecting the whistleblowers better, it is necessary “to create a zero-tolerance culture”. The editor, however, holds the opinion that one also needs to take a look at “the environment that has allowed misconduct to flourish”. In his opinion, there should be the possibility of finding a solution without ruining the career of a scientist, especially in mild cases.

I tend to follow the editor’s reasoning. In my opinion, the zero-tolerance culture already exists to a certain extent, because a scientist convicted of, e.g. faking data, can forget about his career. But the result of such a policy is clear: no-one wants to blow the whistle on a colleague, because they don’t want to end somebody else’s career and because they will make themselves very unpopular. The real problem is the way misconduct is treated at the moment: we want to identify the guilty scientist, and punish him/her.

While this makes sense for the worst cases of fraud, in milder cases one should try and ask the question *why* the misdeed was done. Take, for example, the way hospitals treat mistakes nowadays: they try to find out how it could happen, and how it can be avoided in the future. This is very sensible, because it treats the problem in a proactive way: instead of reacting to the incident by punishing somebody, future incidents are reduced by tackling the things that cause them in the first place.

If there is a lot of pressure to produce as much data as possible in a research group, it is tempting to cut a corner once in a while. Can this not partly be considered the prof’s fault? In a similar way, one should address the working atmosphere in the group in question. The problem with the academic system is that there is no informal institution to turn to, besides your boss, if you are to witness a case of scientific misconduct. So we fall back to the old issue: the only person you can contact in case of problems has all the power over you.

At the University of Toronto, a “Graduate Student Oath”, similar to the Hippocratic Oath, has been tried as a means to strengthen scientific ethics (Science). Although this is an interesting idea, I doubt it will change the behaviour of people very much.

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Discovery of Mg-40, Al-42, and Al-43

Baumann et al. have recently reported the discovery of three new isotopes ⁴⁰Mg, ⁴²Al, and ⁴³Al. The discovery is notable for producing an isotope that neither the finite range droplet model (FRDM) nor the Hartree-Fock-Bogoliubov (HFB-8) predicted should be bound.

Of the 3 isotopes, the discovery of ⁴²Al is an unexpected surprise and thusly the most fascinating. As we all know from undergraduate nuclear chemistry the Weizsäcker’s formula contains a pairing term (d) approximately equal to 34*A^-3/4 MeV. The term increases the binding energy for an even number of protons (Z) and neutrons (N), decreases it for an odd Z and N, and of course is zero for an odd atomic number (A). ⁴²Al contains 13-protons and 29-neutrons, lies on the extreme neutron-rich side, and thus was not predicted to exist in a bound state.

Theory can be seen to be in contradiction from experimental data as seen below.

Reprinted by permission from Macmillan Publishers Ltd: Nature 449, 1022 – 1024 (25 Oct 2007).

To the immediate left of the ⁴³Al dot is the collection of ⁴²Al events. The ⁴³Al event had a probability of ~2 x 10^-3 of arising from the Al-42 cluster of events.The tantalizing conclusion of this work is that the neutron-drip line may reside further than even the next generation nuclear facilities could explore for Z>12.

Link to article: http://dx.doi.org/10.1038/nature06213

Mitch

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