Few researchers were using computers 30 years ago. This quickly changed with the release of several commercially viable personal computers in the 1980s. Since then, processing power has increased and the cost of computers decreased at an exponential rate (see Moore’s Law).
It’s no surprise that computers are now pivotal in chemistry research. We use them in a wide range of calculations – from determining the 40th decimal place of the absolute energy of He to modeling the release and distribution of toxic chemicals in river basins. The software used to address these complex problems is becoming increasingly accessible and easy to use too. There are already a variety of cell phone apps for chemistry related problem solving.
Yet, while the prevalence of software and computer-based research continues to grow, the rules for publishing results and sharing software lags behind. The magical/miracle nature of black-box calculations is disconcerting to individuals that want to know how the answers were obtained (see Sidney Harris cartoon). A palpable concern is growing in the scientific community around the sharing of software – and the foundational source code -necessary to reproduce published results. Two recent opinion pieces, one in Science titled, “Shining Light into Black Boxes” and the other in Nature titled, “The case for open computer programs” are trying to bring attention to this issue. The articles discuss the advantages and apprehensions of sharing,...
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 Chemistry (actually already had this one, but including it for completeness.)
Nature Cell Biology
Nature Chemical Biology
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.
(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...
(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...
Stephen J. Ebbens
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.
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
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
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
Catalyst: Glucose oxidase and Biliruben oxidase
Propulsion: Self electrophoresis
Terrain: Aqueous meniscus
Max Speed: 1 cm/s
Mitch’s Name: The Komatsu Truck (because it is huge)
Article: Bioelectrochemical Propulsion
Catalyst: Synthetic catalse
Terrain: Acetonitrile solution
Max Speed: 35 um/s
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...
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.
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.
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...
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
Saturday there was free food and alcohol at the Marriott for the Younger Chemist Committee (YCC). It was sponsored by the ACS web team. Fortunately, there weren’t many people there so I got more than my share of egg rolls and free booze. That night at the poster session, there was also free alcohol and free turkey which is an interesting combination of food and drink when its already late at night and you’ve been looking at talks all day.
Monday I will be trying to score some more free food and drink at the CHED poster session 2:30-4, I don’t know whether there will be anything, but I’ll shortly find out. The Nuclear division has their social hour at 7-9pm tonight, and there should be plenty of free alcohol there. Since, scimix is from 8-10, I’ll be there from 9 on.
Monday is the first day the exposition opens up to us regular folk. The best booths by far have been the following.
Elsevier: Free personal fan that lights up and says, “I’m hot”. Which is also true… thermally at least.
Corning: Free M&Ms in their new 200mL plastic vessel
Strem: Which has a nice periodic table for your desk. The best thing about it, it’s actually up to date with the newest transactinides (i.e. Roentgenium).
ACS pubs: Free issue of ACS Nano. I dropped by and was hoping to catch an editor there, but the very cute girl from marketing that was managing the desk said they all went home for the day. Mind you, I was there...