Chemistry

On Saturday we are having an economics hackathon in London. I’d love to be there but unfortunately am going to the Eur Sem Web Conf in Montpelier. It’s run by Velichka and colleagues – here’s the sort of reason why (from OKFN blog) Velichka Dimitrova revisted the disgraced Reinhart-Rogoff paper on austerity economics, the perfect evidence of the need for open data in economics – and was picked up by the London School of Economics and the New Scientist. The point is that economists made very serious mistakes and that proper management of the data and tools could have prevented it. We have to work towards reproducible computation in sciences and economics. From Velichka’s blog (and then I set you a puzzle at the end): Another economics scandal made the news last week. Harvard Kennedy School professor Carmen Reinhart and Harvard University professor Kenneth Rogoff argued in their 2010 NBER paper that economic growth slows down when the debt/GDP ratio exceeds the threshold of 90 percent of GDP. These results were also published in one of the most prestigious economics journals – the American Economic Review (AER) – and had a powerful resonance in a period of serious economic and public policy turmoil when governments around the world slashed spending in order to decrease the public deficit and stimulate economic growth. Yet, they were proven wrong. Thomas Herndon, Michael Ash and Robert Pollin from the University of Massachusetts (UMass) tried to replicate the results of Reinhart and Rogoff and criticised them on the basis of three reasons: Coding errors: due to a spreadsheet error five countries were excluded completely from the sample resulting in significant error of the average real GDP growth and the debt/GDP ratio in several categories Selective exclusion of available data and data gaps: Reinhart and Rogoff exclude Australia (1946-1950), New Zealand (1946-1949) and Canada (1946-1950). This exclusion is alone responsible for a significant reduction of the estimated real GDP growth in the highest public debt/GDP category Unconventional weighting of summary statistics: the authors do not discuss their decision to weight equally by country rather than by country-year, which could be arbitrary and ignores the issue of serial correlation. The implications of these results are that countries with high levels of public debt experience only “modestly diminished” average GDP growth rates and as the UMass authors show there is a wide range of GDP growth performances at every level of public debt among the twenty advanced economies in the survey of Reinhart and Rogoff. Even if the negative trend is still visible in the results of the UMass researchers, the data fits the trend very poorly: “low debt and poor growth, and high debt and strong growth, are both reasonably common outcomes.” Source: Herndon, T., Ash, M. & Pollin, R., “Does High Public Debt Consistently Stifle Economic Growth? A Critique of Reinhart and Rogoff, Public Economy Research Institute at University of Massachusetts: Amherst Working Paper Series. April 2013. What makes it even more compelling news is that it is all a tale from the state of Massachusetts: distinguished Harvard professors (#1 university in the US) challenged by empiricists from the less known UMAss (#97 university in the US). Then despite the excellent AER data availability policy – which acts as a role model for other journals in economics – the AER has failed to enforce it and make the data and code of Reinhart and Rogoff available to other researchers. Coding errors happen, yet the greater research misconduct was not allowing other researchers to review and replicate the results through making the data openly available. If the data and code were made available upon publication in 2010, it may not have taken three years to prove these results wrong, which may have influenced the direction of public policy around the world towards stricter aus

The Scholarly Revolution #scholrev is forging ahead. Alexander Garcia Castro is running a fantastic hackathon n Montpelier immediately after the SePublica Polemics workshop.  Join us in Montpellier for a one-day event to hack on scholarly PDFs!Do you have tools that may help us to extract information from PDFs?send us an email so that we can include them in the hackathon.Would you like to extract citations from existing PDFs?Wouldn’t it be cool if we, scholars, did not have to pay for citationdata? What about author disambiguation?Are you interested in identifying and extracting meaningful parts from PDFs?Would you like to have XML/RDF for scholarly PDFs? What if you couldhave access to the actual content of the PDF for supporting the Web ofData?We are interested in all of these issues, send us your tools, ideas,comments and join us in Montpellier. We are also supporting remoteparticipation to the hackathon -hangout and webex.Visit us at http://scholrev.org/hackathon/casey.mclaughlin@cci.fsu.edualexgarciac@gmail.com–Alexander Garciahttp://www.alexandergarcia.name/http://www.usefilm.com/photographer/75943.htmlhttp://www.linkedin.com/in/alexgarciac One the important aspects of a revolution is having the right tools and this hackathon will collect what we’ve got and work out how to deploy them. “Jailbreaking” PDFs is not easy. It’s complex and it’s messy. But we are getting to the stage where we have the tools to: Download PDFs from the open web. Turn them into semantic form Filter the semantics and repurpose them – everything from metadata to citations to chemistry to phylogenetic trees Build a community And since we work with open source everything we do is a step forward. Once we have solved a problem it can’t be unsolved (unlike commercial closed tools which are often withdrawn of locked). There’s a great deal we can do with collaborative action (each person can add a stone to the building. All we have to do is care enough.

I have been very honoured to be invited to lead off a workshop session at the European Semantic Web Conference (ESWC). This workshop is a radical initiative to change the way we think about information. Here’s the description: http://sepublica.mywikipaper.org/drupal/ There is much controversy in the world of publishing and semantic publishing needs to both create waves in publishing and to ride the waves of change approaching in the world of publishing. We therefore invite statements for presentation at a discussion session at SePublica 2013 at ESWC in Montpellier on 26 May 2013.We want radical, controversal and polemical positions to be articulated about semantic publishing and how we should achieve semantic publishing of scholarly works, data and all sorts of stuff. To be presented, statements must be relevant, legal and not too offensive(as judged by the workshop organisers).All acccepted statements wil be presented. Submission will be through easychair; all accepted polemics will bepublished before the meeting on the Knowledgeblog platform (http://www.knowledgeblog.org), where they will be permanently archived, and open for public comments. Submissions should be limited to 500 words. We can accept submissions in most formats, including Word, simple HTML (nothing in the header, no active content) or Latex (again the simpler the better). Presentations on the day wil be restricted to one slide that will be presented for two minutes (we will do this via timed slides) – all slide presentations must be submitted in advance. Presentations will be followed by a vivid discussion.Illustrating what we would like to have…Here’s To The Crazy Ones. The misfits. The rebels. The trouble-makers. The round pegs in the square holes. The ones who see things differently. They’re not fond of rules, and they have no respect for the status-quo. You can quote them, disagree with them, glorify, or vilify them.About the only thing you can’t do is ignore them. Because they change things. They push the human race forward. And while some may see them as the crazy ones, we see genius. Because the people who are crazy enough to think they can change the world – are the ones who DO !” (I [AlexanderGC?] believe this is from Steve Jobs, but I am not sure about the right atribution of sentence.) Welcome to SEPUBLICA 2013 For over 350 years, scientific publications have been fundamental to advancing science. Since the first scholarly journals, Philosophical Transactions of the Royal Society (of London) and the Journal de Sçavans, scientific papers have been the primary, formal means by which scholars have communicated their work, e.g., hypotheses, methods, results, experiments, etc. Advances in technology have made it possible for the scientific article to adopt electronic dissemination channels, from paper-based journals to purely electronic formats. However, In spite of improvements in the distribution, accessibility and retrieval of information, little has changed in the publishing industry so far. The Web has succeeded as a dissemination platform for scientific and non-scientific papers, news, and communication in general; however, most of that information remains locked up in discrete digital documents that are replicates of their print ancestors; without machine-interpretable content they lack the exploitation we have begun to expect from other data. Semantic enhancements to scholarly works would expose both the content of those works and the implicit discourse between those works. Scholarly data and documents are of most value when they are interconnected rather than independent.  This is a tremendous vision and I am deeply honoured to be asked to spark it off. I’ll try and indicate over the next 3-4 days some avenues. Polemics (https://en.wikipedia.org/wiki/Polemic ) are: a contentious argument that is intended to establish the truth of a specific understanding and the falsity of the contrary

A ZnO/TiO2 heterojunction semiconductor photocatalyst in which two reactive TiO2 {001} facets are untouched by the ZnO

TEXAS

Yesterday at the Council for Chemical Research meeting, Dow unveiled a publicly-accessible website with a comprehensive set of lab safety training videos plus additional resources. The website is at safety.dow.com. More details on the development of the site are in my C&EN story on the project. One tidbit that didn't make it into the news story: While the video hosts are professional actors, the supporting roles are played by Dow scientists. Related Posts:Developing laboratory safety certificationAcademic safety culture surveyWebinars: Safety culture and chemical safety committeesDow teams up with universities on lab safety, how'd…Talking about safety culture at #ACSDenver

Training: Resource hosts comprehensive video library

Antibiotics: New highly active inhibitors of quorum sensing show promise as agents against staph infections

A GENTLE pat on the back and a short walk can put a crying baby to sleep. Four-legged newborns, too, calm down when their mothers hold them by the nape of their necks to carry them. Precisely why, though, has remained a mystery. Kumi Kuroda, of RIKEN Brain Science Institute, in Japan, and her colleagues decided to find out.The researchers monitored the heart rates of twelve human infants aged between one to six months under three conditions: while they lay by themselves in a crib, immediately after they were picked by their mothers, and while they were carried around. Specifically, they measure the heart rate variability (HRV), or the tiny differences in the interval between successive heart beats, since previous research showed that lower HRV is tied to higher stress.As the researchers report in Current Biology, true to stereotype, the babies' HRV increased significantly when they were carried, suggesting less stress. The results persisted when controlled for things like crying, which can increase the heart rate considerably and skew HRV readings. Given the ethical constraints on experiments involving human babies, Dr Kuroda and her team then turned to mice. After ascertaining that murine newborns, too, show the same physiological response to carrying as human infants do, they examined the sensory mechanisms which might give rise to the phenomenon. First, they used a local anaesthetic to numb the skin on back of the mice’s neck. This blocked the neural signals that are produced by touch. Anesthetised mice were more fidgety while carried than those that were not.Next, Dr Kuroda gave the mice a large dose of vitamin B6, to strip them of the ability to judge the relative position of their body parts, or proprioception, as it is known in the argot. Mice plied with the vitamin were also friskier than those that weren't, judged both by observed behaviour and physiological measures such as HRV.Finally, the researchers used a drug to suppress the mice's parasympathetic nervous system. This is responsible for unconscious "rest-and-digest" or "feed-and-breed" activities like sexual arousal, salivation or urination, that occur when the body is at rest. When parasympathetic nerves were impaired, the carrying-induced, stress-lowering spike in the HRV was not seen, suggesting that the cardiac effect resulting from carrying did indeed stem from the parasympathetic nerve.Crucially, the nervousness caused by pups' impaired senses meant that murine mothers took longer to carry them to part of the enclosure considered safe. Because the young often squirm when sensing danger, such impairment would make whisking them away from potential threats harder. The calming mechanism, then, appears to have evolved to facilitate such extraction. Although human offsrping are not exposed to as many existential threats as their murine counterparts, their parents will no doubt be grateful anyway.