Chemistry

This is a list of the points I want to cover when introducing the session on Polemics. A list looks a bit dry but I promise to be polemical. And try to show some demos at the end. The polemics are constructive in that I shall suggest how...
This is a list of the points I want to cover when introducing the session on Polemics. A list looks a bit dry but I promise to be polemical. And try to show some demos at the end. The polemics are constructive in that I shall suggest how we can change the #scholpub world by building a better one than the current one. NOTE: Do not be overwhelmed by the scale of this. Together we can do it. It is critical we act now Semantics/Mining is now seen as an opportunity by some publishers to “add value” by building walled gardens. Increasing attempts to convince authors to use CC-NC. We must develop semantic resources ahead of this and push the edges One person can change the world We must create a coherent community Examples: Open Streetmap, Wikipedia Galaxyzoo OKFN Crowdcrafting, Blue Obelisk (Chemistry – PMR), ?#scholrev Visions Give power to authors Discover, aggregate and search (“Google for science”) Make the literature computable Enhance readers with semantic aids Smart “invisible” capture of information Practice before Politics Create compelling examples Add Value Make authors’ lives easier Mine and semanticize current scholarship. Text Tables Diagrams Data Text (chemistry, species) Tables (Jailbreak corpus) Diagrams chemical spectra, phylogenetic trees Data (output). Quixote Material to start with Open information (EuropePMC, theses) “data not copyrightable”. Supp data, tables, data-rich diagrams Push the limits of what’s allowed (forgiveness not permission) Disciplines/artefacts with good effort/return ratio Phylogenetic trees (Ross Mounce + PMR) Nucleic acid sequences Chemical formulae and reactions Regressions and models Clinical/human studies (tables) Dose-response curves Tools, services, resources     We need a single-stop location for tools Research-enhancing tools (science equiv of Git/Mercurial). Capture and validate work continuously Common approach to authoring Crawling tools for articles, theses. PDF and Word converters to “XML” Classifiers NLP tools and examples Table hackers Diagram hackers Logfile hackers Semantic repositories Abbreviations and glossaries Dictionaries and dictionary builders  Advocacy, helpers, allies Bodies who may be interested (speculative, I haven’t asked them): Funders of science major Open publishers Funders of social change (Mellon, Sloane, OSF…) SPARC, DOAJ, etc. (Europe)PMC Crowdcrafting (OKF, am involved with this) Wikipedia
about 1 hour ago
EARLIER this year Asda was among a number of British supermarkets shamed because some of their beef products were found to contain horsemeat. Luckily, consumers are a forgiving lot. Asda reported last week that its sales have already rec...
EARLIER this year Asda was among a number of British supermarkets shamed because some of their beef products were found to contain horsemeat. Luckily, consumers are a forgiving lot. Asda reported last week that its sales have already recovered to pre-scandal levels. Brands have recovered from worse. Take "Soylent Green", a dystopian science-fiction film set in 2022, in which the eponymous nutritious wafer is unveiled as containing recycled humans. Now, nine years early, a product called Soylent is about to hit the shelves in America.Its creator, Rob Rhinehart, a 24-year-old computer scientist, assures Babbage that his version of Soylent contains no human flesh. In fact, Soylent promises to be as tasteless as its name, comprised as it is mostly of powdered starch, milk proteins, olive oil, oat fibre and various trace minerals and vitamins. When reconstituted with water, Soylent becomes a unflavoured beige liquid. "There are no secrets here," says Mr Rhinehart. Just the quantities of every essential nutrient, as recommended by America's Food and Drug Administration, in their "most economical, bioavailable, water-soluble form".Soylent is a complete food replacement for those disinclined or too busy to cook, but lacking the wherewithal to eat out. Mr Rhinehart also touts the environmental benefits of not having to travel to the shops, prepare meals or discard spoiled food. Earlier this year he put his mouth where his money is by subsisting solely on Soylent for three months. He claims never to have felt healthier.That is not to say the process went smoothly. Mr Rhinehart is no nutritionist and early versions of Soylent had their problems. Omitting iron from his original formula made Mr Rhinehart’s heart race and an absence of sulphur caused joint pain, while (deliberate) overdoses of potassium and magnesium resulted in cardiac arrhythmia and burning sensations. He currently lives on Soylent during the week and enjoys conventional food at the weekend.“I wanted everything that could go wrong with Soylent to happen to me first,” he explains. Seven recipes later, he believes it is ready to for wider consumption. A crowdfunding effort on his website has raised nearly $300,000 so far, with thousands of people signing up for either a week’s or a month’s supply of the stuff, due for delivery in August. There are plans afoot for male- and female-specific formulae, as well as a vegan version. “If we raise a lot, we could put money into formal testing and research,” says Mr Rhinehart. Adam Drewnowski, director of the Centre for Public Health Nutrition at the University of Washington, will not be among them. “To some extent, Soylent is an expensive glass of milk,” he says. While Soylent’s $65 weekly price-tag is certainly cheaper than eating out, it compares unfavourably with the cost of cooking for yourself. America's Department of Agriculture recently calculated the weekly cost for a family of four to eat a thrifty but healthy diet at home as $146, even allowing for some spoilage.Mr Drewnowski is also sceptical of Soylent’s environmental credentials. He notes that the bulk of food’s carbon footprint and greenhouse-gas emissions come from production and processing, rather than distribution, cooking or waste. Mr Drewnowski calls the carbon impact of Soylent’s milk protein "not insignificant".Nutritionally complete liquid foods have been around for decades. Examples include milk formula for infants, weight-loss diets like the Cambridge Plan, and medical interventions for people in comas. A French product called Plumpy’Nut, based on peanut butter, provides emergency nutrition for children suffering a famine for less than $10 a week. What makes Soylent different is that it is being aimed at healthy adults who could cook and eat normally but would rather not. Soylent’s crowdfunding success indicates that there is hunger for such fuss-free food. Whether people will want to live by gruel alone in the long run is another matter altogether.
about 4 hours ago
Pincer carbene ligands mediate the coupling of a coordinated acetonitrile ligand and its unusual reactivity opens application in catalysis
Pincer carbene ligands mediate the coupling of a coordinated acetonitrile ligand and its unusual reactivity opens application in catalysis
about 19 hours ago
Spectroscopy: Laser vaporization improves surface-enhanced Raman spectroscopy for cultural heritage research
Spectroscopy: Laser vaporization improves surface-enhanced Raman spectroscopy for cultural heritage research
1 day ago
Senate: Breakthrough bipartisan proposal would update Toxic Substances Control Act
Senate: Breakthrough bipartisan proposal would update Toxic Substances Control Act
1 day ago
Training: Resource hosts comprehensive video library
Training: Resource hosts comprehensive video library
1 day ago
I just had the fastest and cleanest pump oil change of my career, thanks to an invention of my colleague. We use large Welsh DuoSeal belt-driven pumps installed in metal cabinets under the hoods and these beasts are reliable – but ...
I just had the fastest and cleanest pump oil change of my career, thanks to an invention of my colleague. We use large Welsh DuoSeal belt-driven pumps installed in metal cabinets under the hoods and these beasts are reliable – but so heavy: They take over 3 liters of oil to fill and the whole thing weights about 50 kilos. The oil drain valve is inconveniently located right near the bottom so the pump cannot be easily drained inside the cabinet. The normal oil change procedure requires disconnecting the vacuum hose and dragging the pump out. I would prop the pump on an empty solvent barrel, put oil collection bucket beneath the drain valve and keep draining, tilting, flushing, draining, filling, cursing. Lifting the pump requires two pairs of hands, the oil drips everywhere, and given the large and awkward shape of the (very heavy) re-filled pump that has to be then coaxed back in and over the cabinet lip, the vacuum hose reattached and vacuum leaks fixed, it is a pretty unpopular job – one that gets postponed for as long as possible, resulting in pumps sloshing in very tired crud that has the look and smell of burnt molasses. But not any longer! Motivated by his hurt back and desperation, my colleague recently got a brilliant idea to take a large (4L) Erlenmeyer filtration flask closed with a stopper with a tube, attach cheap vinyl transparent tubing (like you would use for water in reflux condensers) and connect it to the oil drain valve at the bottom of the pump. If the spent oil is still warm (from a pump that has been run, so it is less viscous), it can by sucked out through the drain valve into the Erlenmeyer under house vacuum in just few minutes. After a flushing oil fill, 2 min pump run and another suction-assisted drain and final re-fill, the entire oil changing operation can be completed in less than 15 minutes. No mess, no need to take the pump out, no need to disconnect the vacuum hose from the pump. Our biologists of course claimed a credit for the pump oil change idea, having used this sort of setup for sucking off liquor from cells in multi-well plates. But I think the true origin of this pump oil change breakthrough is slightly more disturbing. You see, my colleague who came up with this idea is leaving for medical school in few weeks. In preparation he has taken the anatomy labs already. As I was sucking out nearly a gallon of alarmingly dark rotten sludge from my pump using his gadget, he calmly observed that the really good, top-of-the-line embalming machines can aspirate blood while at the same time injecting the formaldehyde solution back into the empty veins: One just needs to correctly insert the inlet and outlet tubes into the patient, turn on the flush routine and wait until the aspirate finally starts coming out clear…
1 day ago
Tweet of the week: “In discrepancy is discovery” – Lesson learnt from scientific research. — Curious Wavefunction (@curiouswavefn) May 20, 2013 To the network: Artful Science: Was antiquity really so tacky? Cleantech Chemistry: Ne...
Tweet of the week: “In discrepancy is discovery” – Lesson learnt from scientific research. — Curious Wavefunction (@curiouswavefn) May 20, 2013 To the network: Artful Science: Was antiquity really so tacky? Cleantech Chemistry: Never Mind All That: Solar on the upswing Newscripts: In Print: Toys Will Be Toys and Amusing News Aliquots The Safety Zone: Dow launches Lab Safety Academy website The Watch Glass: Teflon: Newcomer to heat exchange and What's That Stuff? Chicken Eggs and Texas City: Portrait of a Chemical Town and C&EN Talks With Mae Jemison and Chemist tried in Chicago riot case Related Posts:This Week on CENtral Science: Harlem Shake, Natural gas, andThis Week on CENtral Science: Whale Fossils, Oscar Noms, UC…This Week on CENtral Science: Mona Lisas, Spider Sex,…This Week on CENtral Science: #scioDC , World's…This Week On CENtral Science: Richard's Lionheart,…
1 day ago
A CYNIC might dismiss the "quantified self" movement, whose adherents use an array of gizmos to record all aspects of their physical existence, as gimmicky navel-gazing by geeky workout nuts, eager to gamify ever bigger chunks of life. T...
A CYNIC might dismiss the "quantified self" movement, whose adherents use an array of gizmos to record all aspects of their physical existence, as gimmicky navel-gazing by geeky workout nuts, eager to gamify ever bigger chunks of life. That, as Babbage has recently come to realise, is unfair. Better information about your actual exertions makes for more informed decisions. This is as true of exercise as it is of personal spending, say. Little wonder that, as monitoring devices become smaller, cheaper and better integrated with smartphones, more people are embracing their quantified selves. For your correspondent, the conversion began a year and a half ago, when he moved his office from rented space into his basement, purchased an adjustable standing desk and, shortly afterwards, a flat treadmill designed to work at low speeds underneath the desk while displaying miles walked. He has become, in other words, a walking worker of the sort described by Susan Orlean in a recent New Yorker story. (Standing turned out easy—and a nice change; learning to type and focus on two computer screens while trundling proved a bigger challenge.)To keep himself motivated, Babbage recently purchased a self-tracker made by Fitbit, a Californian company. Fitbit's devices (similarly to the Nike Fuelband, the Jawbone UP and others) use an accelerometer to track steps. Fancier models include an altimeter to capture ascending stairs and inclines. Smartphone apps pair with these devices, naturally. (Software developers have also created software that relies on the built-in GPS and other sensors in mobiles, with varying accuracy.) Most of the standalone trackers are designed as wristbands, others (like Babbage's Fitbit One) are smaller than a pack of gum and can be slipped into a clip or strapped around a wrist inside a pouch.As the data streams from the sensors to smartphones or computers and on to the device-makers' central servers, the associated apps offer feedback and encouragement based on targets set or reached. The Fitbit app, for example, tells you that a few more steps will take you past the daily target, or give you a pat on the back for exceeding a goal or setting a new all-time high. Small targets, reminders, stretch goals and awards all help nudge you towards personal betterment.The systems increasingly welcome data from other hardware and software. Wi-Fi scales, popular a few years ago, can be linked up to some systems. (Babbage added his to a new Fitbit account.) Smartphone apps like Runkeeper, which use GPS to plot routes and measure distance and altitude changes, can be integrated, too. For a more detailed picture, you can enter food consumed and describe other activities that the devices are unable to capture.Many of the gizmos link directly to an online social network, inviting you to compete with friends. Babbage's long-shinned chum regularly racks up over 125,000 steps in a week. (Your correspondent managed briefly to pass him with about 95,000 after the rival had spent a day away from his own treadmill and another day in transit to Australia; the advantage did not last long.)Goaded, envious or proud—perhaps all three—Babbage has walked about 40 miles each of the past two weeks, a fourfold improvement on pre-tracking times by his reckoning. He has also shed a few pounds and, by slipping the Fitbit inside its wrist strap overnight, has learned how well, or poorly, he sleeps. The system responds to fidgeting and can thus tell deep slumber from light, or from waking. Your correspondent sleeps deeply, it turns out. But the data make one thing clear: he ought to hit the sack a bit earlier.
1 day ago
Beth Halford and I sat down to have a quick chat about the life of postdocs, based on her really interesting article in this week's C&EN. It was really fun and the edited recording is below:Timepoints:0:00 - 2:00: What's been the backgro...
Beth Halford and I sat down to have a quick chat about the life of postdocs, based on her really interesting article in this week's C&EN. It was really fun and the edited recording is below:Timepoints:0:00 - 2:00: What's been the background of postdocs?4:30: The happiness of postdocs6:30: The postdocs that Beth knew7:00: Crowdfunding a postdoc (CJ grossly underestimates the cost of a FTE)8:55: PIs and their postdocs9:50: Should we pay postdocs more? Beth on Paula Stephan11:00: $16/hour12:00: Why do a postdoc?13:30: The finances of postdocs15:11: Jessica Breen's cogent comments on delaying life milestones?17:15: Are postdocs really broader?19:45: The postdoc arms race22:17: The longest postdoc you've heard of23:55: When will the arms race be over?27:55: What should postdocs do about getting a job?Thanks to Beth for a great conversation!
1 day ago