Chemistry

A list of small, useful things (links):John has a great explainer on how to drill a well the right way.Lisa Balbes talks about how most people don't know what to expect in their first job.Andre the Chemist thinks you should move for your...
A list of small, useful things (links):John has a great explainer on how to drill a well the right way.Lisa Balbes talks about how most people don't know what to expect in their first job.Andre the Chemist thinks you should move for your first job.Ken Hanson posts on proposals in his great series on how to get a faculty position. This Dow Lab Safety Academy is interesting; I think it deserves a closer, more critical look than it's gotten so far. Andrew Bisette's 9th #chemclub roundup.I really need to buy this book on Oppenheimer that Ash reviewed. Paul talks about lab manuals.Brandon talks lab SOPs. Vinylogous Aldol writes on academic chemistry salaries. Seems to me there's a step change between full professor salaries and assistant/associate salaries. Chad Jones on diet soda and aspartame. (All I have to say on that issue: from. my. cold. dead. hands.) Readers, did I miss anything?
about 2 hours ago
A list of small, useful things (links):John has a great explainer on how to drill a well the right way.Lisa Balbes talks about how most people don't know what to expect in their first job.Andre the Chemist thinks you should move for your...
A list of small, useful things (links):John has a great explainer on how to drill a well the right way.Lisa Balbes talks about how most people don't know what to expect in their first job.Andre the Chemist thinks you should move for your first job.Ken Hanson posts on proposals in his great series on how to get a faculty position. This Dow Lab Safety Academy is interesting; I think it deserves a closer, more critical look than it's gotten so far. Andrew Bisette's 9th #chemclub roundup.I really need to buy this book on Oppenheimer that Ash reviewed. Paul talks about lab manuals.Brandon talks lab SOPs. Vinylogous Aldol writes on academic chemistry salaries. Seems to me there's a step change between full professor salaries and assistant/associate salaries. Chad Jones on diet soda and aspartame. (All I have to say on that issue: from. my. cold. dead. hands.) Readers, did I miss anything?
about 2 hours ago
My sincere apologies with the relatively quiet posting recently. I do indeed have a Process Wednesday post in the works, but I found this to be such an interesting framing of the issue by Alyssa Rosenberg, commenting on Sheryl Sandberg's...
My sincere apologies with the relatively quiet posting recently. I do indeed have a Process Wednesday post in the works, but I found this to be such an interesting framing of the issue by Alyssa Rosenberg, commenting on Sheryl Sandberg's Lean In and her approach to looking at childcare costs that I had to post it:Similarly, Sandberg suggests a different way to look at the cost of child care. Rather than considering nannying or preschool costs as a dilemma, something that wipes out a woman’s earnings, or that’s discretionary spending to allow a woman to continue doing something that she likes, Sandberg once again reframes the question, acknowledging that “Child care is a huge expense, and it’s frustrating to work hard just to break even. But professional women need to measure the cost of child care against their future salary rather than their current salary…Wisely, Anna and other women have started to think of paying for child care as a way of investing in their families’ future.” Sandberg makes a very interesting point and one that I hadn't considered. When I calculate child care for our family budget, I usually do the math against our income (numerator = child care, denominator = wages). I had not taken into account that, over time, the wages term goes up...[One should point out that for those, like Ms. Sandberg, who have/desire offices in the C-suite, the beginning years of one's career probably play much more of a role in future income than those of us to aspire to more mundane titles like "group leader" or "senior principal fellow."]
about 3 hours ago
My sincere apologies with the relatively quiet posting recently. I do indeed have a Process Wednesday post in the works, but I found this to be such an interesting framing of the issue by Alyssa Rosenberg, commenting on Sheryl Sandberg's...
My sincere apologies with the relatively quiet posting recently. I do indeed have a Process Wednesday post in the works, but I found this to be such an interesting framing of the issue by Alyssa Rosenberg, commenting on Sheryl Sandberg's Lean In and her approach to looking at childcare costs that I had to post it:Similarly, Sandberg suggests a different way to look at the cost of child care. Rather than considering nannying or preschool costs as a dilemma, something that wipes out a woman’s earnings, or that’s discretionary spending to allow a woman to continue doing something that she likes, Sandberg once again reframes the question, acknowledging that “Child care is a huge expense, and it’s frustrating to work hard just to break even. But professional women need to measure the cost of child care against their future salary rather than their current salary…Wisely, Anna and other women have started to think of paying for child care as a way of investing in their families’ future.” Sandberg makes a very interesting point and one that I hadn't considered. When I calculate child care for our family budget, I usually do the math against our income (numerator = child care, denominator = wages). I had not taken into account that, over time, the wages term goes up...[One should point out that for those, like Ms. Sandberg, who have/desire offices in the C-suite, the beginning years of one's career probably play much more of a role in future income than those of us to aspire to more mundane titles like "group leader" or "senior principal fellow."]
about 3 hours ago
I'm going to have to start posting more frequently. My last post was about solar firms going bankrupt in China and now my cleantech news is about how solar is set to rebound. Seems like something should have happened in between that post...
I'm going to have to start posting more frequently. My last post was about solar firms going bankrupt in China and now my cleantech news is about how solar is set to rebound. Seems like something should have happened in between that post and this one. Actually, a few biobased chemical deals were announced. Thanks BASF and Evonik! Making a better solar cell. Credit: University of Stuttgart Institute of Photovoltaics Anyway – back to solar. Earlier this week, Lux Research (a rather skeptical gang generally) put out a summary of a new research report titled “Solar's Great Recovery: Photovoltaics Reach $155 Billion Market in 2018.” Actually, solar had a great 2012 – at last in the U.S. – but that was mainly due to installations of several large utility projects. The business of producing those solar modules had hit some major potholes. Around five years ago, solar demand was hindered by high prices – held up by shortages of key polysilicon raw material, but balanced by huge subsidies in Europe, especially in Spain and Germany. Then – in the nature of boom and bust cycles – the high prices prompted huge polysilicon capacity increases. Then prices fell, Europe cut subsides, the recession hit… and all that new capacity made solar prices tank and inventories piled up. Whew – what a tale. In a fun new twist, according to Lux analyst Ed Cahill, the solar crisis will become a boon as record low prices boost demand. (And after that what will happen? Stay tuned). The rise will take place as those cheaper installations (especially utility and commercial rooftop) become routine and spread into new markets. U.S., China, Japan, and India are expected to speed up installations. That will help to power (no pun intended) a compound annual growth rate in the industry of 10.5% over the next three years. A few other things might help – according to this New York Times article, the U.S. and Europe are both working to smooth over trade disputes with China. Regional pricing schemes may take the place of tariffs. China had been accused of exporting solar modules at prices less than the cost of production (a practice called “dumping”). China, in turn, accused polysilicon makers in the U.S. and Europe of doing the same thing. All of this fun news is not likely to help revive solar module manufacturing in the U.S. or in Germany. But new technology might. My colleague Alex Scott flagged a news item from the University of Stuttgart's Institute for Photovoltaics. Researchers there have tested a crystalline silicon solar cell with a 22% sunlight conversion efficiency. It is difficult to say how much a module made of these cells would convert, but a traditional module is normally around 15%. The secret to the team's work is a design that puts the metal contacts on the back layer of the cell, using a laser. While hanging out on the back of the cell, the material will not block light hitting the front of the cell. Ta-da! More electrons. Related Posts:They're the Tops: Leading Solar Module ProducersGermany Unwinds Solar Gravy TrainNo Magic In China's Solar IndustrySolar Boom in Japan, with Battery to MatchEpic Fail: Solyndra files for bankruptcy
about 4 hours ago
APPLE defends its tax practices, Yahoo buys Tumblr and an Indian cyber-spying group re-emerges
APPLE defends its tax practices, Yahoo buys Tumblr and an Indian cyber-spying group re-emerges
about 9 hours ago
I am really excited about the #scholrev hackathon program put together as “Jailbreaking the PDF”: some additional information at http://duraspace.org/jailbreaking-pdf-hackathon From Alexander Garcia and Alex Garcia-Castro M...
I am really excited about the #scholrev hackathon program put together as “Jailbreaking the PDF”: some additional information at http://duraspace.org/jailbreaking-pdf-hackathon From Alexander Garcia and Alex Garcia-Castro Montpellier, France  The upcoming “Jailbreaking the PDF” hackathon (http://scholrev.org/hackathon) will be held Monday, May 27 in Montpellier, France at the Agence Bibliographique de l’enseignement Superieur (ABES): http://www.abes.fr/Connaitre-l-ABES/Presentation-de-l-ABES. Currently, the bulk of peer-reviewed scientific knowledge is locked up in PDF documents, which are difficult to get information. We want to change that. If you’re interested in hacking on PDFs and exploring ways to access scholarly data in modern ways, this hackathon is for you. There is no registration fee–the event is free.  Bring yourself your favorite laptop, and we’ll supply the food, drinks wifi, repository, and everything else necessary to hack away. Future announcements will be posted at http://scholrev.org/hackathon. As with all hackathons we’ll work it out on the day (and possibly some on the night before). There are some suggested projects at http://wehack.it/hackathons/47-jailbreaking-the-pdf (I have put #ami2 in), but the important thing is to come up with things we can do on the day that will make a real impact. It’s a great chance to show that there is a critical mass of people in #scholrev and that we can achieve things. The key thing is that we all want to change the world – in this case by repurposing PDFs to liberate information and by doing that working out how we change our ways of communicating (“publishing”) to humans and machines. What makes Jailbreak different is the Open approach – our tools are Open , our data and results are Open. And it is more important that WE succeed rather than I succeed. There are several reasons for developing technology and they include: Creating a business and a market Being the first to create something and gain (academic) recognition Changing the world So I and colleagues have been developing #AMI2, a toolset for turning PDF content into semantic form. I’m not interested in creating a business (at present) and I have the luxury of not needing academic glory. I shall be happy to submit a paper in due course as there are novel aspects but citations aren’t the primary driver. No, this is my contribution to a toolkit to change the world. Because scholarly publishing critical needs a revolution and it’s not coming from conventional sources. Hacking PDFs can be a major part of the game-changer. And if the software is Open, then we can grow it. I’m delighted to see that there are other people hacking PDFs and I shall meet some at this workshop. What will I feel if someone else has developed a tool that does things that AMI2 can’t do or does them better? It may surprise you, but I shall feel pleased. And I hope others would feel the same way. Because it advances us all and makes the overall task easier and quicker. We’ve found this in chemistry software with the Blue Obelisk (http://en.wikipedia.org/wiki/Blue_Obelisk ) where over 20 groups write F/OSS software. Each is independent – we don’t try to aggregate this into one monster toolkit (it wouldn’t work). But each looks to see what the others are doing, keeps in gentle touch and avoids needless duplication. I expect this spirit to develop in Jailbreak. In any case hacking PDFs requires a large amount of heuristics. Examples are: Translating undocumented fonts to Unicode Dealing with graphics Interpreting figures Publisher – and journal-specific annotations Recognising and processing tables Hacking references and metadata Many of these are never-ending jobs. Many are also boring. But many are ideal for a shared approach. I am very interested to see what the CERMINE: Content ExtRactor and MINEr does: CERMINE is a comprehensi
about 11 hours ago
Just how many different small-molecule binding sites are there? That's the subject of this new paper in PNAS, from Jeffrey Skolnick and Mu Gao at Georgia Tech, which several people have sent along to me in the last couple of days. This ...
Just how many different small-molecule binding sites are there? That's the subject of this new paper in PNAS, from Jeffrey Skolnick and Mu Gao at Georgia Tech, which several people have sent along to me in the last couple of days. This question has a lot of bearing on questions of protein evolution. The paper's intro brings up two competing hypotheses of how protein function evolved. One, the "inherent functionality model", assumes that primitive binding pockets are a necessary consequence of protein folding, and that the effects of small molecules on these (probably quite nonspecific) motifs has been honed by evolutionary pressures since then. (The wellspring of this idea is this paper from 1976, by Jensen, and this paper will give you an overview of the field). The other way it might have worked, the "acquired functionality model", would be the case if proteins tend, in their "unevolved" states, to be more spherical, in which case binding events must have been much more rare, but also much more significant. In that system, the very existence of binding pockets themselves is what's under the most evolutionary pressure. The Skolnick paper references this work from the Hecht group at Princeton, which already provides evidence for the first model. In that paper, a set of near-random 4-helical-bundle proteins was produced in E. coli - the only patterning was a rough polar/nonpolar alternation in amino acid residues. Nonetheless, many members of this unplanned family showed real levels of binding to things like heme, and many even showed above-background levels of several types of enzymatic activity. In this new work, Skolnick and Gao produce a computational set of artificial proteins (called the ART library in the text), made up of nothing but poly-leucine. These were modeled to the secondary structure of known proteins in the PDB, to produce natural-ish proteins (from a broad structural point of view) that have no functional side chain residues themselves. Nonetheless, they found that the small-molecule-sized pockets of the ART set actually match up quite well with those found in real proteins. But here's where my technical competence begins to run out, because I'm not sure that I understand what "match up quite well" really means here. (If you can read through this earlier paper of theirs at speed, you're doing better than I can). The current work says that "Given two input pockets, a template and a target, (our algorithm) evaluates their PS-score, which measures the similarity in their backbone geometries, side-chain orientations, and the chemical similarities between the aligned pocket-lining residues." And that's fine, but what I don't know is how well it does that. I can see poly-Leu giving you pretty standard backbone geometries and side-chain orientations (although isn't leucine a little more likely than average to form alpha-helices?), but when we start talking chemical similarities between the pocket-lining residues, well, how can that be? But I'm even willing to go along with the main point of the paper, which is that there are not-so-many types of small-molecule binding pockets, even if I'm not so sure about their estimate of how many there are. For the record, they're guessing not many more than about 500. And while that seems low to me, it all depends on what we mean by "similar". I'm a medicinal chemist, someone who's used to seeing "magic methyl effects" where very small changes in ligand structure can make big differences in binding to a protein. And that makes me think that I could probably take a set of binding pockets that Skolnick's people would call so similar as to be basically identical, and still find small molecules that would differentiate them. In fact, that's a big part of my job. But in general, I see the point they're making, but it's one that I've already internalized. There are a finite number of proteins in the human body. Fifty thousand? A couple of hundred thousand? Probably not a millio
about 11 hours ago
FLASHOVER is something dreaded by firefighters. It is the point at which the temperature in a room has risen so far that everything inflammable ignites spontaneously. In days gone by, when houses were draughty and thus cooler, and rooms ...
FLASHOVER is something dreaded by firefighters. It is the point at which the temperature in a room has risen so far that everything inflammable ignites spontaneously. In days gone by, when houses were draughty and thus cooler, and rooms were filled with furniture made from natural materials that were slow to burn, it could take 15 minutes or more for a fire to reach the point of flashover. Now, though, buildings are better insulated and furnishings are stuffed with hydrocarbon-based foams. In these conditions flashover can happen within three.This means that whereas firefighters once had time, after they had arrived at a blaze, to scout it out before it had taken hold, they are now confronted with situations that could flashover at any moment. This difference can be deadly.Ironically, modern fireproof suits may have made the situation worse. In the past, a firefighter would have felt the heat building up towards flashover and would thus have been forced to retreat. Today’s fully encapsulated suits mean he must rely instead on visual clues that flashover is imminent, such as flames rolling across the ceiling or a scrumpled-up ball of paper bursting alight as it reaches its flashpoint (supposedly 451º Fahrenheit, according to Ray Bradbury’s novel of almost that title). These sorts of warnings, though, are dangerously imprecise.For the past five years, researchers at the Worcester Polytechnic Institute in Massachusetts, led by Kathy Notarianni, have been trying to understand flashovers—the better to predict exactly when they will occur. The team have carried out a series of test burns that simulated different types of house fires, in wooden structures built to mimic standard American homes. One included an actual sofa, armchairs, television, carpeting, doors, windows and curtains.Dr Notarianni’s team found that high air temperatures alone are not enough to trigger flashover. What is needed is a layer of particularly hot gas just below the ceiling. This radiates heat into the room below, causing flashover even when the air temperature in the rest of the room is relatively low. Older, draughtier rooms let these gases leak out, and slower-burning furniture means there is less hot gas in the first place. Dr Notarianni found, though, that as she added things like plasterboard sheeting to the ceilings of her experimental rooms, gas accumulated more easily, and flashover became more likely.In light of this knowledge the team have devised a system that uses hardened thermocouples and thermal flux sensors to feed data to a computer program which follows the progression of the fire and constantly re-calculates the countdown to flashover. In the early stages of a fire, this program’s predictions vary a lot from moment to moment, but as the point of flashover approaches they become more and more accurate. Within the final, crucial, 30 seconds the prediction becomes very accurate indeed, giving firefighters enough warning to get out without having caused them to evacuate needlessly early.The next stage is to miniaturise the hardware, so that it can be fitted to a firefighter’s helmet. To do that, Dr Notarianni has received a grant from the Federal Emergency Management Agency. There is, though, one further problem to solve. The prototype gives its best results when the sensors are about 30cm beneath the ceiling. But not only are firefighters not tall enough for their helmets to be at that height when they are standing up, they also tend to navigate burning buildings on their hands and knees. Ideally, then, a better way of interpreting what is going on based on temperatures near the floor needs to be developed—though with luck this will only mean tweaking the software. That done, the new flashover detector should liberate firefighters from constantly having to keep an eye on screwed up balls of paper, and thus let them get on with trying to put the fire out before flashover happens.
about 11 hours ago
Just how many different small-molecule binding sites are there? That's the subject of this new paper in PNAS, from Jeffrey Skolnick and Mu Gao at Georgia Tech, which several people have sent along to me in the last couple of days. Thi...
Just how many different small-molecule binding sites are there? That's the subject of this new paper in PNAS, from Jeffrey Skolnick and Mu Gao at Georgia Tech, which several people have sent along to me in the last couple of days. This question has a lot of bearing on questions of protein evolution. The paper's intro brings up two competing hypotheses of how protein function evolved. One, the "inherent functionality model", assumes that primitive binding pockets are a necessary consequence of protein folding, and that the effects of small molecules on these (probably quite nonspecific) motifs has been honed by evolutionary pressures since then. (The wellspring of this idea is this paper from 1976, by Jensen, and this paper will give you an overview of the field). The other way it might have worked, the "acquired functionality model", would be the case if proteins tend, in their "unevolved" states, to be more spherical, in which case binding events must have been much more rare, but also much more significant. In that system, the very existence of binding pockets themselves is what's under the most evolutionary pressure. The Skolnick paper references this work from the Hecht group at Princeton, which already provides evidence for the first model. In that paper, a set of near-random 4-helical-bundle proteins was produced in E. coli - the only patterning was a rough polar/nonpolar alternation in amino acid residues. Nonetheless, many members of this unplanned family showed real levels of binding to things like heme, and many even showed above-background levels of several types of enzymatic activity. In this new work, Skolnick and Gao produce a computational set of artificial proteins (called the ART library in the text), made up of nothing but poly-leucine. These were modeled to the secondary structure of known proteins in the PDB, to produce natural-ish proteins (from a broad structural point of view) that have no functional side chain residues themselves. Nonetheless, they found that the small-molecule-sized pockets of the ART set actually match up quite well with those found in real proteins. But here's where my technical competence begins to run out, because I'm not sure that I understand what "match up quite well" really means here. (If you can read through this earlier paper of theirs at speed, you're doing better than I can). The current work says that "Given two input pockets, a template and a target, (our algorithm) evaluates their PS-score, which measures the similarity in their backbone geometries, side-chain orientations, and the chemical similarities between the aligned pocket-lining residues." And that's fine, but what I don't know is how well it does that. I can see poly-Leu giving you pretty standard backbone geometries and side-chain orientations (although isn't leucine a little more likely than average to form alpha-helices?), but when we start talking chemical similarities between the pocket-lining residues, well, how can that be? But I'm even willing to go along with the main point of the paper, which is that there are not-so-many types of small-molecule binding pockets, even if I'm not so sure about their estimate of how many there are. For the record, they're guessing not many more than about 500. And while that seems low to me, it all depends on what we mean by "similar". I'm a medicinal chemist, someone who's used to seeing "magic methyl effects" where very small changes in ligand structure can make big differences in binding to a protein. And that makes me think that I could probably take a set of binding pockets that Skolnick's people would call so similar as to be basically identical, and still find small molecules that would differentiate them. In fact, that's a big part of my job. But in general, I see the point they're making, but it's one that I've already internalized. There are a finite number of proteins in the human body. Fifty thousand? A couple of hundred thousand? Probably no
about 11 hours ago