Chemistry

Last week a new science festival came to town. For 3 days, 15 different pubs in London, Oxford and Cambridge invited local scientists to share their work with the punters for a Pint of Science. Each city hosted talks on the brain, the body and biotechnology and I attended two of the biotechnology evenings held in Cambridge. On Wednesday, Colin Davidson and Chris Lowe asked ‘Can you live without your mobile?’ With the UN predicting that there will be more phones than people in the world by the end of 2014, and the majority of the growth in mobile phone use now in the developing world, both Colin and Chris are interested in exploiting the concept of mobile healthcare for the benefit of society. Their talks reminded me of some of the research we’ve covered in Chemistry World, including this app for detecting food allergens.  Mobile phone based technologies are (obviously) more portable and often easier to use, so ideal for improving or monitoring health in traditionally poorly served hard-to-reach areas. Apparently Android is ahead of Apple when it comes to the development of mobile technology for science – good to know; I’m in the market for a new smartphone… The overriding conclusion of the evening was that the role smartphones play in helping to alleviate modern healthcare problems is only going to increase, so for mobile healthcare at least, the future really is bright. On Thursday, Annabel Murphy and Alison Smith discussed generating energy and chemicals using microorganisms. Oil-derived petrochemicals are used to make a lot of things other than fuel by the pharmaceutical and chemical industry but Alison made a good case for using microorganisms to reduce our reliance on fossil fuels. Chemical production using microorganisms is already a well established technology and she mentioned how very recently yeast has been used to make the antimalarial drug, artemisinin. There are a number of advantages to this approach, as ‘nature is a much better chemist than we are.’ There was a mini-pub quiz in the interval, and I’m sorry to admit that we did very badly. Do you know which country has had a mandatory blending of biofuel with gasoline since 1976? Despite our abysmal performance, it did get us all thinking and led nicely into Alison’s talk. Alison spoke about the potential for using algae to sustainably generate energy. Plants and algae have been photosynthesising for millions of years so it makes sense to harness this process. Cultivating algae at scale is, however, a major challenge, as is public acceptance of the idea. (On a side note, Alison provided some comments for the feature on algae biofactories in the May issue of Chemistry World  – it’s definitely worth a read.) Both evenings were very much focussed on the background to the topics, and although this offered a really good grounding in each subjects, I was a little disappointed not to hear more about the researchers’ actual work. It left me unclear as to who the target audience was – the mildly science literate person, as I would class myself, or an interested lay person. Personally, I found the presentations quite long and would have preferred more time for discussion – this is when the audience really became engaged with the science. Despite these small quibbles, the events were very enjoyable and I came away feeling like I had learnt something. Hearing about research direct from the researchers is more than just learning facts and figures – we’re given a view into the personalities and the lives of the real people behind the science.  It would be wrong to underestimate how worthwhile it can be for the public to hear about research first-hand. According to their twitter account, @pintofscience, the organisers have already started planning the events for next year. Follow them there or visit their website for news of future events. Who else had a pint of science last week? Jennifer Newton

I’m writing blog posts to collect my thoughts for the wonderful workshop at SePublica http://sepublica.mywikipaper.org/drupal/ where I am leading off the day. [This also acts as a permanent record instead of slides. Indeed I may not provide slides as such as I often create the talk as I present it.] My working title is Why and how can we make Scholarship Semantic? [If you switch off at "Semantics" trust me and keep reading… There's a lot here about changing the world.] Why should we strive to create a semantics web/world? I “got it” when I head TimBL in 1994. Many people have “got it”. There are startups based on creating and deploying semantic technology. My colleague Nico Adams (who understands much more about the practice of semantics than me) has a vision of creating a reasoning engine for science (he’s applied this to polymers, biotechnology, chemistry). I completely buy his vision. But it’s hard to sell this to people who don’t understand. Any more than TimBL could sell SGML in 1990. (Yes there were whole industries who bought into SGML, but most didn’t). So what TimBL did was to build a system that worked (The WWW). And this often seems to be the requirement for Semantic Web projects. Build it and show it working. SePublica will probably be attended by the converted. I don’t think I have to convince them of the value of semantics. But I do have to catalyse: The creation of convincing demonstrators (examples that work) Arguments for why we need semantics and what it can do. So why are semantics important for scholarly publishing ? The following arguments will hopefully convince some people: They unlock the value of the stuff already being published. There is a great deal in a single PDF (article or thesis) that is useful. Diagrams and tables are raw exciting resources. Mathematical equations. Chemical structures. Even using what we have today converted into semantic form would add billions. They make information and knowledge available to a wider range of people. If I read a paper with a term I don’t know then semantic annotation may make it immediately understandable. What’s rhinovirus? It’s not a virus of rhinoceroses – it’s the common cold. That makes it accessible to many more people (if the publishers allow it). They highlight errors and inconsistencies. Ranging from spelling errors to bad or missing units to incorrect values to stuff which doesn’t agree with previous knowledge. And machines can do much of this. We cannot have reproducible science until we have semantics. They allow the literature to be computed. Many of thre semantics define objects (such as molecules or phylogenetic trees) which are recomputable. Does the use of newer methods give the same answer? They allow the literature to be aggregated. This is one of the most obvious benefits. If I want all phylogenetic trees, I need semantics – I don’t want shoe-trees or B-trees or beech trees. And many of these concepts are not in Google’s public face (I am sure they have huge semantics internally) They allow the material to be searched. How many chemists use halogenated solvents. (The word halogen will not occur in the paper). With semantics this is a relatively easy thing to do. Can you find second-order differential equations? Or Fourier series? Or triclinic crystals? (The words won’t help) AMI2 will be able to. They allow the material to linked into more complex concepts. By creating a data base of species , a database of geolocations and links between them we start to generate an index of biodiversity. What species have been reported when and where? This can be used for longitudinal analyses – is X increasing/decreasing with time? Where is Y now being reported for the first time? They allow humans to link up. If A is working on Puffinus Puffinus (no, it’s not a Puffin, that’s Fratercula Artica) in the northern hemisphere

RNA Interference: Nanocoatings on bandages and other medical materials could deliver RNAs capable of shutting off genes related to disease

We’ve got a splendid collection of about 600 Open PDFs for our jailbreak hackathon. They seem to have a medical focus. They are of very variable type and quality. Some are reports, guidelines , some academic papers. Some are born digital but at least one is scanned OCR where the image and the text are superposed. (BTW I am taking it on trust that the papers are Open – some are from closed access publishers and carry their copyright. It’s time we starting marking papers as Open ON THE PAPER). I have given these to #AMI2 – she processes a paper in about 10 secs on my laptop so it’s just over an hour for the whole lot. That gives me a chance to blog some more. In rev63 AMI was able to do tables so here, without any real selection, I’m giving some examples. (Note that some tables are not recognised as such – especially when the authors don’t use the word “table”. But we shall hack those in time…). Also, as HTML doesn’t seem to have a tableFooter that manages the footnotes I have temporarily added this to the caption as a separate paragraph From Croat Med J. 2007;48:133-9: The table in the PDF  AMI’s translation to HTML: Table 1. Scores achieved by 151 Croatian war veterans diagnosed with posttraumatic stress disorder on the Questionnaire on Traumatic Combat and War Experiences (USTBI-M), Mississippi Scale for Combat-Related Post-Traumatic Stress Disorder (M-PTSD), and Minnesota Multiphasic Personality Inventory (MMPI)-201 (presented as T values) *Abbreviations: L – rigidity in respondents’ approach to the test material; F – lack of understanding of the material; K – tendency to provide socially acceptable answers.  Score  Questionnaire (mean ± standard deviation) Cut-off score USTBI-M 77.8 ± 14.3 Maximum: 120 M-PTSD 122.1 ± 22.9 107 MMPI-201 scales*   L 51.1 ± 2.0 70 F 73.2 ± 6.3 70 K 42.4 ± 3.2 70  87.6 ± 5.1 70  96.7 ± 6.6 70  88.2 ± 4.7 70  67.3 ± 4.8 70     79.3 ± 5.8 70 Pt ( psychastenia ) 75.4 ± 5.7 70  72.1 ± 7.4 70  52.3 ± 2.6 70  COMMENT: Some of the row labels/ headings are omitted, but I think that can be solved. (Remember this is AMI’s first attempt so we call it alpha) Here’s another: And what AMI translates it to Table 2 The comparison of quality of life among study groups using analysis of variance and post-hoc tests *Group-by-group comparisons that were significant at the level of P QOL dimension/status Groups N Mean ± SD F; P Post-hoc differences* Physical PTSD + LBP (I) 79 75.44 ± 11.33    PTSD (II) 56 78.43 ± 11.54 49.18; I-III, I-IV, II-III,  LBP (III) 84 87.43 ± 13.84 II-IV, III-IV  Controls (IV) 134 94.42 ± 11.65    Total 353 85.97 ± 14.40   Psychological PTSD + LBP (I) 76 63.74 ± 14.60    PTSD (II) 58 67.45 ± 15.92 79.05; I-III, I-IV, II-III,  LBP (III) 90 80.27 ± 14.59 II-IV, III-IV  Controls (IV) 132 90.67 ± 10.76    Total 356 78.51 ± 17.44   Social PTSD + LBP (I) 80 33.40 ± 8.89    PTSD (II) 58 35.93 ± 9.98 70.19; I-III, I-IV, II-III,  LBP (III) 91 41.58 ± 8.78 II-IV, III-IV  Controls (IV) 134 49.22 ± 7.13    Total 363 41.70 ± 10.6   Enviromental PTSD + LBP (I) 79 92.81 ± 20.78    PTSD (II) 58 100.76 ± 19.79 66.27; I-III, I-IV, II-IV,  LBP (III) 88 108.36 ± 17.71 III-IV  Controls (IV) 130 126.06 ± 14.27    Total 355 110.14 ± 22.02   Satisfaction with personal health status PTSD + LBP (I) 80 1.84 ± 0.74    PTSD (II) 59 2.36 ± 0.85 127.48; I-II, I-III, I-IV, II-IV,  LBP (III) 95 2.70 ± 0.98 III-IV  Controls (IV) 135 4.03 ± 0.85    Total 369 2.94 ± 1.23   Overall self-reported quality of life PTSD + LBP (I) 73 2.82 ± 1.14    PTSD (II) 49 3.29 ± 1.28 24.04; I-II, I-III, I-IV, II-III,  LBP (III) 75 4.04 ± 1.25 II-IV  Controls (IV) 42 4.48 ± 0.80    Total 239 3.59 ± 1.31     I think she’s got it completely right (the typos “Enviromental” and “Unhomogenous” are visible in the PDF). AFAIK there is no automatic Open extractor of tables so we are very happy to contribute this to the public pool

Duke University engineers have developed a new safer method for catalytic hydrogen production. According to the authors of the study, it does not require high temperatures and produces smaller amounts of toxic chemicals than other industrial hydrogen production technologies.... Shodiya, T., Schmidt, O., Peng, W., & Hotz, N. (2013) Novel nano-scale Au/?-Fe2O3 catalyst for the preferential oxidation of CO in biofuel reformate gas. Journal of Catalysis, 63-69. DOI: 10.1016/j.jcat.2012.12.027 Novel nano-scale Au/?-Fe2O3 catalyst for the preferential oxidation of CO in biofuel reformate gas

APPLE defends itself against accusations of immoral tax practices, joining several other international brands already under fire

YAHOO has bought Tumblr for a hefty sum, but users fear the takeover will result in the blog site losing its distinctive style

Linguistics of adolescent phonetics If you don't get it, then I just have one thing to say and it's: “A voiced alveolar stop and breathy-voiced low-back unrounded vowel, with advanced tongue root” – duuuuh… (That latter words is described by James Harbeck in his accompanying article as aiming to sound as stupid as possible. Of course, the stupidity being communicated is not that of the articulator but of you, dear listener, or did you not get that either? Meh.) Translating teenage grunts is a post from the science blog of David Bradley, author of Deceived Wisdom Subscribe to our Email Newsletter

A CYBER-SPYING network has re-emerged in India. But who are they taking their orders from?

FiercePharma has some good figures to back up my posts the other day on R&D spending versus marketing. I mentioned how many people, when they argue that drug companies spend more on marketing than they do on research, are taking the entire SG&A number, and how companies tend to not even break out their marketing numbers at all. Well, the folks at Fierce had a recent article on marketing budgets in the business, and they take Pfizer's numbers as a test case. That's actually a really good example: Pfizer is known as a mighty marketing machine, and for a long time they had what must have been the biggest sales force in the industry. They also have a lower R&D spend than many of their peers, as a percentage of sales. So if you're looking for the sort of skewed priorities that critics are always complaining about, here's where you'd look. Pfizer spent $622 on advertising last year. Man, that's a lot of money. It's so much that it's not even one-tenth of their R&D budget. Ah, you say, but ads are only part of the story, and so they are. But while we don't have a good estimate on that for Pfizer, we do have one for the industry as a whole: DTC spending is only part of the overall sales-and-marketing budget, of course. Detailing to doctors costs a pretty penny, and that's where drugmakers spend much of their sales budget. Consumer advertising spending dropped by 11.5% in 2012 to $3.47 billion. Marketing to physicians, according to a Johns Hopkins Bloomberg School of Public Health study, amounted to $27.7 billion in 2010; that same year, DTC spending was just over $4 billion. That's a total for 2010 of more than $31 billion, the best guess-timate we can come up with on short notice. According to FierceBiotech's 2010 R&D spending report, the industry shelled out $67 billion on research that year--more than twice our quick-and-dirty marketing estimate. So let's try for a Pfizer estimate then. If they stayed at roughly that ratio, then they would have spent seven times as much marketing to physicians as they did on advertising per se. That gives a rough number of $4.3 billion, plus that $622 million, for a nice round five billion dollars of marketing. That's still less than their R&D budget of $7.9 billion, folks, no small sum. (And as for that figure from a couple of years ago about how it only costs $43 million to find a new drug, spare me. Spare everyone. Pfizer is not allocating $7.9 billion dollars for fun, nor are they planning on producing 184 new drugs with that money at $43 million per, more's the pity.) So let me take a stronger line: Big Pharma does not spend more on marketing than it does on R&D. This is a canard; it's not supported by the data. And let me reiterate a point that's been made here several times: no matter what the amount spent on marketing, it's supposed to bring in more money than is spent. That's the whole point of marketing. Even if the marketing budget was the same as the R&D, even if it were more, it still wouldn't get rid of that point: the money that's being spent in the labs is money that came in because of marketing. Companies aren't just hosing away billions of dollars on marketing because they enjoy it; they're doing it to bring in a profit (you know, that more-money-than-you-spend thing), and if some marketing strategy doesn't look like it's performing, it gets ditched. The response-time loop over there is a lot tighter than it is in research. There. Now the next time this comes up, I'll have a post to point to, with the numbers, and with the links. It will do no good at all. Note: I am not saying that every kind of drug company marketing is therefore good. Nor am I saying that I do not cringe and roll my eyes at some of it. And yes indeed, companies can and do cross lines that shouldn't be crossed when they get to selling their products too hard. Direct-to-consumer advertising, although it has brought in the money, has surely damaged the industry from other directions. All th