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				<title>bjoern.brembs.blog : a neuroscientist's blog</title>
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				<description>This is the personal blog of biologist Björn Brembs. It features neuroscientific research, sports and various political or personal topics.</description>

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				<pubDate>Mon, 13 Jul 2009 14:00:13 -0400</pubDate>
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						<title>Flies are creatures of habit, too</title>
<link>http://bjoern.brembs.net/news.php?item.531.3</link>
<description><![CDATA[My latest paper has appeared a few days ago at <a href="http://current-biology.org" rel="external">Current Biology</a>, with the title "Mushroom-bodies regulate habit formation in Drosophila". In it I describe experiments which I interpret as showing habit formation in fruit flies. What I did was to train flies to attempt turning in one direction. I used heat punishment to get them to do it and helped them by using colors to indicate which direction was which, e.g. when the fly attempted left-rurning, the computer controlling the experiment turned the fly's environment green and when they attempted to turn right, it switched off green and turn on blue illumination. One of the two situations then was punished with the heat. This of course was all done with <em>Drosophila </em>in stationary flight at the flight simulator:<br /><div height="344" width="425"><div></div><div></div><div></div><object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=6,0,40,0" width="425" height="344"><param name="width" value="425" /><param name="height" value="344" /><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="src" value="http://www.youtube.com/v/K_6BDf-CjiI&amp;hl=en&amp;fs=1&amp;" /><embed type="application/x-shockwave-flash" width="425" height="344" allowfullscreen="true" allowscriptaccess="always" src="http://www.youtube.com/v/K_6BDf-CjiI&amp;hl=en&amp;fs=1&amp;"></embed></object><br />The flies 'get' the task after only about 8 minutes of training and keep clear of the punished color/turning direction even if the heat was switched off afterwards. When I analyzed what the flies have learned, the turning, the colors or both, it turned out they learned only the colors. I tested the color memory by asking them to choose colors with a different behavior. The experiment for the flies can be imagined like first learning to drive a car in the US or the European continent, only to then have to drive a car in the UK or Australia, with everything reversed. After 8 minutes of training, the flies could switch from one car to another. When I did the same analysis after 16 minutes of training, I found that both the behavior and the colors had been learned. In the transfer test, the flies now failed to choose the previously unpunished color with the novel behavior. In the car example, if you practice car driving long enough, driving in a different car in a different traffic system becomes much harder then if you've just started learning how to drive. Basically, it becomes difficult to kick the habit, even if you're a fly. These results don't only match well with vertebrate and human studies, it also dovetails nicely with <a href="http://brembs.net/rut-pkc/">our recent discovery</a> that the behavior-learning and the world-learning (for the flies: turning and color-learning, respectively) systems can be distinguished at the molecular level.<br />Once we saw the interaction between behavior and world-learning, we started to use the genetic toolkit that comes with the model system <em>Drosophila </em>and found that a very well-studied insect brain region, the mushroom-bodies, is involved in some of the interactions underlying the regulation of habit formation in flies.<br />These results now allow us for the first time to tease apart the mechanisms of interacting memory systems at the molecular and the circuit level. If you think that's interesting, you can <a href="request87.html">get the new paper in the download section</a>.<br /></div>]]></description>
<author>bjoern&lt;bjoern@nospam.com&gt;</author>
<pubDate>Wed,  8 Jul 2009 14:59:05 -0400</pubDate>
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						<title>Libel law forcing Nature to abandon core scientific principles?</title>
<link>http://bjoern.brembs.net/news.php?item.530.11</link>
<description><![CDATA[This story would be almost comical in a Monty-Python sort of way, if it wasn't for a fairly serious backdrop.<br /><br /><div height="344" width="425"><div></div><div></div><div></div><object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=6,0,40,0" width="425" height="344"><param name="width" value="425" /><param name="height" value="344" /><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="src" value="http://www.youtube.com/v/9JKvJaJKPPk&amp;hl=en&amp;fs=1&amp;" /><embed type="application/x-shockwave-flash" width="425" height="344" allowfullscreen="true" allowscriptaccess="always" src="http://www.youtube.com/v/9JKvJaJKPPk&amp;hl=en&amp;fs=1&amp;"></embed></object></div><br />In <a href="http://network.nature.com/groups/naturenewsandopinion/forum/topics/4856" rel="external">this thread</a> on <em><a href="http://networks.nature.com" target="_blank">Nature Networks</a></em> on science journalism, I left the following comment <div class='indent'>the problem is not access to that one single paper the press release cites. The problem is access to the papers the one under embargo should have cited but didn't. The problem is access to the papers it cites, in order to be able to tell what they have done and if it was done the right way. The problem is access to all the literature from which a journalist can form his/her own opinion if what the authors claim is really novel or just something reproduced from 10 years ago, such as this <a href="http://www.nature.com/nature/journal/v454/n7205/full/nature07090.html" target="_blank"><em>Nature</em> paper</a> which unwillingly only reproduced <a href="http://learnmem.cshlp.org/content/5/1/179.long" target="_blank">this earlier article</a> and didn't even cite it. In this particular case, the other, un-cited article was at least accessible, but the problem remains: reviewers have trouble getting access to all the relevant literature for them to competently review submitted manuscripts. If journalists are evolving into a science watch-dog, as James Randerson from the Guardian claims in the <em>Nature</em> podcast, how can that watch-dog grow teeth without full access?<br />Without open access, any journalistic watch-dog must remain toothless - and toothless watch-dogs certainly won't last long.<br />I find Randerson's argument fairly interesting (as the entire <em>Guardian Science Weekly </em>podcast is one of the best science podcasts out there), especially given the pressures to publish in certain journals, the closeness of some scientists to some editors in said journals (I'm speaking from personal experience in my circle of colleagues here) and especially the fact that peer-review isn't perfect. Post-publication review/scrutiny will become even more important than it already is and journalists are in a unique position to fill a critical niche in the checks and balances that have to arise in the crazy world science has become.<br />The bottom line is: if journalists don't have full access to the literature, they won't be more than amplifiers of press releases and that would definitely be the end of the line for science journalism.</div> A few days later, I received a note from <em>Nature Network </em>that my post had been taken down. I was rather surprised to learn that it was taken down because NN thought I had accused someone of plagiarism: <div class='indent'>I’m sending you a response I made at Nature Network to your accusation that a Nature paper is plagiarised. This is an extremely serious accusation, not least as you provide no reasoning for it, and I suggest that a more appropriate and professional approach would be to contact the journal directly, according to the journal’s procedures in such matters.</div>Apparently, the problem was this clause in my comment: “such as this Nature paper which unwillingly only reproduced this earlier article” With ‘unwillingly’ I meant to say ‘inadvertently’, but that wasn’t the problem. The problem was ‘reproduced’. <span>'Reproduction', in the publishing business can mean to reproduce from a template, i.e. copying. </span>However, scientifically, “<strong>Reproducibility</strong> is one of the main principles of the <a href="http://en.wikipedia.org/wiki/Scientific_method" title="Scientific method"><span>scientific method</span></a><span>” (<a href="http://en.wikipedia.org/wiki/Reproducibility" target="_blank">Wikipedia</a>), which is what I was referring to, obviously. When I wrote back to <em>Nature </em>asking for a clarification, they replied: <div class='indent'>any reasonable person inside or outside science, would construe [“reproduced”] to mean "copied" and yes, this is actionable in English law - but even if it were not, it is denigrating other scientists and is inappropriate on the normal grounds of courtesy and discourse.</div>At this point it needs to be mentioned that I have already <a href="comment-n519.html" target="_blank">blogged about this <em>Nature </em>paper</a> and have pointed out how the new experiments in this paper show pretty much the same results as the somewhat different experiments from the earlier paper. A reproduction in the finest sense: different people, variation of experimental conditions, ten years apart, yet qualitatively same/similar results. Reproducibility is definitely a good thing in science! Reproducibility wasn't the reason I blogged about this paper. The problem with this <em>Nature </em>paper was that the authors claimed to have shown something else, but did not control for the effect shown in the earlier paper. Thus, the uncontrolled, known effect could be an alternative explanation for the novel effect the authors actually wanted to study. Not necessarily, but without the proper control experiment, it is impossible to tell. Apparently, neither the handling editor at <em>Nature</em>, nor the reviewers noticed this. One may speculate, since the older paper wasn’t cited, that the authors simply didn’t know about the earlier paper. In science, this sort of thing happens every day. Authors, editors and reviewers are humans and things slip through their radar. Not such a big deal, really. There are ~24,000 scholarly journals, so of course you can miss an important paper buried in there somewhere. Happens even at <em>Nature</em>, has happened before and will happen again. It's almost impossible to keep on top of <em>everything </em>that's going on. Future experiments will find out if indeed the alternative explanation can be ruled out or not, this is how science goes. This sort of thing is also where post-publication review comes in handy, which is why I posted my review on the blog and explained the shortcomings of the paper to undergraduate students after a lecture on temperature sensation. Online, informal post-publication review is a relatively recent and valuable addition to the scientific discourse, as it can instruct future experiments.<br />What is not new, of course, is to publicly criticize published research about technical or conceptual shortcomings. It’s how science progresses, by challenging our current state of knowledge. Criticism is vital to the scientific method. Konrad Lorenz famously once wrote: “It is a good morning exercise for a research scientist to discard a pet hypothesis every day before breakfast. It keeps him young. “ and WH Newton-Smith wrote that “no one disputes the importance of criticism in science” (<a href="http://books.google.com/books?id=D-M5ilhhBs8C&amp;pg=PA22&amp;lpg=PA22&amp;dq=%22no+one+disputes+the+importance+of+criticism+in+science%22&amp;source=bl&amp;ots=IC-T9ugxG8&amp;sig=2nxPJSxjpXKqLLntbopO1wq745U&amp;hl=en&amp;ei=_0FUSs2aCZGInQPyg5UF&amp;sa=X&amp;oi=book_result&amp;ct=result&amp;resnum=1" target="_blank">Karl Popper: philosophy and problems</a>, O’Hear, editor, Cambridge). Apparently, <em>Nature </em>disputes it: even if I had not accused the authors of plagiarism, but had criticized their paper for a lack of control experiments (which is what I did), according to <em>Nature</em>, I would be “denigrating other scientists and is inappropriate on the normal grounds of courtesy and discourse”.<br />Thus, given this very brief exchange, one could make the case that <em>Nature</em> appears to be giving up on two of the main principles of the scientific method: reproducibility and criticism.</span> Clearly<span>, one can only speculate about the motivations behind such actions, and I would never rule out misunderstandings on my part. However, if I did not misunderstand the messages from <em>Nature</em>, I'd hazard a guess that the <a href="http://www.guardian.co.uk/science/2009/jun/04/simon-singh-libel-british-chiropractic-association-bca" target="_blank">Singh affair</a> and the impact UK libel-law has on the scientific discourse may be to blame. There is <a href="http://friendfeed.com/rpg/92853972/nature-network-rolls-over-and-exposes-its-belly" target="_blank">precedence for censorship at <em>Nature Network</em> for precisely this reason</a>. If UK libel-laws were indeed the motivation also in this case, this situation reminds us that the </span><span><em>raison d'être </em>of </span><span>scientific publishers is not to facilitate the scientific discourse, this is merely one of their many services. Commercial publishers, like all private companies, exist to make a profit and libel suits reduce profit. To be fair, <em>Nature </em>has <a href="http://www.nature.com/nature/journal/v459/n7248/full/459751a.html" target="_blank">weighed in on the Singh-Affair in defense of Singh</a> and has recorded an extra issue of its podcast on the story (which I have yet to listen to). Thus, I think it's fairly clear on what side <em>Nature </em>stands on in this affair. If only actions would follow <em>Nature</em>’s words.</span> On the other hand, I can see the kind of trade-offs private companies have to make, especially in the critical state all traditional journalism is in these days.]]></description>
<author>bjoern&lt;bjoern@nospam.com&gt;</author>
<pubDate>Wed,  8 Jul 2009 03:08:53 -0400</pubDate>
<guid isPermaLink="true">http://bjoern.brembs.net/news.php?item.530.11</guid>
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						<title>Science and art: romantic machines</title>
<link>http://bjoern.brembs.net/news.php?item.529.5</link>
<description><![CDATA[I think my interest in modern art was sparked by the <a href="http://de.wikipedia.org/wiki/Documenta_8" rel="external">Documenta 8</a> in Kassel in 1987. I was a high school student at the time, joining a trip there organized by the art students. Since then I've been trying to find the time to enjoy modern art. Unfortunately, finding time was often not easy. Despite trying hard, I missed every single Documenta since then, to my great regret. Two years ago, on a flight to a conference in the US, I was thrilled to learn I was sitting next to a curator, <a href="http://www.marcwellmann.de" target="_blank">Marc Wellman</a>, who was on his way to open an exhibition he had curated in New York. We talked about all kinds of things and he promised to keep me informed of the exhibitions he would curate here in Berlin. Weirdly enough, we were on the same flight back, this time almost next to each other on opoposite sides of the aisle. Back in Berlin, Marc kept his promise and I've been receiving his invitations ever since. Typical for scientists constantly experimenting, travelling and publishing just to be able to keep a job, it took me two years to make time to actually see one of his openings. This past Saturday we went to the <a href="http://www.georg-kolbe-museum.de" target="_blank">Georg-Kolbe-Museum</a> for the exhibit "<a href="http://www.georg-kolbe-museum.de/romantische_maschinen.htm" target="_blank">Romantische Maschinen</a>" (romantic machines, <a href="http://www.georg-kolbe-museum.de/pdfs/RM_Folder.pdf" target="_blank">program in PDF</a>) and we were not disappointed!<br />Fittingly enough, the exhibition started with a piece from the Documenta 8, the movie "<a href="http://en.wikipedia.org/wiki/The_Way_Things_Go" target="_blank">Der Lauf der Dinge</a>" (<a href="http://icarusfilms.com/cat97/t-z/the_way_.html" target="_blank">the way things go</a>):<br /><div height="344" width="425"><div></div><div></div><div></div><object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=6,0,40,0" width="425" height="344"><param name="width" value="425" /><param name="height" value="344" /><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="src" value="http://www.youtube.com/v/QfEkPgfA7wo&amp;hl=en&amp;fs=1&amp;" /><embed type="application/x-shockwave-flash" width="425" height="344" allowfullscreen="true" allowscriptaccess="always" src="http://www.youtube.com/v/QfEkPgfA7wo&amp;hl=en&amp;fs=1&amp;"></embed></object><br />As you can see, the video shows a long sequence of various mechanical and chemical cause-and-effect sequences, a chain reaction. Some of these sequences are difficult to comprehend and believe without some basic chemistry and physics. The intricacy of the design is impressive and the whole sequence does make one think about determinism in the macroscopic world. It made me reflect about my own work on <a href="http://brembs.net/spontaneous">spontaneous behavior</a>, which, while not uncaused (it's caused by a biological mechanism in the animal), lacks the external sensory trigger which is commonly taken for granted.<br />The next piece was something for all senses: an old cement mixer, refurbished to roast popcorn:<br /><a href="http://bjoern.brembs.net/e107_images/newspost_images/kolbe_03.jpg"><img src="http://bjoern.brembs.net/e107_images/newspost_images/kolbe_03_small.jpg" style="border: 0px solid black; width: 300px; height: 400px" alt="kolbe_03_small.jpg" /></a><br />When it was running, the machine was loud, the entire museum smelled of popcorn and if you wanted, you could eat the freshly popped corn. A very ironic way of fusing the sensations during the procedure with associations one has with the original purpose of the machine and with the smell and taste of the popcorn.<br />The third object was a very fragile-looking piece, seemingly cobbled together from what the artist had standing around:<br /><a href="http://bjoern.brembs.net/e107_images/newspost_images/kolbe_02.jpg"><img src="http://bjoern.brembs.net/e107_images/newspost_images/kolbe_02_small.jpg" style="border: 0px solid black; width: 400px; height: 396px" alt="kolbe_02_small.jpg" /></a><br />It was not the first time I was really angry that the iPhone 3G can't record videos! What you can't see on this picture is that the sheets of paper are rotating against one another such that they are always pushing against each other. This arrangement elicited the most peculiar impression and was surprisingly aesthetic. We even thought we could build something like this (maybe with light) for the livingroom... beautiful.<br />The next piece was the one that captivated me the most. For me it embodied the essence of 'romantic machines'. It's "<a href="http://www.robertbarta.de/017_work_en_time_machine.html" target="_blank">Time Machine</a>" (there's also video on that page) by <a href="http://www.robertbarta.de" target="_blank">Robert Barta</a>:<br /><a href="http://bjoern.brembs.net/e107_images/newspost_images/kolbe_01.jpg"><img src="http://bjoern.brembs.net/e107_images/newspost_images/kolbe_01_small.jpg" style="border: 0px solid black; width: 400px; height: 300px" alt="kolbe_01_small.jpg" /></a><br />There is a small, red electric locomotive (which so reminded me of "<a href="http://en.wikipedia.org/wiki/The_Little_Engine_That_Could" target="_blank">the little engine that could</a>") running on a big horizontal wheel. The wheel is rotating at such a speed, that the engine is basically at a standstill, with reference to the room. The wheel and the train are both symbols for some of humanity's greatest inventions, yet the tiny engine on the gigantic wheel feels like almost a <a href="http://en.wikipedia.org/wiki/Metropolis_(film)" target="_blank">Metropolis</a>ian allegory of insignificant beings running as fast as they can only to stay where they are. Talk about a romantic machine! The little engine also reminded me of today's scientists struggling to balance experiments, teaching, writing and conference traveling just to get from one short-term-contract to the next in this publish-or-perish world.<br />A very dynamic exhibit was O2 by <a href="http://www.spencerbrownstonegallery.com/Artists/Zilvinas_Kempinas/Kempinas_images.html" target="_blank">Zilvinas Kempinas</a>. There was a fan which kept a loop of magnetic tape (video recording tape) hovering on the wall. Whenever your hand got into the airstream, the loop changed shape, seemingly alive. This video is pretty similar:<br /><div height="344" width="425"><div></div><div></div><div></div><object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=6,0,40,0" width="425" height="344"><param name="width" value="425" /><param name="height" value="344" /><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="src" value="http://www.youtube.com/v/mt4298sfybg&amp;hl=en&amp;fs=1&amp;" /><embed type="application/x-shockwave-flash" width="425" height="344" allowfullscreen="true" allowscriptaccess="always" src="http://www.youtube.com/v/mt4298sfybg&amp;hl=en&amp;fs=1&amp;"></embed></object></div>I was mesmerized at the sight of the hovering band and felt why it fitted very well into the category of 'romantic machines'.<br />The next exhibit that invited me to stop and think was a mirror my <a href="http://www.oberwelt.de/projects/2007/Smiatek.htm" target="_blank">Johanna Smiatek</a>. This mirror would start to vibrate when you got too close, making it impossible to discern any details any more. This one was reminiscent of <a href="http://en.wikipedia.org/wiki/Narcissus_(mythology)" target="_blank">Narcissus</a>, who fell in love with his image in a pool. If you get too close to the surface and touch it, you also destroy the image.<br />The technically most advanced exhibit was the bit.reflection installation by Julius Popp of <a href="http://www.youtube.com/watch?v=avGZoKnw8sI" target="_blank">bit.fall</a> fame:<br /><a href="http://bjoern.brembs.net/e107_images/newspost_images/kolbe_05.jpg"><img src="http://bjoern.brembs.net/e107_images/newspost_images/kolbe_05_small.jpg" style="border: 0px solid black; width: 400px; height: 181px" alt="kolbe_05_small.jpg" /></a><br />The mirrors reflect the light onto the wall and form words, pulled from news-sites on ther internet. At first, only a few letters appear, then the whole word, which quickly becomes illegible as it's transformed into the next word. Very much like bit.fall, it captures nicely the ephemeral nature of news these days. For a few media cycles, something incredibly impressive or important happens, reverberates in the various media, only to be dropped and forgotten and sometimes destroyed soon after. You can find videos here and here which show the machine working in grerat detail. The video below shows several Julius Popp pieces and starts bit-reflection at 2:57.<br /><br /><div height="344" width="425"><div></div><div></div><div></div><object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=6,0,40,0" width="425" height="344"><param name="width" value="425" /><param name="height" value="344" /><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="src" value="http://www.youtube.com/v/gTY7Lb_vxRM&amp;hl=en&amp;fs=1&amp;" /><embed type="application/x-shockwave-flash" width="425" height="344" allowfullscreen="true" allowscriptaccess="always" src="http://www.youtube.com/v/gTY7Lb_vxRM&amp;hl=en&amp;fs=1&amp;"></embed></object><br />On the outside, in a wall separating two parts of a central yard, is a bee-hive from <a href="http://www.baerbel-rothhaar.de/de/bienen_01.html" target="_blank">Bärbel Rothaar</a>:<br /><a href="http://bjoern.brembs.net/e107_images/newspost_images/kolbe_04.jpg"><img src="http://bjoern.brembs.net/e107_images/newspost_images/kolbe_04_small.jpg" style="border: 0px solid black; width: 400px; height: 176px" alt="kolbe_04_small.jpg" /></a><br />Working at an institution where most people work on honeybees, this was of course of particular interest to me. The piece sits in front of a webcam, so you can see a few videos of the bees buzzing away <a href="http://kunstundumwelt.umweltbundesamt.de/talking-heads/" target="_blank">here</a>.<br />It seems, science and technology have now become so dominant in our culture (this sounds almost like I think it's a bad thing! <img src='http://bjoern.brembs.net/e107_images/emotes/yellow/laugh.png' alt='' style='vertical-align:middle; border:0' /> , that the arts are increasingly drawing inspiration and topics from them. Art is always also a method of answering the questions of who and what we are. In that respect, it is akin to science. Maybe the cross-fertilisation seen between them is not all too surprising. Maybe it is more surprising the transfer seems to be going only in one direction, or isn't it? I often find that the scientific and the artistic method often complement each other very well, finding different perspectives on similar answers. Certainly, my science dominated (it's basically a monopoly!) life would be seriously impoverished without this alternative, artistic perspective.<br />The exhibition will be on until September 6 and if you're in Berlin and are the least interested in these sorts of things, have a look, we had a great time there.<br /></div></div>]]></description>
<author>bjoern&lt;bjoern@nospam.com&gt;</author>
<pubDate>Mon, 29 Jun 2009 10:13:53 -0400</pubDate>
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						<title>PLoS One largest journal in the world 2010?</title>
<link>http://bjoern.brembs.net/news.php?item.528.5</link>
<description><![CDATA[Managing Editor of PLoS One, Peter Binfield, recently published a paper entitled "<a href="http://conferences.aepic.it/index.php/elpub/elpub2009/paper/view/114" rel="external">PLoS One: background, future development, and article-level metrics</a>"in which he outlines some of the recent upgrades at PLoS One and future plans for article-level metrics.<br />What Pete also mentioned in the article is the doubling in articles published every year:<br /><ul><li>2007: 1,231 articles</li><li>2008: 2,722 articles</li><li>2009: ~4,300 articles</li><li>2010: ~1% of PubMed?</li></ul>If this trend indeed continues until 2010, PLoS One will be the largest journal on the planet, if measured by number of articles published (PubMed lists thousands of journals). Today, PLoS One already has more than 800 Academic Editors (I'm one of them) donating their time for handling peer-review and 30,000 authors have published with PLoS One.<br />I wonder whether this growth is just siphoning off excess publication pressure, or if some smaller journals are already seeing their submission numbers decrease. I take this growth also as a sign that people are fed up with our publishing system and embrace a publishing venue where they know they will get published if only their sience is sound.]]></description>
<author>bjoern&lt;bjoern@nospam.com&gt;</author>
<pubDate>Fri, 26 Jun 2009 09:13:42 -0400</pubDate>
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						<title>Science journalists should be the strongest Open Access proponents</title>
<link>http://bjoern.brembs.net/news.php?item.527.11</link>
<description><![CDATA[Listening to this week's <a href="http://nature.com/nature" rel="external"><em>Nature</em></a> podcast I became aware of something I haven't read anywhere else so far. Since this issue of <em>Nature </em>(and the podcast) has "science journalism" as the theme and <a href="http://friendfeed.com/science-online/b833cee4/end-of-line-for-science-journalism-from-nature" target="_blank">Maxine Clarke</a> asked us to contribute some discussion, I thought I could write down what I was pondering about whilst listening to the podcast.<br />It was a comment from The Guardian's <a href="http://www.journalisted.com/james-randerson" target="_blank">James Randerson</a>, IIRC, which got me thinking, He was talking about the history of science journalism and how it was all gung-ho in the early days and now has matured more into a watch-dog of sorts. Well, I haven't seen all that many investigative reports that uncover fraud or expose a paper as hype. Now that may be because of my reading habits or because there is very little fraud or because it's only the hype that sells or some other reason. However, it may also be because the journalists have no chance of actually investigating anything. With yearly subscription rates for scholarly journals ranging between US$1200-3000 and about 24,000 journals, journalists face the same problem as scientists: they can never afford to subscribe to all the relevant journals in order to do a thorough investigation of whatever topic they're investigating. Some journalists tell me they don't have access to any journals and have to go by the press-releases! No way any journalist can be a watchdog without information. So what can the journalists of today do who want to investigate? They have to call the scientists up. Either the scientists who did the study in question, or colleagues, to get other opinions. All of this is, of course, the far worse option than to read the literature and form your own opinion.<br />I agree with James Randerson that science journalists didn't used to be watchdogs. I tend to believe in the vast majority of cases, they didn't have to. Given the current pitiful state of affairs in science, I regret to say, journalists may have to assume the watchdog role. For one, we have way too many scientists for the few positions and thus tremendous competition not for fame, but to put food on the table. This situation is aggravated by a publishing system in which it is more important <em>where </em>you publish than <em>what </em>you publish. That one publication in a high-profile journal can decide if a scientist will get tenure at a university or has to flip burgers. Given that fraud rarely is detected in a way that has any serious consequences for the fraudster, once he has achieved tenure, we have a system that provides all the incentives for fraud, even for people who would otherwise never dream of committing anything like that. It is very conceivable that the rate of scientific misconduct is in the middle of scyrocketing right now.<br />As deplorable as it might seem, if we don't change the way we hire our scientists and remove the incentives for scientific misconduct, we will soon be needing a science police. Journalists are well-trained in science and are in a unique position to fill the role of a science police. In order to police scientists, to be the watch-dog James Randerson talked about, journalists need access to all the literature. However, I don't see journalists demanding that access, yet.This is the more timely as science bloggers are also moving somewhat into this direction. Many science bloggers work at scientific institutions and have access to a lot of journals. In fact, <a href="comment-n519.html">I recently blogged</a> about a paper in <em>Nature </em>myself, where a crucial citation and crucial control experiments were missing. Science journalists will not be able to compete without open access to the scientific literature.]]></description>
<author>bjoern&lt;bjoern@nospam.com&gt;</author>
<pubDate>Fri, 26 Jun 2009 07:20:14 -0400</pubDate>
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						<title>A unified scholarly database is not a monopoly</title>
<link>http://bjoern.brembs.net/news.php?item.526.11</link>
<description><![CDATA[It has been the main argument against unifying scholarly literature and data in a single database that monoplies are always bad. I won't go into any political arguments here. Markets have their place, but they also have their limitations. In a recent email exchange with a fellow scientist, we fired these arguments (among others) at each other.<br />He wrote:<br /><div class='indent'>But what I'm not sure is whether a single platform for publication is the right way to go. I believe that competition is still important to prevent corruption. So, if we have many PLoS ONE-like platforms with different bodies of peer reviewers that would be ideal.</div>I replied:<br />If competition were really so important, why does each university have one library system? Why hasn't that been outsourced to whatever provider provides the best library service? What is there to corrupt when all that is required for publication is scientific soundness? What is there to be corrupted when where you publish is irrelevant, but what you publish? And besides, with currently 1.5 million papers being published every year, you need so many people that if for some reason you get into a feud with someone, there's plenty of others to chose from. And if someone publishes nonsense, post-publication review takes care of that.<br /><br />So I don't buy into the competition argument at all. Markets work. But nor everywhere and not for all purposes.<br />To which he replied:<br /><div class='indent'>Where I work I see corruption everywhere.<br />In my University, many things are monopolized by single committees or single regulatory bodies and this always produces favoritism, nepotism, power abuse etc.</div>But nobody owns the standard. The system depends critically on a standard to which all libraries subscribe. Think of it like email. Who owns smtp, or http? There is one single system, yet, no mafia, only spam (and that's what peer-review is for: not to eliminate, but at least to reduce spam).<br /><div class='indent'>A corrupt Editor-in-Chief can and does favor his relatives, his students, his protégés and publishes many things that make no sense or are sometimes fake. On the other hand, this same EiC blocks another person's papers from being published, and this makes his "mafia" get promoted faster so that he can control the department, etc...</div>Happens now and will be less later - because just publishing isn't rewarded. What is published is being rewarded, not just publishing.<br /><div class='indent'>I didn't mean competition in a political sense; I'm not exactly pro-free-market (nor against). However, any monopoly is scary to me. I'm thinking what if Google or Facebook decides suddenly to blackmail me, for example? I'm significantly dependent on them, and they have substantial amounts of my private communications. In addition, if there is no Microsoft or Yahoo, wouldn't Google slowdown the development of new tools etc.?</div>A standard in publishing is as much like a monopoly as http or smtp...<br />Of course existing publishers can join the standard, but why would they? There's no financial incentive for them anymore, because libraries provide the same service for less.<br /><div class='indent'>I don't trust post-publication tools will work very well.</div>Yet people love to publish papers falsifying someone else's papers. Science is a single, gigantic post-publication tool, that's how it works. What else is a paper other than a comment to all the papers listed in the references? It's just the formats that vary and that just takes acclimatization. With a common standard and a single database, all we're doing is just tapping the potential of something that has been there all along: multi-level communication. What I'm advertising is not the creation of something new - it's merely trying to stop historical baggage to prevent the potential discourse that is inherent to science from unfolding.]]></description>
<author>bjoern&lt;bjoern@nospam.com&gt;</author>
<pubDate>Wed, 24 Jun 2009 16:10:44 -0400</pubDate>
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						<title>I just talked 3.5h to Bob Doyle on the phone!</title>
<link>http://bjoern.brembs.net/news.php?item.525.5</link>
<description><![CDATA[I've just hung up the phone and need to write a short note to mark the occasion. <a href="http://en.wikipedia.org/wiki/Bob_Doyle" rel="external">Bob Doyle</a> had contacted my PhD supervisor <a href="http://en.wikipedia.org/wiki/Martin_Heisenberg" target="_blank">Martin Heisenberg</a> about his <a href="http://www.nature.com/nature/journal/v459/n7244/full/459164a.html" target="_blank"><em>Nature </em>article on free will</a> with a <a href="http://gfp.typepad.com/the_garden_of_forking_pat/2009/05/martin-heisenberg-on-free-will.html" target="_blank">blog post on the article</a>. Heisenberg then introduced Bob to me and our <a href="http://brembs.net/spontaneous">work on spontaneous behavior</a>. After a few exchanges, we quickly realized that we had come to very similar conclusions from basically opposite starting points, concerning the problem of free will. In a nutshell, <a href="http://informationphilosopher.com/freedom/cogito/" target="_blank">Bob's approach</a> entails to separate the 'free' from the 'will' and we think  we have <a href="http://www.plosone.org/doi/pone.0000443" target="_blank">found evidence</a> for a biologically plausible mechanism. So we scheduled a phonecall for this afternoon and it was amazing.<br />We covered not only free will and found that a bunch of people seemed to have been thinking along the same lines as we only that they neither knew of each other or had the possibility or the education to combine thoughts from such disparate fields as philosophy, physics and biology. We concluded that it is the internet which now brings all these ideas together. We went on and covered the <a href="http://informationphilosopher.com/solutions/experiments/ergodic_hypothesis/" target="_blank">ergodic hypothesis</a>, <a href="http://informationphilosopher.com/solutions/experiments/schrodingerscat/" target="_blank">Schrödinger's cat</a>, and eventually got back to the internet and how Bob was involved in the <a href="http://www.econtentmag.com/Articles/Column/I-Column-Like-I-CM/The-First-Podcast-13515.htm" target="_blank">first podcast</a>, and in the development of open source content management systems (he even knew <a href="http://e107.org">e107</a>, the CMS which this blog runs on) as well as collaboration software such as <a href="http://wiggio.com" target="_blank">Wiggio</a> which his sons are developing. The latter was especially interesting to me because we have just submitted a <a href="http://docs.google.com/Doc?id=ddwhqd6k_114dzdkxd2k" target="_blank">grant to develop collaboration systems for scientists</a>. From there we went onto the semantic web (a semantic organization is at the core of our grant proposal) and how he had introduced the <a href="http://www.memeticweb.org/" target="_blank">memetic web</a> back in 2005, a sort of crowd-sourced version of the semantic web. The whole time the evolution of the term "information" was weaved into the conversation, not surprisingly given his <a href="http://www.informationphilosopher.com" target="_blank">domain name</a>. As such, entropy, of course, was also a recurring topic.<br />Finally, Bob confessed he was now also thinking of getting his hads dirty: he was thinking about ethics! He thinks (and I tend to agree) that there probably is a pretty good correlation between acts we generally consider "good" and how well these acts preserve information (or generate negative entropy). I really liked that concept.<br />In total, I'm very energized and enthusiastic about the potential future of science in general. Now we just need to reform scholarly publishing to make it all a reality <img src='http://bjoern.brembs.net/e107_images/emotes/yellow/smile.png' alt='' style='vertical-align:middle; border:0' /><br /><br />At the very end of the conversation was a neat little event. I mentioned how much I had enjoyed our conversation and how quickly time had passed. I quoted the saying from the <em>Drosophila</em> community that "time's fun when you're having flies". Bob then told me that he had a flashback to his undergraduate university, Brown University, and a line that was written on one of the bathroom doors, which he hadn't thought about in 40 years but which was brought back with my little line:<br />Time flies<br />You can't - they go too fast<br /><br /><img src="http://bjoern.brembs.net/e107_images/emotes/yellow/elated.png" style="border: 0px none " alt="elated.png" /><br /><br />BTW, you can all congratulate Bob on his 73rd birthday it was exactly 5 days ago!]]></description>
<author>bjoern&lt;bjoern@nospam.com&gt;</author>
<pubDate>Wed, 24 Jun 2009 15:56:04 -0400</pubDate>
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						<title>Elsevier's on a run - towards more bad PR that is</title>
<link>http://bjoern.brembs.net/news.php?item.524.11</link>
<description><![CDATA[Publishing giant <a href="http://www.elsevier.com" rel="external">Elsevier</a> is really on a non-stop campaign for bad PR lately:<br /><ol><li>In April/May it became known that they had used funds from the pharmaceutical industry to create fake journals in a "stealth marketing campaign to Australian Doctors" (<a href="http://www.the-scientist.com/blog/display/55679/" target="_blank">The Scientist</a>). Elsevier statement: "This was an unacceptable practice, and we regret that it took place."</li><li>At about the same time, Elsevier's parent corporation, <a href="http://www.reed-elsevier.com" target="_blank">Reed Elsevier</a>, <a href="http://www.reed-elsevier.com/annualreport08/Pages/Home.aspx" target="_blank">reported</a> that 2008 was a record year both for the parent and Elsevier itself in terms of revenue and profit. When almost every other company on this planet was taking losses, a publisher relying mainly on taxpayer money raked in a whopping 716 million € in adjusted profits, a solid 3% more than the previous year (see presentation below for charts).</li><li>Now <a href="http://www.timeshighereducation.co.uk/story.asp?sectioncode=26&amp;storycode=407046&amp;c=1" target="_blank">this month</a>, Elsevier attempts to get universities to link to Elsevier's online content instead of hosting their own Open Access repositories.</li><li>A <a href="http://www.insidehighered.com/news/2009/06/23/elsevier" target="_blank">few days later</a>, the news surfaces that Elsevier has offered money for positive book reviews (for their own books, of course) on Amazon.com. Elsevier statement: "request(s) should be unbiased, with no incentives for a positive review, and that's where this particular e-mail went too far."</li><li>And finally, just <a href="http://digital-scholarship.org/digitalkoans/2009/06/23/elsevier-fails-to-block-release-of-its-licensing-contract-with-washington-state-university/" target="_blank">a few days ago</a>, Elsevier lost a lawsuit where they wanted to prevent their licensing practices from becoming public. Something they have to hide in their pricing schemes?</li></ol>And that's just the last three months. I wonder what's next? They're going to offer $25 discounts in their page charges for every Elsevier-citation in a manuscript published with them? Or add $25 to the page charges for every non-Elsevier citation? Seriously, would it surprise you?<br />Here some more info on other things wrong with how scientists do busieness these days, with quite a bit on Elsevier:<br /><br /><div style="width: 425px; text-align: left"><a href="http://www.slideshare.net/brembs/whats-wrong-with-scholarly-publishing-today-ii?type=powerpoint" title="What's wrong with scholarly publishing today? II" style="margin: 12px 0pt 3px; font-family: Helvetica,Arial,Sans-serif; font-style: normal; font-variant: normal; font-weight: normal; font-size: 14px; line-height: normal; font-size-adjust: none; font-stretch: normal; display: block; text-decoration: underline">What's wrong with scholarly publishing today?<br /></a><div style="margin: 0px" height="355" width="425"><div></div><div></div><div></div><object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=6,0,40,0" width="425" height="355"><param name="width" value="425" /><param name="height" value="355" /><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="src" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=whatswrong4ss-090619091933-phpapp02&amp;stripped_title=whats-wrong-with-scholarly-publishing-today-ii" /><embed type="application/x-shockwave-flash" width="425" height="355" allowfullscreen="true" allowscriptaccess="always" src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=whatswrong4ss-090619091933-phpapp02&amp;stripped_title=whats-wrong-with-scholarly-publishing-today-ii"></embed></object></div><div style="font-size: 11px; font-family: tahoma,arial; height: 26px; padding-top: 2px"><br /></div></div>]]></description>
<author>bjoern&lt;bjoern@nospam.com&gt;</author>
<pubDate>Wed, 24 Jun 2009 03:30:44 -0400</pubDate>
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						<title>Two positions in our lab</title>
<link>http://bjoern.brembs.net/news.php?item.523.5</link>
<description><![CDATA[I have now started the process of advertising for two positions in <a href="http://lab.brembs.net">our lab</a> (lab-site under construction; see also my <a href="publications.php">publications</a>). We have funds for 3 (maybe 5) years for a full-time technician and a graduate student. We are a small group of about 4-6 undergraduate students, a postdoc and me. We work in invertebrate neuroscience, in particular on the neurobiology of spontaneous behaviors, decision-making and operant learning in the fruit fly <em>Drosophila</em>. These topics not only fall within neuroscience, but also touch more general areas such as free will or the interactions of genes and environment. All of our experiments are computer-controlled, the data are digital and we try to use the latest social tools for communicating and organizing the lab. Therefore. an affinity towards using computers on a regular basis is definitely well-received in our lab.<br />The lab is located in Berlin, a vibrant city in the heart of Europe with a consumer price index below any other western metropolis. Close to our lab are other neuroscience institutes and we collaborate with other groups not only in our but also the other universities in Berlin.<br /><ul><li>The main job of the technician would be to take care of the fly stocks, prepare (and maybe conduct and evaluate) behavioral experiments, order consumables, prepare fly food and deliver corporal punishment to every member of the lab who doesn't clean up after him/herself (just kidding <img src="http://bjoern.brembs.net/e107_images/emotes/yellow/devilmad.png" style="border: 0px none " alt="devilmad.png" />). There may be one or the other standard method to be used, such as histology, immuno-assays, various blots or <em>in situ </em>hybridizations.</li><li>The project of the graduate student is to localize the neuronal circuitry necessary for <a href="http://brembs.net/spontaneous">spontaneous behavior</a> in the fruit fly. The student would learn all the tricks of the trade of modern <em>Drosophila </em>neurogenetics. Specifically, he/she will be crossing flies to express various manipulators of neuronal function in various areas of the brain and then evaluate the behavior of the flies. There is the opportunity to learn programming for the evaluation (in <a href="http://www.mathworks.com/" rel="external">MatLab</a>) as well as for setting up the computer-controlled experiments, but candidates with pre-existing proficiency in programming will of course have an advantage.</li></ul>]]></description>
<author>bjoern&lt;bjoern@nospam.com&gt;</author>
<pubDate>Fri, 19 Jun 2009 11:11:26 -0400</pubDate>
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						<title>Berlin university president anonymously accused of being a creationist</title>
<link>http://bjoern.brembs.net/news.php?item.522.5</link>
<description><![CDATA[Yesterday, there was an anonymous flyer posted on the door of our institute alleging that the president of our university, the <a href="http://www.fu-berlin.de/" rel="external">Freie Universität Berlin</a>, <a href="http://www.fu-berlin.de/en/einrichtungen/praesidium/praesident.html" target="_blank">Dieter Lenzen</a>, had come out as an "intelligent design" creationist. The first part of the flyer quoted from an <a href="http://www.tagesspiegel.de/meinung/kommentare/Dieter-Lenzen-Religion-Pro-Reli;art141,2780991" target="_blank">article by Lenzen in the Berlin newspaper "Tagesspiegel"</a> (my translation): <div class='indent'>I don't know if there is a god. Nobody knows that. What I do know is that the world around me, from the smallest molecule to the mechanics of the planets is an intelligent construction, which leads some to ask: Who has thought this up? To whom does this belong? Religion and religious education cannot give a definitive answer to that, but they can offer an answer: good religious education will not paint this god as a person, but rather as an acting principle."</div>This article was written just before a referendum on if and how public schools in Berlin schould have mandatory religious education. Hence, it mainly deals with ethics and morals and how to best teach school children morals and ethics. Nothing about evolution in that article. The referendum specifically asked the voters if the current ethics classes should be replaced by religious education classes (the referendum eventually failed and no mandatory religious education was introduced in Berlin). Lenzen is very qualified to write about how to teach children, as <a href="http://www.aktionsrat-bildung.de/index.php?id=20" target="_blank">he is professor of education science</a>. Taken in the context of the whole article, the quote may seem a little unfortunately worded, but hardly any evidence of underlying creationism.<br />In addition, creationism in Germany is quite a non-issue. Most people I talk to have never even heard the term and ask what it means. My own students don't really believe me, when I tell them that people still actually believe in creationism until they see some US websites (after seeing them they ask: do they also believe the earth is flat?). Any public voice that happens to have picked up some US-based rhetoric and regurgitates it in Germany is usually quickly laughed into oblivion. However, the flyer's second part cited from minutes that student Sebastian Schneider had written down from memory after a session of the "<a href="http://www.fu-berlin.de/en/einrichtungen/gremien/senat/index.html" target="_blank">Academic Senate</a>" of which Lenzen is the head. According to the flyer, Lenzen had confirmed his statement in the article with the following words (again my translation): <div class='indent'>It is proven that biology cannot sufficiently describe the origin of species. Phenomena like bifurcation, for instance, can be observed in so many different areas of biological development, that one has to assume an intelligent construction.</div>This statement is much less ambiguous. However, this quote comes from a member of the <a href="http://www.astafu.de/english/asta" target="_blank">AStA</a>, a general student council which is elected once a year by the student parliament and administers the affairs of the student body. In a <a href="http://www.astafu.de/aktuelles/archiv/a_2009/presse_04-28" target="_blank">press release which cites Schneider</a>, the AStA calls for the resignation of Lenzen, because of his alleged creationism. At least parts of the student body are also actively seeking to oust president Lenzen and <a href="http://annapanek.picturepush.com/album/34980/p-GER,-Berlin,-Nov-5th-2008:-Students%60-protest.html" target="_blank">have staged public protests against him before</a>.<br />From these accounts it all seemed highly unlikely that Lenzen is a creationist. The quote is ambiguous and out-of-context. The alleged statement in the senate from a student body known to oppose Lenzen, even asking for his resignation. Still, it appeared from his position on the referendum (his article argued for the introduction of mandatory religious education in public schools) that Lenzen might be religious. Furthermore, he is well-versed in the humanities, which sometimes (but by no means necessarily) comes with a certain lack of scientific understanding. It was thus conceivable that he could have picked up some IDiotic blurb somewhere, which has found its way into his article. Thus, despite the admittedly low probability, but because I thought it was an important enough question, I asked for a less ambiguous statement from the president of my university. Today I have received a very unambiguous answer from his press spokesman (paraphrased): <div class='indent'>FU President Lenzen is not a creationist. His sentences in the article are taken out of context. He has clarified these sentences in the senate and a motion to censure has been voted off, also by students present at the session.</div>Well, I guess that solves that issue. The question now is: who goes around posting anonymous accusations on the doors of our institute?]]></description>
<author>bjoern&lt;bjoern@nospam.com&gt;</author>
<pubDate>Thu,  4 Jun 2009 10:14:14 -0400</pubDate>
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						<title>Will science ride the Google Wave into the 21st century?</title>
<link>http://bjoern.brembs.net/news.php?item.521.3</link>
<description><![CDATA[Ok, I'll try to refrain from wave-puns as much as possible in this post, but it'll be hard, given the wave of  comments and opinion hitting the innerwebz these days. Oops, sorry. <img src="http://bjoern.brembs.net/e107_images/emotes/yellow/grin.png" style="border: 0px none " alt="grin.png" /><br />If you don't know what Google Wave is, there's plenty to read by now: The <a href="http://wave.google.com" rel="external">Google Wave site</a>, of course, <a href="http://www.techcrunch.com/2009/05/28/google-wave-drips-with-ambition-can-it-fulfill-googles-grand-web-vision/" target="_blank">TechChrunch</a>, <a href="http://www.web-strategist.com/blog/2009/05/29/google-wave-to-brings-web-20-lifestyle-to-work/" target="_blank">WebStrategist</a>, the official <a href="http://googleblog.blogspot.com/2009/05/went-walkabout-brought-back-google-wave.html" target="_blank">Google blog</a>, naturally, or <a href="http://radar.oreilly.com/2009/05/google-wave-what-might-email-l.html" target="_blank">O'Reilly</a>.<br />Or, you can just watch the 1:20hrs video of the keynote presentation, which is what I did and I did not regret it:<br /><br /><div height="340" width="560"><div></div><div></div><div></div><object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=6,0,40,0" width="560" height="340"><param name="width" value="560" /><param name="height" value="340" /><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="src" value="http://www.youtube.com/v/v_UyVmITiYQ&amp;hl=en&amp;fs=1" /><embed type="application/x-shockwave-flash" width="560" height="340" allowfullscreen="true" allowscriptaccess="always" src="http://www.youtube.com/v/v_UyVmITiYQ&amp;hl=en&amp;fs=1"></embed></object><br /><br />I've found three posts, so far which cover Google Wave from a scientist's perspective. Martin Fenner asks that <a href="http://network.nature.com/people/mfenner/blog/2009/05/28/google-wave-dont-forget-the-scientists" target="_blank">Google Wave mustn't forget the scientists</a>, Ricardo Vidal dreams of the <a href="http://my.biotechlife.net/2009/05/29/using-the-google-wave-to-surf-the-streams/" target="_blank">perfect (Google) Wave to surf the streams</a> and Cameron Neylon thinks that<a href="http://blog.openwetware.org/scienceintheopen/2009/05/30/omg-this-changes-everything-or-yet-another-wave-of-adulation/" target="_blank"> everything has changed in his wave of adulation</a>. Of course, I first learned about Google Wave from the <a href="http://friendfeed.com/cameronneylon/9864a4e7/omg-this-changes-everything-or-yet-another-wave" target="_blank">various </a><a href="http://friendfeed.com/cameronneylon/341021e4/finally-managed-to-get-end-of-google-wave" target="_blank">threads </a>on <a href="http://friendfeed.com/the-life-scientists/4d88961c/signing-up-to-be-notified-about-google-wave-wish" target="_blank">FriendFeed</a>.<br />It's not without some irony that the brain child of scientists - the internet - is now developing at such a rate, that we hopelessly outpaced scientists feel the urge to plead to a private company to not abandon us poor scientists. Some of us, after all, are spending roughly 5 billion € on the <a href="http://en.wikipedia.org/wiki/Large_Hadron_Collider#Cost" target="_blank">most complex experiment in the history of humanity</a>. Embarrassingly, I would posit that most of today's scientists use the internet for science at roughly the level of 1994: Browsing and e-mail. However, this should not keep us from joining the evolution of Web 3.0 and help develop Science 2.0 (see, even in our versioning we lag behind the general public). What could Google Wave do to bring the way science is done into the 21st century?<br /><ol><li>A great example of the abovementioned anachronism in science is paper writing. The bread-and-butter task in our publish-or-perish world. How do today's scientists write papers? They edit documents in MS Word and then send each other versions via e-mail. Which is what we have been doing since about 1994...<br />There have since been a few developments which a few scientists have picked up. Social bookmarking à la <a href="http://www.connotea.org/user/brembs" target="_blank">Connotea</a> or <a href="http://www.citeulike.org/user/brembs" target="_blank">citeUlike</a> is one area and social networks such as <a href="http://friendfeed.com/brembs" target="_blank">FriendFeed</a> or <a href="http://network.nature.com/people/brembs/profile" target="_blank">Nature Networks</a> is another (and many scientists use<a href="http://facebook.com" target="_blank"> Facebook</a> privately). One of the latest of them which I also use is <a href="http://www.mendeley.com" target="_blank">Mendeley</a>. Mendeley cooperates with citeUlike such that you can add papers from a website to your collection and then add/edit the references in your manuscript from your collection. Having had a look at the editing capabilities of Google Wave, it is clear that one of the first things we as scientists should do is to add collaborative reference management and figure/table numbering to the rich text editing capabilities. Martin Fenner lists this feature on <a href="http://network.nature.com/people/mfenner/blog/2009/05/28/google-wave-dont-forget-the-scientists" target="_blank">his blog post</a> and we're discussing it at <a href="http://friendfeed.com/the-life-scientists/f714a1f1/so-how-about-mendeley-being-first-to-write">FriendFeed</a>. Of course, collaborative editing doesn't stop at papers: grants, lab-wikis, institute websites, manuals, protocols, fridge content, who's up for journal club?, which machine is currently broken/working, where is item X?, who's going to the conference? Which posters are you going to look at?.... the list goes on and on! Google Wave has solutions for all of these processes - today.<br />Obviously, any sort of peer-review is also set to profit tremendously from such collaborative editing - isn't that one definition of peer-review?<br /></li><li>Another workflow that is seriously outdated is the way collaborations are run <em>during </em>the project. Today, hardly a project is conducted by the lone researcher in a dark lab. Mostly, it's (international, transcontinental) teams of scientists with various specialisations. How do scientists today update each other on their various projects? Scientist A meets scientist B at a conference: "Oh, and by the way, we found that thing we were supposed to be looking for - it's not what you thought". Or: scientist A emails scientist B: "hey, it just occurred to me it's been like forever. Have you guys found that thing yet?". If as many scientists will be using Google Wave as are using e-mail today, the progress is posted (automatically, if the experiment is automated) to the wave of the project for all participants to see in real time. This is actually a feature of a grant proposal we just sent to the German funding agency (<a href="http://www.dfg.de/aktuelles_presse/information_fuer_die_wissenschaft/andere_verfahren/info_wissenschaft_09_09.html" target="_blank">DFG</a>). We used a predecessor of Google Wave, <a href="http://docs.google.com/Doc?id=ddwhqd6k_114dzdkxd2k" target="_blank">Google documents, to draft the proposal</a>. We might as well now tell the funding agency that the methodology we said we would employ in our grant proposal is already outdated and that we'll be looking into using Google Wave. See also our<a href="http://friendfeed.com/brembs/505f8f9e/funding-opportunity-for-open-science-in" target="_blank"> discussion of this grant on FriendFeed</a>. Automated data logging aspect was also covered in <a href="http://blog.openwetware.org/scienceintheopen/2009/05/30/omg-this-changes-everything-or-yet-another-wave-of-adulation/" target="_blank">Cameron Neylon's post</a>.<br /></li><li>If everybody is using Google Wave as people are using e-mail today, every contribution of each scientist to every project will be logged and timestamped. Author contributions, database developments/contributions, expriments, ideas, interpretations, anything could be used and attributed. We'd have an entirely new reputation system at our hands, one that could finally replace the centuries old 'publish-or-perish'. If people are saying that <a href="http://venturebeat.com/2009/05/28/does-google-wave-mean-the-death-of-gmail-and-google-docs/" target="_blank">e-mail died last Thursday</a>, the<a href="comment-n397.html"> Impact Factor</a> died along with it.</li></ol>A main factor driving adoption (besides the features and potential) of Google Wave will be that it's going to be Open Source as well as a new standard (federal) protocol, similar to the SMTP on which e-mail is running today. This means, you could set up your own version of Google Wave and keep it and any contents in it entirely secret and hidden from public view, just like current intranets. It will be interesting how companies like Facebook and Friendfeed will react to Google Wave, as their functionality is in serious competition by Google Wave. Some think <a href="http://nicolas.lehuen.com/index.php/post/2009/05/29/FriendFeed-might-actually-benefit-from-Google-Wave" target="_blank">Friendfeed might actually benefit</a>.<br /><br />In all this hype and enthusiasm, it only remains to wonder what a company could possibly gain from making more than two years of R&amp;D open source and to push for an open standard. Surely, Google will not give all this effort away for free. They may speculate on a head start in developing Wave clients (or servers). They may release basically unusuable code in to the open. Who knows. True non-profit standards are rarely developed by for-profit industries, so scientists need to remain skeptical and prepared to find their own solutions until we have all the code in our hands.<br /><br />UPDATE: There's a <a href="http://www.suntimes.com/business/1606282,ihnatko-google-wave-060309.article" target="_blank">great article</a> over at the Chicago Sunday Times explaining what exactly Google Wave is.<br /></div>]]></description>
<author>bjoern&lt;bjoern@nospam.com&gt;</author>
<pubDate>Sun, 31 May 2009 12:28:12 -0400</pubDate>
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						<title>In which a Nature paper fails on several levels</title>
<link>http://bjoern.brembs.net/news.php?item.519.3</link>
<description><![CDATA[<span style="padding: 5px; float: left"><a href="http://www.researchblogging.org"><img src="http://www.researchblogging.org/public/citation_icons/rb2_mid.png" style="border: 0pt none " alt="ResearchBlogging.org" /></a></span> Ok, so what else is new? We all love to rip GlamMag paperz to shreds in our journal clubs. This paper by <a href="http://www.nature.com/nature/journal/v454/n7205/full/nature07090.html" rel="external">Hong et al.</a> last year in <em><a href="htp://nature.com/nature" target="_blank">Nature</a> </em>stands out of the crowd in two main ways. For one, it shows how failing to realize alternative explanations can easily break your entire publication. Moreover, it shows how generating large datasets doesn't replace using your brain when generating and evaluating them. Apparently, the editors and reviewers at <em>Nature </em>handling this particular manuscript failed to take this into account this one time.<br />The authors went through unbelievable efforts to test an enormous number of different wild type, mutant and transgenic <em>Drosophila </em>strains for their temperature preference. Based on only 8 authors, it seems to me these authors must have worked 24/7 for many, many months to get all this data, evaluate them and discuss and compile all the results. Here's their experiment:<br /><br /><img src="http://bjoern.brembs.net/e107_images/newspost_images/hong1.jpg" style="border: 0px solid black; width: 450px; height: 516px" alt="hong1.jpg" /><br /><br />Pretty self explanatory: the flies walk around in a chamber with a temperature gradient and where they spend most of their time determines their temperature preference. From this sort of data, the authors calculate a preference index for high or low temperatures, respectively:<br /><br /><img src="http://bjoern.brembs.net/e107_images/newspost_images/hong2.jpg" style="border: 0px solid black; width: 450px; height: 390px" alt="hong2.jpg" /><br /><br />According to their graph, flies walking around incessantly score an AI of zero both for high temperatures and for low temperatures (center pane of the graph). There is a structure in the <em>Drosophila </em>brain that is associated with hyperactivity: the mushroom-bodies. The study was published exactly ten years before Hong et al.: <a href="http://learnmem.cshlp.org/content/5/1/179.long" target="_blank">Mushroom bodies suppress locomotor activity in <em>Drosophila melanogaster</em></a>. Apparently, the authors are unaware of this publication, as they don't even cite it. However, the authors of this previous paper have used a very similar setup (horizontal tubes) and tested flies for their walking activity:<br /><br /><a href="http://learnmem.cshlp.org/content/5/1/179/F4.large.jpg" target="_blank"><img src="http://learnmem.cshlp.org/content/5/1/179/F4.medium.gif" style="border: 0px solid black" /></a><br /><br />In this graph (Fig. 2 from Martin et al., 1998), the mutant mbm1 as well as transgenic fly strains which have synaptic activity blocked in various parts of the mushroom-bodies (line 201Y, H24 and 17D) show increased walking activity. Now let's see how these flies perform in the temperature assay from Hong et al. (Fig. 1, modified to show just selected strains):<br /><br /><img src="http://bjoern.brembs.net/e107_images/newspost_images/hong3.jpg" style="border: 0px solid black; width: 462px; height: 300px" alt="hong3.jpg" /><br /><br />As expected, the flies show an AI of around zero (with black bars denoting AI low and grey bars AI high). But Hong at al. have not suspended critical thought entirely before they submitted the results of their intensely laborious screening efforts. They realized there was a need to control for some sort of locomotion defects in the flies they tested. However, their control also fails on several levels: a) they used a climbing assay when in their temperature assay the flies were walking horizontally and b) the climbing performance in their assay could only decline and not increase:<br /><br /><img src="http://bjoern.brembs.net/e107_images/newspost_images/hong4.jpg" style="border: 0px solid black; width: 553px; height: 212px" alt="hong4.jpg" /><br /><br />Thus, the authors could not detect the increase in walking performance that inhibiting mushroom-body function conveys (Martin at al., 1998).<br /><br />In summary: Hong et al. conclude that the mushroom-bodies are involved in temperature preference by using a locomotor assay that reproduces the results of an experiment published ten years earlier (Martin et al. 1998). Somehow adding insult to injury, they tested an absolutely incredible number of fly strains (more than 120, by my count), yielding no less than <a href="http://www.nature.com/nature/journal/v454/n7205/extref/nature07090-s1.pdf" target="_blank">30 pages of supplementary material</a> with many figures, tables, text and references (but again, no citation of Martin et al. 1998 in there). Yet, they only manage to show the same thing as Martin et al. in 1998 with 10% the number of strains.<br /><br /><u>Important</u>: Of course, all this does not <em>exclude </em>that the mushroom-bodies and the processes in the neurons there controlling cAMP level indeed may be involved in temperature sensing and temperature preference. It's only that Hong et al. haven't shown that, yet.<br /><br /><hr><strong class='bbcode bold'>References:</strong><br /><br /> <span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Nature&rft_id=info%3Adoi%2F10.1038%2Fnature07090&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=cAMP+signalling+in+mushroom+bodies+modulates+temperature+preference+behaviour+in+Drosophila&rft.issn=0028-0836&rft.date=2008&rft.volume=&rft.issue=&rft.spage=0&rft.epage=0&rft.artnum=http%3A%2F%2Fwww.nature.com%2Fdoifinder%2F10.1038%2Fnature07090&rft.au=Hong%2C+S.&rft.au=Bang%2C+S.&rft.au=Hyun%2C+S.&rft.au=Kang%2C+J.&rft.au=Jeong%2C+K.&rft.au=Paik%2C+D.&rft.au=Chung%2C+J.&rft.au=Kim%2C+J.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CResearch+%2F+Scholarship%2CNeuroscience%2CBehavioral+Biology%2C+Ecology%2C+Evolutionary+Biology%2C+Genetics%2C+Zoology">Hong, S., Bang, S., Hyun, S., Kang, J., Jeong, K., Paik, D., Chung, J., &amp; Kim, J. (2008). cAMP signalling in mushroom bodies modulates temperature preference behaviour in Drosophila <span style="font-style: italic;">Nature</span> DOI: <a rev="review" href="http://dx.doi.org/10.1038/nature07090">10.1038/nature07090</a></span><br><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Learning+and+Memory&rft_id=info%3Adoi%2F10.1101%2Flm.5.1.179&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Mushroom+Bodies+Suppress+Locomotor+Activity+in+Drosophila+melanogaster&rft.issn=&rft.date=1998&rft.volume=5&rft.issue=&rft.spage=179&rft.epage=191&rft.artnum=http%3A%2F%2Flearnmem.cshlp.org%2Fcontent%2F5%2F1%2F179.long&rft.au=1.+Jean-Ren%C3%A9+Martin&rft.au=2.+Roman+Ernst&rft.au=3.+Martin+Heisenberg&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CNeuroscience%2CBehavioral+Biology%2C+Genetics%2C+Zoology%2C+Behavioral+Neuroscience%2C+Molecular+Neuroscience">1. Jean-René Martin, 2. Roman Ernst, &amp; 3. Martin Heisenberg (1998). Mushroom Bodies Suppress Locomotor Activity in Drosophila melanogaster <span style="font-style: italic;">Learning and Memory, 5</span>, 179-191 DOI: <a rev="review" href="http://dx.doi.org/10.1101/lm.5.1.179">10.1101/lm.5.1.179</a></span>]]></description>
<author>bjoern&lt;bjoern@nospam.com&gt;</author>
<pubDate>Sun, 17 May 2009 10:21:01 -0400</pubDate>
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