I think my interest in modern art was sparked by the Documenta 8 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, Marc Wellman, 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 Georg-Kolbe-Museum for the exhibit "Romantische Maschinen" (romantic machines, program in PDF) and we were not disappointed! Fittingly enough, the exhibition started with a piece from the Documenta 8, the movie "Der Lauf der Dinge" (the way things go):
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 spontaneous behavior, 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. The next piece was something for all senses: an old cement mixer, refurbished to roast popcorn: 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. The third object was a very fragile-looking piece, seemingly cobbled together from what the artist had standing around: 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. The next piece was the one that captivated me the most. For me it embodied the essence of 'romantic machines'. It's "Time Machine" (there's also video on that page) by Robert Barta: There is a small, red electric locomotive (which so reminded me of "the little engine that could") 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 Metropolisian 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. A very dynamic exhibit was O2 by Zilvinas Kempinas. 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:
I was mesmerized at the sight of the hovering band and felt why it fitted very well into the category of 'romantic machines'. The next exhibit that invited me to stop and think was a mirror my Johanna Smiatek. 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 Narcissus, 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. The technically most advanced exhibit was the bit.reflection installation by Julius Popp of bit.fall fame: 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.
On the outside, in a wall separating two parts of a central yard, is a bee-hive from Bärbel Rothaar: 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 here. It seems, science and technology have now become so dominant in our culture (this sounds almost like I think it's a bad thing! , 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. 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.
Managing Editor of PLoS One, Peter Binfield, recently published a paper entitled "PLoS One: background, future development, and article-level metrics"in which he outlines some of the recent upgrades at PLoS One and future plans for article-level metrics. What Pete also mentioned in the article is the doubling in articles published every year:
2007: 1,231 articles
2008: 2,722 articles
2009: ~4,300 articles
2010: ~1% of PubMed?
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. 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.
Listening to this week's Nature podcast I became aware of something I haven't read anywhere else so far. Since this issue of Nature (and the podcast) has "science journalism" as the theme and Maxine Clarke asked us to contribute some discussion, I thought I could write down what I was pondering about whilst listening to the podcast. It was a comment from The Guardian's James Randerson, 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. 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 where you publish than what 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. 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, I recently blogged about a paper in Nature 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.
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. He wrote:
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.
I replied: 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.
So I don't buy into the competition argument at all. Markets work. But nor everywhere and not for all purposes. To which he replied:
Where I work I see corruption everywhere. In my University, many things are monopolized by single committees or single regulatory bodies and this always produces favoritism, nepotism, power abuse etc.
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).
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...
Happens now and will be less later - because just publishing isn't rewarded. What is published is being rewarded, not just publishing.
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.?
A standard in publishing is as much like a monopoly as http or smtp... 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.
I don't trust post-publication tools will work very well.
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.
Wednesday 24 June 2009 - 16:10:44
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I've just hung up the phone and need to write a short note to mark the occasion. Bob Doyle had contacted my PhD supervisor Martin Heisenberg about his Nature article on free will with a blog post on the article. Heisenberg then introduced Bob to me and our work on spontaneous behavior. 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, Bob's approach entails to separate the 'free' from the 'will' and we think we have found evidence for a biologically plausible mechanism. So we scheduled a phonecall for this afternoon and it was amazing. 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 ergodic hypothesis, Schrödinger's cat, and eventually got back to the internet and how Bob was involved in the first podcast, and in the development of open source content management systems (he even knew e107, the CMS which this blog runs on) as well as collaboration software such as Wiggio which his sons are developing. The latter was especially interesting to me because we have just submitted a grant to develop collaboration systems for scientists. 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 memetic web 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 domain name. As such, entropy, of course, was also a recurring topic. 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. 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
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 Drosophila 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: Time flies You can't - they go too fast
BTW, you can all congratulate Bob on his 73rd birthday it was exactly 5 days ago!
Wednesday 24 June 2009 - 15:56:04
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Publishing giant Elsevier is really on a non-stop campaign for bad PR lately:
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" (The Scientist). Elsevier statement: "This was an unacceptable practice, and we regret that it took place."
At about the same time, Elsevier's parent corporation, Reed Elsevier, reported 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).
Now this month, Elsevier attempts to get universities to link to Elsevier's online content instead of hosting their own Open Access repositories.
A few days later, 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."
And finally, just a few days ago, Elsevier lost a lawsuit where they wanted to prevent their licensing practices from becoming public. Something they have to hide in their pricing schemes?
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? Here some more info on other things wrong with how scientists do busieness these days, with quite a bit on Elsevier:
I have now started the process of advertising for two positions in our lab (lab-site under construction; see also my publications). 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 Drosophila. 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. 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.
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 ). There may be one or the other standard method to be used, such as histology, immuno-assays, various blots or in situ hybridizations.
The project of the graduate student is to localize the neuronal circuitry necessary for spontaneous behavior in the fruit fly. The student would learn all the tricks of the trade of modern Drosophilaneurogenetics. 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 MatLab) as well as for setting up the computer-controlled experiments, but candidates with pre-existing proficiency in programming will of course have an advantage.
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."
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 he is professor of education science. Taken in the context of the whole article, the quote may seem a little unfortunately worded, but hardly any evidence of underlying creationism. 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 "Academic Senate" 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):
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.
This statement is much less ambiguous. However, this quote comes from a member of the AStA, a general student council which is elected once a year by the student parliament and administers the affairs of the student body. In a press release which cites Schneider, 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 have staged public protests against him before. 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):
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.
Well, I guess that solves that issue. The question now is: who goes around posting anonymous accusations on the doors of our institute?
Thursday 04 June 2009 - 10:14:14
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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. If you don't know what Google Wave is, there's plenty to read by now: The Google Wave site, of course, TechChrunch, WebStrategist, the official Google blog, naturally, or O'Reilly. Or, you can just watch the 1:20hrs video of the keynote presentation, which is what I did and I did not regret it:
I've found three posts, so far which cover Google Wave from a scientist's perspective. Martin Fenner asks that Google Wave mustn't forget the scientists, Ricardo Vidal dreams of the perfect (Google) Wave to surf the streams and Cameron Neylon thinks that everything has changed in his wave of adulation. Of course, I first learned about Google Wave from the various threads on FriendFeed. 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 most complex experiment in the history of humanity. 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?
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... There have since been a few developments which a few scientists have picked up. Social bookmarking à la Connotea or citeUlike is one area and social networks such as FriendFeed or Nature Networks is another (and many scientists use Facebook privately). One of the latest of them which I also use is Mendeley. 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 his blog post and we're discussing it at FriendFeed. 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. Obviously, any sort of peer-review is also set to profit tremendously from such collaborative editing - isn't that one definition of peer-review?
Another workflow that is seriously outdated is the way collaborations are run during 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 (DFG). We used a predecessor of Google Wave, Google documents, to draft the proposal. 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 discussion of this grant on FriendFeed. Automated data logging aspect was also covered in Cameron Neylon's post.
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 e-mail died last Thursday, the Impact Factor died along with it.
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 Friendfeed might actually benefit.
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&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.
UPDATE: There's a great article over at the Chicago Sunday Times explaining what exactly Google Wave is.
Ok, so what else is new? We all love to rip GlamMag paperz to shreds in our journal clubs. This paper by Hong et al. last year in Naturestands 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 Nature handling this particular manuscript failed to take this into account this one time. The authors went through unbelievable efforts to test an enormous number of different wild type, mutant and transgenic Drosophilastrains 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:
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:
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 Drosophilabrain that is associated with hyperactivity: the mushroom-bodies. The study was published exactly ten years before Hong et al.: Mushroom bodies suppress locomotor activity in Drosophila melanogaster. 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:
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):
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:
Thus, the authors could not detect the increase in walking performance that inhibiting mushroom-body function conveys (Martin at al., 1998).
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 30 pages of supplementary material 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.
Important: Of course, all this does not exclude 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.
References:
Hong, S., Bang, S., Hyun, S., Kang, J., Jeong, K., Paik, D., Chung, J., & Kim, J. (2008). cAMP signalling in mushroom bodies modulates temperature preference behaviour in DrosophilaNature DOI: 10.1038/nature07090 1. Jean-René Martin, 2. Roman Ernst, & 3. Martin Heisenberg (1998). Mushroom Bodies Suppress Locomotor Activity in Drosophila melanogaster Learning and Memory, 5, 179-191 DOI: 10.1101/lm.5.1.179
Today, I have finished ther ancient and rather anachronistic procedure of habilitation. First, I had to show that I had enough teaching experience and then write a habilitation monograph which, thankfully, consisted of summarizing and discussing a selection of my publications. Then I had to wait for a long time and in this time do some more teaching. After the teaching I had to show that I could also teach about subjects which were far outside of my area of expertise, so I talked about "Microbe wars: the ecology and toxicology of bacterial toxins".
Finally, after about 25 minutes of questions after this 30 minute lecture and an additional deliberation time for the committee, I was handed the habilitation diploma:
So now I'm officially allowed to apply for tenured professorships in Germany (if there were any which would suit my specialty, that is) . In about 4 weeks time, I will be allowed to call myself not only Dr. Brembs, but even Dr. habil. Brembs. Not that anybody really cares, lol
Wednesday 13 May 2009 - 12:47:52
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I was recently alerted to a group of theoretical publications which deal with the issue of apparent 'noise' in neuronal populations. The Nature Reviews Neuroscience article "Neural correlations, population coding and computation" by Bruno B. Averbeck, Peter E. Latham & Alexandre Pouget covers this area quite well. Basically, the authors claim that the variability one can see when recording from the brain when the same stimulus is presented repeatedly is noise and must be detrimental for the tranmission of information and hence a problem the brain must solve:
Part of the difficulty in understanding population coding is that neurons are noisy: the same pattern of activity never occurs twice, even when the same stimulus is presented. Because of this noise, population coding is necessarily probabilistic. If one is given a single noisy population response, it is impossible to know exactly what stimulus occurred. Instead, the brain must compute some estimate of the stimulus (its best guess, for example), or perhaps a probability distribution over stimuli.
It needs to be noted that the authors do not refer to sensory neurons, which code sensory information with great precision. Instead, they look at neurons deep in the mammalian brain, many synapses away from the primary sensory afferents. What I don't understand from their article is why this should be considered 'noise'. Obviously, if high fidelity between the site of sensory input and the site of recording were required, there would be a single axon going there, and not via many syapses. Synapses are time consuming and energetically expensive. During development, unused synapses are being pruned throughout the brain. Thus, the variability must reflect some computation which takes place in the synapses from the site of sensory input to the site of recording. Let me illustrate this with a picture:
Of course, if one records from neuron NR and stimulates sensory neuron NS, as in A, there is a lot of processing going on in the synapses along N1-4. This is happening even without any external input into the single conveyor belt of information. Of course, there never is such a conveyor belt, that idea is already misleading. After the very first synapse (from wherever you start), there are always inputs from other sites, feed-forward and feedback connections, etc. But even in this simplest model of information transmission, every synapse is a computational component and not just a link between neurons adding variability to the sensory signal for no reason. These synapses would not be there if this processing was not some important brain function. This is illustrated in B: if simple and reliable information transmission from NS to NR were important, there would only be one single axon from NS to NR, without any additional processing.
I would really like to hear good arguments as to why the recorded variability should be 'noise' and a problem for information coding, rather than a reflection of the brain doing what it's supposed to do: finding out what the best action is under the current circumstances. Averbeck, B., Latham, P., & Pouget, A. (2006). Neural correlations, population coding and computation Nature Reviews Neuroscience, 7 (5), 358-366 DOI: 10.1038/nrn1888
I arrived a few days early on the big island of Hawaii, for the conference of the Society for the neural control of movement. Probably not surprisingly, for a European, there's plenty of exotic wildlife to observe. Unfortunately, I don't have the right equipment for taking pictures of small creatures, so these crude attempts will have to do as a teaser of how much fun we're having here and what kind of animals we've seen so far. If anybody knows the species of these animals, please leave a message in the comments section:
Now what's up with creationists that they think being a naked vegetarian is so appealing? This item on Friendfeed reminded me of the cognitive dissonance: On the one hand, religious fundamentalists of any religion abhorr nudity and evangelicals in the US (the main religion supporting creationism) are no exception. I've also never read anything about christian veganism, on the contrary, they delight in ceremonious cannibalism (wafers turning into Jesus?). On the other hand, they firmly believe that god's original plan was to hang out in a garden full with naked vegetarians. I think they should try and raise some money for a bus campaign:
Imagine a young scientist (Daniel) who has discovered the mechanism by which the stress caused by constant social defeat leads to epigenetic modifications in the germline of rats. These modifications lead to submissive behavior in the offspring of the stressed rats. Now this scientist is put under pressure from his corporate sponsors to test his results in humans in order to 'cure' the social underclass from their loser mentality. In his plight, Daniel tests his ideas on the poor guy who delivers his experimental rats (Korn). Korn is a typical underdog who keeps getting beat down by the system, can't hold a job and is just the kind of person Daniel has been looking for. Just as his secret experiments are being discovered, Korn is kidnapped... If you think this sounds like an interesting and entertaining plot, you should see "Wild Werden. Ein Notstand". It plays at the Staatstheater Karlsruhe on May 20, 2009, 8pm. It has premiered there on February 22, you can see some pictures here. There's also a critique available at the site of the theater. I have been somewhat invovled in some aspects of the script, as the two directors of the play, Jörn J. Burmester and Stefan Nolte have been discussing their ideas with me and asked for my scientific advice. I haven't seen the play, yet, but I plan to travel to Karlsruhe to see how it has turned out. The play uses the outlined plot to address the issue of what our society considers "sick" and in need of a cure. What is the 'better' human? When does scientific innovation turn to hubris?
Wednesday 08 April 2009 - 10:45:09
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I promised in another post that I would link to my article in the German periodical "Laborjournal" as soon as it would appear online. Well, it has happened! The article is basically a how-to describing the necessary steps for publishing your scientific method in the peer-reviewed video journal JoVE. All German-speaking scientists can now go ahead and read it
Thursday 02 April 2009 - 13:03:47
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Maybe I should consider myself lucky. Only now has the credit crunch hit somewhere close to home. And it's not even that close. Many, many others have of course suffered much, much worse. Nevertheless, I feel these recent developments as a personal setback. What has happened? In a somewhat unusual way, I have discovered that the online video journal JoVE has gone closed access. This is unusual, because I'm an Associate Editor at JoVE and had no clue what was going on. Of course, it would've been less of a sudden hit if I had been warned ahead of time. Albeit, the people running JoVE apparently had more pressing things to do than keeping equally busy editors abreast. Which goes to show how the young startup is struggling to make ends meet in the current financial climate. Other people have also weighed in with their opinions. Noah Grey blogged at Nature Networks and Abishek Tiwari criticises "blind supporters of open access". This development is cause for concern. The FriendFeed discussion covers a lot of the issues. The main problem in my eyes is that funds need to be shifted from libraries (=recipients) to the individuals who are producing the content (=contributors). This is a general OA problem which becomes easier as publication costs keep plummeting due to online publishing. If the costs are comparatively low, contributors can pay to publish. However, this ideal seems to fail with high-quality video publishing which still is very expensive. A regular publication in JoVE costs many times the price of a regular paper in a traditional scientific journal. For this simple reason, JoVE faced the choice of closed access video methods or no video methods. Given this choice, of course closed access video methods is better than no video methods. Therefore, I support this decision and will talk to my library about subscribing to JoVE. Going forward, it will be a challenge to sustain a constant revenue stream for JoVE. It's still too new to have prestige to publish in it and the reputation for quality which generates demand. I remain cautiously optimistic, though, as JoVE is a great journal and eventually people will realize what an asset to science JoVE is.
Slowly but surely, PLoS One is starting to roll out the eagerly awaited article-level metrics. Of course, I feel more than a little flattered that our paper on "Order in spontaneous behavior" is one of the first articles showing off the new features. From the information the PLoS One Academic Editors received:
This redesign represents the start of a very important new project to begin placing contextual information on each PLoS article (not just PLoS ONE), in order to provide readers with new ways to evaluate the usefulness of that article and to help them find other related articles that might be of interest to them.
Each article now shows three different tabs:
Article: Much of the content in the right hand column has been moved into the other tabs to make way for new features. Links to the appropriate issue or collection appear in the right hand column of the article page. In PLoS ONE related subject categories have been added to the right hand column to allow easy access to other related articles. We've also designed the right hand column to allow for some new feature growth in the future (e.g. user tags).
Related Content: Data from external sources is provided on the this tab. Sources include the number of citations from PubMed Central and Scopus; the number of bookmarks from CiteULike and Connotea; and the number of blog posts linking to the article from Postgenomic, Nature Blogs and Bloglines. More sources will be added in the future.
Comments: All of the comments, minor corrections and formal corrections are easily viewed in one location.
More details on the upgrade to the latest Topaz version can be found on the PLoS blog. This is an exciting development! These new features (and more will be coming!) put PLoS One at the forefront of the new developments leading to actually measuring the effect individual articles have on the scientific and general community, rather than just assuming that some individual article must be 'good' simply because it was published in a journal where some other 'good' articles have been published.
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, 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.
). There may be one or the other standard method to be used, such as histology, immuno-assays, various blots or in situ hybridizations.
