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Jun02

Cut out the parasitic middle men!

In: science politics • Tags: libraries, open access, publishing, SciELO

Academic publishers have been parasitizing the public purse for long enough now. Steffen Böhm, director of the Essex Sustainability Institute, said it best:

By cutting out the parasitic publishing middle men, the academy could reclaim control of its knowledge, funding and labour.

In his article, he mentions the successful SciELO project in South America. In a lot of ways, SciELO (scielo.org) is quite close to what I have been arguing for: SciELO means “Scientific Electronic Library Online” and is supported by the Brazilian and Chilean government. It currently publishes about 900 scientific journals which are all fully openly accessible. The Latin American and Caribbean Center on Health Sciences Information (BIREME – Biblioteca Regional de Medicina) spearheaded conception, design and implementation of SciELO, with special assistance from the US National Library of Medicine. Ten of SciELO’s 15 national collections are funded more or less directly by governments, five by universities. SciELO publishes and archives everything in marked-up full-text, meaning that the entire full-text is machine-readable and hence exquisitely (re-)useful. In essence, with a decentralized database like SciELO, any and all possible metrics (if one really wants/needs them) are just a few lines of code away.

The success of SciELO demonstrates that our institutions, our libraries, big and small, collectively have all it takes to cut out the parasitic middle men that annually gobble up billions and tax funds that are dearly missed in our budgets. We have the know-how, the infrastructure, that funding, the workforce, the technology and even plenty of examples where such a take-over (actually, take-backs) has worked on a smaller scale. All we need to do is to get some coordination among major players going and there will be many birds hit with one stone:

  • Immediate, fully open access to all publicly funded research world wide – text, data and software
  • The equivalent of approximately 4 billion US dollars saved annually
  • An incredible market for innovation, e.g.
    • what are the best ways to present scientific data in the most flexible way?
    • can we write programs that construct (and test) hypotheses by crawling this vast scientific space?
    • What possible additional uses can be developed from such a resource?
  • A single place to find scientific information
  • Long-term archive security
  • Any functionality of the current journal system still deemed relevant is easily copied.

The only thing keeping us from this digital utopia are commercial publishers and the politicians they buy with our money (either directly or via lobbying). Oh and then, of course, there is the tiny issue of journal rank. Big Smile


UPDATE: Approximate cost for a paper in SciELO is ~90US$. Given an annual world-wide publication output of roughly two million papers per year, that would amount to a total cost of publishing new articles of around 180 million US$ for the entire planet. Add to that approximately 200k US$ annually for infrastructure and related costs, and you are still way below 200m total annual costs for academic publishing, fully open access. If that were shared only between the roughly 9000 universities world-wide (i.e., without additional contributions from governments directly), the total average cost per university and year would amount to just over 20,000 US$. With every German library spending, on average >600k on subscriptions, this would entail windfall savings for each institution.

Compare that to the current academic publishing market running at an estimated 12 billion in sales. With about 30% or 4b in publisher profits, current costs of academic publishing are inflated by more than 7.8b. In other words, switching to a library/institution-based publishing system akin to that realized in SciELO would provide savings closer to 11b than to 4b.

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Posted on June 2, 2013 at 17:06 Comments Off on Cut out the parasitic middle men!
May30

Dissecting a fly’s course control system

In: researchblogging • Tags: Drosophila, inverting goggles, neurogenetics, operant, optomotor, rol sol

ResearchBlogging.orgUntil 1986, it was thought that so-called optomotor responses, i.e., the tendency of all animals and humans to follow moving visual stimuli with their eyes or their bodies, were a prerequisite for gaze or trajectory stabilization: whenever the scenery in your gaze moves, you adjust gaze or body orientation to compensate for the shift. The main concept was that these behaviors were responses to external stimuli, e.g., shift to the left elicits a counter movement to compensate for the shift. Without such simple input-output processes, it was thought, it would be impossible to maintain course or gaze. However, in 1986, Wolf and Heisenberg reported on experiments in Drosophila fruit flies with drastically reduced optic lobes, the primary visual processing centers of insects. These flies with the double mutation rol (reduced optic lobes) sol (small optic lobes, see figure 1) were incapable of performing optomotor responses to rotating stimuli, but nevertheless fixated a stripe in their frontal visual field if they were allowed to control the position of that stripe with turning maneuvers that were simultaneously recorded. In other words, the flies could not see in which direction the stripe was moving, but nevertheless managed to move the stripe in a way that fixated it preferentially in front of the flies. Further experiments showed that the only way the flies could possibly accomplish this feat is by ‘trying out’ which turning maneuver led to the stripe staying in the frontal part of their visual field – an operant (or, as one would also say today, goal-directed) behavior. For more details on this and two related classic experiments from the Heisenberg lab see “The Importance of Being Active“.

rolsol

Fig. 1: Side by side comparison of the brains of wild type (WT) and rol sol double mutant flies (click to enlarge).

Now Bahl et al. in the lab of Alexander Borst (a graduate student of Heisenberg‘s from 1982-84) have not only replicated this seminal study, they have done so in an impressively sophisticated and meticulous manner, avoiding many if not all of the methodical problems of the original experiments and adding exciting new findings to our body of knowledge along the way. Their fabulous publication constitutes a shining example of the power of combining today’s genetic technology with state-of-the-art behavioral physiology and computational modeling. Technically, it doesn’t get any better than that in our field today. A major procedural concern with the 1986 Wolf & Heisenberg paper had always been that none of the potential side-effects of the drastic double mutation rol sol were known. Granted, the optic lobes were vanishingly tiny in these mutants (see figure 1) and almost any visual capability seemed like a surprise, but which other processes were affected and in what way was completely unknown. Rather than almost ablating the entire optic lobes of the flies, Bahl et al.’s genetic manipulations specifically affected only two sets of interneurons, T4/5, in the flies’ visual system which the Borst lab had previously reported as abolishing all optomotor responses. Not only was it known that these highly specific manipulations abolished optomotor responses, it was also known why this happened: these neurons are a crucial component of the fly’s visual motion detector. Thus, these flies were exclusively motion-blind and all other faculties were unaltered. Amazingly, despite this highly specific manipulation, these flies behaved exactly like the rol sol flies: they did not respond to moving visual cues, but when allowed to control a black stripe with turning maneuvers, they kept the stripe in their frontal visual field. The authors not only replicated this aspect of the flies’ behavior, they also did so using walking flies, while the original study had examined flying flies, thus extending and generalizing the findings of Wolf and Heisenberg. Moreover, the authors found out, by careful and detailed dissection of the flies’ behavior, that optomotor responses improve fixation by increasing the tendency of the fly to move the stripe to the front of its visual field. For more details see the original publication or an excellent news-type article by Masson & Goffard. This news-article also emphasizes, btw, the relevance of fly work for our general understanding of gaze stabilization even in vertebrate systems.

Fig. 2: “Inverting goggles” experiment. Whenever the tethered fly attempts a turning maneuver, the fly's visual panorama is rotated in the same direction. In the depicted example, a right turning maneuver leads to a rotation of the panorama to the right. In this situation, any attempts of the fly to follow the stripe will lead to a catastrophic feedback of increasing speed of the stripe and yaw torque of the fly in the same direction. Nevertheless, flies learn to generate turning maneuvers in the opposite direction in order to establish a zero net rotation of the stripe (optomotor balance). Fly drawing courtesy of Reinhard Wolf.

Fig. 2: “Inverting goggles” experiment. Whenever the fly attempts a turning maneuver, the fly’s visual panorama is rotated in the same direction. Fly drawing by R. Wolf.

Very much like Wolf & Heisenberg in 1986, Bahl et al. come to the conclusion that there is, in addition to the well-studied optomotor system, a less well-studied position system that acts in parallel during object fixation/course control. Specifically, and this is where they differ markedly from Wolf & Heisenberg, the authors assume that both systems operate according to more or less fixed input-output rules, i.e., “turn left on stimuli moving to the left” or “turn right if the bar is on the right”. However, the single most critical condition in the experiments by Wolf & Heisenberg was the one where a right turn of the fly led to a rotation of the visual field to the right, instead of to the left (the ‘inverting goggles‘ experiment, see figure 2). The rol sol flies showed no difference in stripe fixation between both conditions, whereas control flies took much longer to fixate the stripe under ‘inverting goggles’ conditions. This decisive experiment showed that “turn right when the stripe is on the right” (i.e., the conclusion Bahr et al. arrive at) cannot explain fixation in these motion blind flies. Had the rol sol flies performed this function exclusively, they would not have been able to fixate the stripe. The same then also holds for the flies from Bahr et al.: if their flies also fixate the stripe equally well in the regular as well as the inverted situation, their entire explanation for their results falls apart. Regrettably, Bahl et al. did not perform this very crucial, essential experiment, not in their flies, nor in the computer model they derived from their data. Hopefully, their next publication will contain these exciting experiments.

UPDATE: I have visited Axel Borst’s lab yesterday and they are working on the inverting goggles experiment. For now, the flies have trouble stopping the stripe from rotating at all, so there may be some technical problems using walking flies instead of flying flies for this kind of experiment, or simply the right parameters have not been found, yet. Either way, as I speculated, they are working on it!


Bahl, A., Ammer, G., Schilling, T., & Borst, A. (2013). Object tracking in motion-blind flies Nature Neuroscience, 16 (6), 730-738 DOI: 10.1038/nn.3386
Wolf, R., & Heisenberg, M. (1986). Visual orientation in motion-blind flies is an operant behaviour Nature, 323 (6084), 154-156 DOI: 10.1038/323154a0

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Posted on May 30, 2013 at 10:18 Comments Off on Dissecting a fly’s course control system
May23

A wonderful example of Open Science

In: own data • Tags: c105, c105c232, c232, data, GAL4, gene expression, open science

In our new lab here in Regensburg, we are currently re-establishing the method of confocal microscopy. To start with, we used the fly lines which show a defect in the temporal structure of their spontaneous behavior (a project of one of our graduate students). this fly line uses two transgenic constructs (c105 and c232) to drive expression in specified neurons in the fly brain, i.e., the merged expression patterns of c105 and c232. In this case, the transgenes drive expression of green fluorescent protein (GFP). Around 7pm on the evening right after the dissections and the confocal imaging, I reconstructed the image stacks as a 3D video of the expression pattern in the brain and uploaded it to my YouTube channel:

Only an hour or so after I posted the video, Douglas Armstrong sent me an email:

Are you sure c232 is in there? most of its neurons are missing, looks like c105 though

Cheers,

D

https://flytrap.inf.ed.ac.uk/html/enhancer/c105/
https://www.fly-trap.org/html/enhancer/c232/

And sure enough, upon closer inspection and comparison with the data displayed in the two links Douglas sent along, it seemed as if only the c105 expression pattern is visible. So as we are establishing the technique here, we need to pay extra attention to threshold effects, preparation and the imaging settings at the two different confocal microscopes we have here. In addition, we need to image flies with the individual drivers, to make sure nothing is wrong with the fly strain that should contain both drivers.

All of these things are important and we probably would have not paid special attention to them as we thought the double driver line was simply a good line to start optimizing the method.

In other words, if I had never published the data online right after we got them, I probably might have spent quite some time not being aware of potential problems with this fly strain.

Thanks so much, Douglas!

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Posted on May 23, 2013 at 10:54 2 Comments
May21

PostDoc opportunity in our lab now advertized

In: news • Tags: career, job, postdoc

I have now posted the job ads for the PostDoc position in our lab at Nature, Science, SfN and FENS. If you’re interested in the neurobiology of spontaneous behavior and are into open science, have a look at the job ad and send your application to me at bjoern.brembs@ur.de.

Below is the text of the advertisement:


Universität Regensburg with its over 20,000 students is an innovative and interdisciplinary working university which provides a broad variety of research projects and disciplines for German and foreign students. The laboratory of Prof. Björn Brembs (see https://lab.brembs.net) in the Institute of Zoology at Universität Regensburg, Germany, is offering a position as

Postdoctoral fellow (m/f) – neurobiology of spontaneous behavior and operant learning in Drosophila

The full time position is initially limited to two years (with possible extension). The position is paid according to the German pay scale 13 TV-L.

Job description:

Our lab focuses on the neurobiology of spontaneous behavior and operant learning using Drosophila as a neurogenetic model organism. Methods include computer-controlled behavioral experiments with wildtype, mutant and transgenic flies, neuroanatomy using standard and confocal microscopy as well as some molecular biology such as qPCR to determine the effectiveness of RNAi-mediated gene knock-down.

Selected references:

  • Maye, A.; Hsieh, C.; Sugihara, G.; Brembs, B. (2007): PLoS ONE 2(5): e443

[wpdm_file id=15]

  • Brembs, B.; Plendl, W. (2008): Curr. Biol. 18(15):1168-1171

[wpdm_file id=12]

  • Brembs, B. (2009): Curr. Biol. 19(16): 1351-1355

[wpdm_file id=13]

  • Brembs, B. (2011): Proc. Roy. Soc. B. 278(1707), 930-939

[wpdm_file id=14]

Requirements:

Outstanding candidates (m/f) holding a PhD in a relevant field and interested in this topic as well as being enthusiastic about working in an open science lab are encouraged to apply. The position is fully funded for 2 years, with possible extension. Nonetheless, ideal candidates are expected to have or develop a publication record allowing them to apply for competitive external funding. Candidates with a background in Drosophila biology, coding experience, (R, MatLab, Python, LabView et al.) or psychology will be given priority; proficiency in all three areas is an advantage, but not required. Comprehensive oral and written communication skills in English are also important.

Employment:

The fulltime position is a university-paid, fixed-term position along the funding scale outlined by the TV-L E13, according to seniority and including medical and social benefits, as well as a retirement plan. The position includes a teaching requirement of 5 SWS which can be fulfilled in either English or German.

Universität Regensburg is committed to the compatibility of family and career (for more informa­tion, please visit https://www.uni-regensburg.de/equal-opportunities). Severely disabled applicants are given preference in instances where applicants demonstrate an equal level of qualification. Please mention any severe disabilities, if applicable, in the application.

Applications:

Starting date for the position is October 1, 2013 and applications before July 1, 2013 will receive preferred treatment, but applications will be considered until the position is filled. Applications including a short statement of research objectives, a CV, as well as the names and coordinates of three references should be sent in a single PDF file to: bjoern.brembs@ur.de

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Posted on May 21, 2013 at 13:00 Comments Off on PostDoc opportunity in our lab now advertized
May17

Official call for an end to journal rank

In: science politics • Tags: DORA, impact factor, journal rank, publishing

While our own manuscript on journal rank is almost through the peer-review process, this morning I received several messages announcing the DORA (San Francisco declaration on research Assessment), which I signed immediately. Echoing some of the sentiments we also refer to in our article, part of the declaration reads:

The Journal Impact Factor is frequently used as the primary parameter with which to compare the scientific output of individuals and institutions. The Journal Impact Factor, as calculated by Thomson Reuters, was originally created as a tool to help librarians identify journals to purchase, not as a measure of the scientific quality of research in an article. With that in mind, it is critical to understand that the Journal Impact Factor has a number of well-documented deficiencies as a tool for research assessment. These limitations include: A) citation distributions within journals are highly skewed [1–3]; B) the properties of the Journal Impact Factor are field-specific: it is a composite of multiple, highly diverse article types, including primary research papers and reviews [1, 4]; C) Journal Impact Factors can be manipulated (or “gamed”) by editorial policy [5]; and D) data used to calculate the Journal Impact Factors are neither transparent nor openly available to the public [4, 6, 7].

Of course I wholeheartedly agree with this declaration and with all the recommendations mentioned in it (which is why I signed it). However, while the recommendations are great, they merely echo what people have been editorializing about for at least a decade, some even longer. I also fail to see any clear vision as to how publication reform is supposed to happen. Finally, since our paper isn’t out, yet, (other than on arxiv) they cannot include in their statement that there is absolutely no evidence that research published in high-IF journals are in any way better than those in journals with a lower IF: there is not a single study that I know of where there is a positive correlation of anything that could be construed as a direct measure of any aspect of scientific quality with Impact Factor.

In the absence of such evidence, the appeal in the declaration to drop journal rank as an evaluation signal is just that: an appeal – it lacks evidence-based reasoning and substance, as one could simply argue that the flaws of the IF just need to be fixed.

Nevertheless, such a public and widespread declaration is justified, comes at the right time and carries the right message, so it deserves our full support, even if it may not go quite far enough in its demands for reform. Clearly, being a platform seeking the most widespread support, some compromises have to be made.

Now go and sign the declaration already, what are you waiting for?

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Posted on May 17, 2013 at 18:30 Comments Off on Official call for an end to journal rank
May11

A new home for bjoern.brembs.blog

In: server • Tags: blog, e107, WordPress

After Mike Taylor kept complaining about how horrible my old e107 platform was (which obviously it isn’t: I love this CMS), I finally gave in and moved everything over to a new home. The entire brembs.net domain with all its subdomains is no longer hosted in the good old US of A, where its home was since about 2000, when I moved there myself. After almost ten years back in Germany, I’ve now brought my online presence back home as well. As of this post, all my blogging will be done on WordPress.

The 912 old posts from the last ten years are still accessible, of course, at blogarchive.brembs.net. I should have everything set up in a way that even all the original links should be redirected to the archive, such that nobody should really notice much more than a slight difference in appearance.

I’ll now slowly adjust all the content and design on this place, until the required functionality and look-and-feel is in place. Let me know if there is anything you’d like to see here in terms of plug-ins or other functionality, or if any of the design is off-putting. Also, if you will, could you test the commenting system and let me know if anything, what needs to be modified/adjusted?

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Posted on May 11, 2013 at 07:42 3 Comments
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