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Jun21

Funder mandates: Are scientists like junkies?

In: science politics • Tags: funders, mandates, open access, publishing

Mike Taylor wrote about how frustrated he is that funders don’t issue stronger open access mandates with sharper teeth. He acknowledges that essentially, the buck stops with us, the scientists, but mentions that pressures on scientists effectively prevent them from driving publishing reform. Obviously, from the scientist’s perspective, this is a classic collective action problem: every scientist who would start boycotting corporate publishers would be risking their livelihood. On the other hand, if we all started to publish exclusively in a world-wide, federated scholarly communication system, based on a collective of SciELO or SHARE-like platforms, we would not only save billions in publishing costs every year and provide fully open access as an added benefit, but also no scientist would risk anything.

As I see it, there are two (clearly not mutually exclusive) approaches to this problem:

1. Ask for outside help. One can see scientists like junkies: they are addicted to publishing in the journals of parasitic publishers and can’t possibly wean themselves from their fix. This appears to be Mike’s position and Stevan Harnad‘s (although they probably might disagree on green vs. gold details). There is no doubt that this would work, if implemented as Mike and Stevan (and many others) argue. Thus, of course, it would be foolish to not embrace and welcome funder mandates.

2. Work on removing the pressures on scientists that prevents them from collective action. The fix is essentially mediated by the hierarchy of journals which bestows prestige on scientists and which decides who gets to keep their livelihoods and who don’t. To address this issue, we recently published a paper in which we outline that there is no empirical foundation for journal rank, in an attempt to effectively remove the fix.

While both approaches need to be pursued, personally, I strongly favor the second route. It annoys the hell out of me that we scientists creep and crawl on all fours to politicians, funders, publishers asking them to force us to do something we should bloody well be able to do ourselves: we broke the system, we fix it. Begging others to save us from the hell we created for ourselves is probably the one single most annoying aspect of the entire situation. We’re already living and researching off of people’s taxes and now we ask yet more for help – isn’t there anything we can do ourselves? Can’t we even get our own house in order without the help from someone who doesn’t have any direct responsibility for the quagmire?

I just can’t get over the humiliation that urging funders to do what we should be doing is essentially like saying: “we’re too weak to do it ourselves, please, in addition to all the money we’re already getting from you, could you please also do the mandates for us and, while you’re at it, shell out the dough to police and enforce the mandates?”

Funder mandates are great. They have been instrumental in getting us as far as we have gotten and while they are humiliating, they get the job done and work as advertised. Mike is correct in that they could have more teeth, but at least the funders have gotten the ball rolling with approach #1. When will we start to do our part and launch approach #2? Where’s the response from scientists saying: “thank you funders, here’s what we will do!” Instead, we keep pleading for yet more help.

Where’s the quid pro quo from us scientists? Does it always have to be a one-way highway of public service to the scientific community and none out of it? Is the scientific community really such a black-hole of public goods? Or is that just my myopic perspective?

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Posted on June 21, 2013 at 15:27 2 Comments
Jun20

Free will: it’s not what you think it is

In: science • Tags: brain, free will, magic, nonlinearity

To my knowledge, no neuroscientist hypothesizes that there is magic in our heads. However, it appears this is a hypothesis that flies by the editors at the New York Times. The title of this op-ed piece says it all: “beyond the brain”. The author, David Brooks, claims: “The brain is not the mind.” Last I looked (which was a few seconds ago, I admit), beyond the brain was the Pia mater, the subarachnoid space, the Arachnoid, the dura mater and the skull. I wonder, just where precisely does the magic mind sit, if it’s not the brain? In the subarachnoid space, squeezed between layers of connective tissue and blood vessels? Or is it even beyond the skull, hovering above our heads? Now, Mr. Brooks doesn’t mention the Psychokinetic Energy Meter, but he makes it sound as if in his world this is the scientific instrument with which one would measure the capacity of the mind to move the body. Probably most disappointingly, Mr. Brooks bolsters his magic-mind hypothesis with the classic argument from incredulity: ‘I don’t understand it, so it must be magic’: “It is probably impossible to look at a map of brain activity and predict or even understand the emotions, reactions, hopes and desires of the mind.” This is like saying “it’s probably impossible to build a heavier-than-air flying machine” before the Wright brothers’ first flight. More disturbingly, it’s like saying: “I don’t understand no evilution, therefore magic man dunnit”.

Mr. Brooks caps his magic-mind hypothesis off with a few short paragraphs essentially saying “we have free will because I think so, free will is magic, so there’s magic in the head – and science is too limited to get into magic, don’t you forget that!” Given that his main point is that the mind is magic, one can only assume that he means neuroscience is too limited to understand free will sort of like medicine is too limited to understand homeopathy and physics is too limited to understand astrology. This final point is probably the only accurate statement of the entire piece: magic in the head is about as thoroughly debunked as homeopathy or astrology.

What we call ‘mind’ exists in a similar way as colors exist: our brain creates it. Colors are real in the sense that our brain makes colors real, it constructs a reality with colors, but spectral properties of light are not colors. Just like colors, the mind, free will, are real, but not in the way Mr. Brooks apparently thinks: they’re not magic. Neural activity makes our minds just as real as colors, but neither are magic nor do they exist outside of our heads. The fact that we don’t understand, yet, how the brain does that, is not a valid reason to explain our ignorance away with magic, but a boon to neuroscientists (or we’d be unemployed). The correct answer to the question: “what is the mind?” is not “magic”, but “we don’t know how, but all the evidence says it’s our brain that somehow creates it”.

This very fundamental insight of the last 40 years or so of neuroscience, obviously entails that with every discovery we will be better able to predict future actions. If that seems disappointing, tough luck, live with it. Today, we clearly cannot “take pretty brain-scan images and […] use them to predict what product somebody will buy”, this is pop-neuroscience. However, much like we got better at predicting the weather by studying it, we will get better at predicting future actions by studying the brain – as we have already become much better over the last decades. Importantly, and I cannot stress this enough, we don’t need magic to understand that we will nevertheless, not even with unlimited time and resources, never be able to fully predict human behavior. Just like no neuroscientist postulates magic in our heads, no meteorologist would postulate that it’s magic that prevents us from making accurate weather forecasts and no astrophysicist would claim that magic messes with Pluto’s unpredictable orbit. Apparently, it will take a few more decades until it sinks in that the brain is a little more complex than the weather or our solar system. Anybody who thinks that the brain needs magic to bring about the mind with free will thoroughly underestimates it. Everybody and their grandma today has already realized that complex nonlinear dynamics (“butterfly effect”, “chaos” – coincidentally coined in the same decade that dualism essentially died) prevent accurate weather forecasts on a principle basis, not out of technical problems. These effects even make the orbit of Pluto unpredictable! The data from brain recordings and behavioral studies show mathematically analogous nonlinearities, which lead to the predictability of behavior to decay exponentially with the forecasting period even in flies. Clearly, one can assume that humans are less nonlinear and more predictable than flies as apparently Joshua Greene at Harvard seems to postulate, but even as a fly researcher, I find that somewhat hard to accept. But hey, what does a fly guy know? Be that as it may, as long as humans are equally or less predictable than fruit flies, the data from our own little lab alone already alleviate Mr. Brooks’ fears: brains will not become fully predictable with more neuroscience, only gradually more so.

It seems there is a deep-seated frustration that science explains away magic, even in otherwise science-o-phile individuals. More and more research (some of it reviewed here) is accumulating that demonstrates that not only our flies, but many, perhaps all animals have the capacity, given the right circumstances, to make different decisions under identical circumstances. In fact, as has often been argued (review here) before, such protean behavior is a prerequisite and an inevitable outcome of evolution. Why should animal brains possess this capacity and human brains not? If this kind of free will disappoints you, tough luck, live with it. Free will is the capacity of the brain to make decisions that are influenced by all the events leading up to the decision, but not determined by them. Free will is a brain capacity that is of course determined by neural activity, but the neural activity is no more deterministic than the weather is. In fact, I would postulate that our brains are even less deterministic than the weather. Call it wiggle-room, or elbow room, the nonlinearity of decision-making relegates the question of just how deterministic the brain really is to a (highly interesting!) academic debate: in practice, brains will always be less predictable than the weather, irrespective of any quantum effects playing a role or not. This modern, scientific concept of free will emphasizes that our freedom can of course not be absolute. Freedom is always a matter of degree, of shades of gray between the blacks and whites of determinism and stochasticity. In fact, this is precisely how such nonlinearities operate, by implementing deterministic and stochastic components to create phenomena that are neither fully deterministic nor completely stochastic. As we understand the deterministic components better, we get better at predicting nonlinear behavior, but the very nature of all of these systems fundamentally prevents fully accurate forecasts. In reality, we create robots with free will, we even start to understand the neurophysiological mechanisms by which neural processes become unpredictable, but Mr. Brooks writes in the NYT that because he doesn’t understand how the neurons are doing it, it must be magic.

For the life of me, I have no idea what is getting into people like Mr. Brooks who at least give off the very succinct impression that they fear that the human brain needs magic, or else we might one day understand it too well for our own good. Have they no respect for the lump of tissue between their ears? At least he gets a thorough bashing in the many of the comments and of course by the inimitable Neurocritic.

One of our graduate students might have just discovered the neural circuit that allows fly brains to decide which way to turn, even in a virtual environment without any cues. Now please excuse me while I go back to explaining away some magic by studying fly neurons.

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Posted on June 20, 2013 at 19:30 8 Comments
Jun19

One more reason to publish negative results

In: science • Tags: cartoon, fun, negative results, open science

It might just save your life (via Upturned Microscope):

negative results

BTW, even if your life is not at stake, someone else’s may be. So you should publish your results if you are sure something definitely will not work, for instance in F1000 Research, where you can publish negative results for free until August 31, 2013. Your colleagues will be grateful.

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Posted on June 19, 2013 at 20:15 Comments Off on One more reason to publish negative results
Jun10

SHARE: Library-based publishing becoming a reality?

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

The recently released development draft for SHared Access Research Ecosystem (SHARE), authored by the Association of American Universities (AAU), the Association of Public and Land-grant Universities (APLU) and the Association of Research Libraries (ARL) in response to the OSTP memo on public access to federally funded research in the US sounds a lot like the library-based publishing system I’ve been perpetually arguing for. It’s even in our paper on the pernicious consequences of journal rank. Could this be the initial step to break the stranglehold publishers have on scholarly communication? Here some key excerpts from the document:

universities have invested in the infrastructure, tools, and services necessary to provide effective and efficient access to their research and scholarship. The new White House directive provides a compelling reason to integrate higher education’s investments to date into a system of cross-institutional digital repositories that will be known as SHared Access Research Ecosystem (SHARE).

[…]

Universities already own and operate key pieces of the infrastructure, including digital institutional repositories, Internet2, Digital Preservation Network (DPN)2, and more.These current capacities and capabilities will naturally be extended over time. Universities have also invested in recent years in working with Principal Investigators and other campus partners on developing digital data management plans to comply with agency requirements.

[…]

University-based digital repositories will become a public access and long-term preservation system for the results of federally funded research. SHARE achieves the mission of higher education by providing access to and preserving the intellectual assets produced by the academy, in particular those that are made openly available.

[…]

Agencies that choose to develop their own digital repositories, or work with an existing repository such as PubMed Central, could simply adopt the same metadata fields and practices to become a linked node in this federated, consensus-based system. Discipline-based repositories, some of which are housed at universities, will be included.

[…]

The SHARE workflow is straightforward, and using existing protocols can be fully automated.

  1. PI or author submits manuscript to journal as currently occurs.
  2. Journal publisher coordinates peer review, accepts, and edits manuscripts as currently occurs.
  3. Journal submits XML version of the final peer reviewed manuscript (including the abstract) to the PI’s designated repository, or the author submits the final peer-reviewed and edited manuscript accepted for publication (including the abstract) to the PI’s designated digital repository.

In principle, this sounds almost verbatim like the system I advocate, with a few exceptions. Clearly, SHARE is still a ‘green’ OA route, meaning that regular journal publishing still occurs. I see no major issue with this, as some transition period will inevitably be required. The import part is that we wrestle at least some control over our literature back from the publishers.

I also find it important to point out the combined effort of these organizations to integrate the data mandates with the literature. Now we are only missing software requirements – I wonder why these are missing?

Another task not mentioned will be to integrate the back-archives of all the published literature into SHARE. Once we could get that incorporated, we’d potentially be able to offer a superior search, filter and discovery system than anything currently on the market – a system which I would guess to be crucial for weaning ourselves from publishers altogether, eventually.

In conclusion, this might be a very first, baby-step of our emancipation from corporate publishers. If we take the example of SciELO, and inspire  concerted action of a critical mass of institutions of higher education and research, we might just be able to achieve a fully functional scholarly communication system, perhaps even within this generation. Now is the time to provide our feedback to this draft. I think open access activists should get together and tell them what needs to happen.

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Posted on June 10, 2013 at 09:16 Comments Off on SHARE: Library-based publishing becoming a reality?
Jun03

Everybody already knows journal rank is bunk

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

Today, finally, our manuscript on journal rank is accepted for publication at Frontiers in Human Neuroscience. One may wonder how a paper that reviews the empirical findings around journal rank ends up in a journal about human neuroscience. After all, our main conclusions after the literature survey can be summarized like this:

  • Journal rank (as measured by impact factor, IF) is so weakly correlated with the available metrics for utility/quality/impact that it is practically useless as an evaluation signal (even if some of these measures become statistically significant).
  • Less practically, but statistically, journal rank (as measured by IF) is slightly better than chance when filtering for novelty/importance
  • Less practically, but statistically, journal rank (as measured by IF) is worse than chance when filtering for scientific quality (i.e., inverse journal rank is better than chance and throwing dice is better than IF-based journal rank)

Colloquially speaking: if you prefer the hip but shoddy science, read GlamMagz, but if you value substance over style, read the regular journals.

The two most notable exceptions to these general conclusions are retractions and subjective journal rank. As detailed before, among the few really strong correlations with IF-based journal rank are the rate at which papers are retracted: the higher up in the rank, the more likely your paper is to be retracted. Worse still, most of these retractions are due to suspected or demonstrated scientific misconduct or outright fraud. The data say that the reasons for this strong correlation are twofold:

  1. The methodological quality of publications in high-ranking journals is either not better or worse than that of publications in lower ranking journals
  2. The prestige correlates with IF and hence the incentives for submitting sloppy/fraudulent work increase as do the incentives for error-detection

The second strong correlation with impact factor is subjective journal rank, i.e., how well IF captures the perceived, subjective prestige/quality/impact of a particular journal. Given the human potential for confirmation bias paired with the circularity of self-selection by sending only the one’s ‘best’ work to the high-ranking journals, this result is not hard to explain. Moreover, given the history of gaming by abusing the flagrant violations of transparency and basic scientific methodology of the impact factor, it is not inconceivable that the numbers published by Thomson Reuters each year match public perception so well, because also Thomson Reuters know the subjective journal ranking in the heads of their customers and that violations of these expectations could potentially harm a very lucrative business.

Now, why is all this published in a journal on human neuroscience? Well, certainly not for the psychology of confirmation bias and self-selection. We did of course submit our manuscript to the journals with the general readership. Especially, since the data in the literature were new to us and virtually every one of our colleagues that we asked. So here is what the editors of these journals had to say about the conclusions mentioned above and in our article. This is what Nature‘s Joanne Baker had to say:

we will decline to pursue [your manuscript] further as we feel we have aired many of these issues already in our pages recently

and this is what Science’s Brooks Hanson replied:

we feel that the scope and focus of your paper make it more appropriate for a more specialized journal

While Nature felt they had already written enough about how the high-ranking journals publish unreliable research, Science had the impression the topic of journal rank and how it threatens the entire scientific enterprise was not general enough for their readership. Since there are not that many general science journals with sections fitting a review like ours, we next went to PLoS Biology. There, at least, the responsible editor, Catriona MacCallum (whom I respect very much and who is exceedingly likable) sent our manuscript out for review. To our surprise, the reviewers essentially agreed with Nature, that there wasn’t anything new in our conclusions: everybody already knows that high-ranking journals publish unreliable science, e.g.:

“While I am in agreement with the insidious and detrimental influences on scientific publishing identified and discussed in this manuscript, most of what is presented has been covered thoroughly elsewhere.”

[…]

“The authors make sound points, and for doing so can rely on years of solid research that has investigated the pernicious role of journal rank and the impact factor in scholarly publishing.

Overall, I deem this a worthy and valid “perspective” that merits publication, but do want to make the following reservations.

The particular arguments that the authors make with respect to the deficiencies of the journal impact factor (irreproducible, negotiated, and unsound) have already been made extensively in the literature, in online forums, in bibliometric meetings, etc to the point that very little value is gained by the authors restating them in this perspective.

Most of the points dedicated to the retractions and decline effect, and the relation between journal rank and scientific unreliability are also extensively made in the literature that the authors cite.

In other words, very few new or novel insights are made in this particular perspective, other than to restate that which has already been debated extensively in the relevant literature.”

For the full reviews and the letter of the editor, scroll down on our Google Doc.

Thus, essentially, Nature and PLoS Biology officially agree with our assessment that one should read high-ranking journals with more than the regular dose of caution. Therefore, I hope it is now clear that in order to convince readers that the conclusions we draw from the literature are reliable, we had to publish in a journal with an impact factor of 2.339 – and don’t you skimp on any of those decimals!

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Posted on June 3, 2013 at 14:45 5 Comments
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
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