Björn Brembs

Data broker RELX is represented on Twitter by their Chief Communications Officer Paul Abrahams. Due to RELX subsidiary Elsevier being one of the largest publishers of academic journals, Dr. Abrahams frequently engages with academics on the social media platform.

Should you trust Elsevier?

More and more experts are calling for the broken and destructive academic journal system to be replaced with modern solutions. This post summarizes why and how this task can now be accomplished. It was first published in German on the blog of journalist Jan-Martin Wiarda.

 Front cover of

the now-vanished

 Australasian Journal of Bone &amp; Joint Medicine

. Source: Scan from the-scientist.com website

The trinity of failures

According to a recent study, employee surveillance is rampant in today’s corporate work environment. This study documents how, often under the pretense of cybersecurity or risk analysis (sort of like academic publishers, actually), companies analyze the behavioral data they collect from their employees to help them make “evidence-led”, i.e., algorithmic employment decisions.

Algorithmic employment decisions in academia?

There are regular discussions among academics as to who should be the prime mover in infrastructure reform. Some point to the publishers to finally change their business model. Others claim that researchers need to vote with their feet and change how they publish. Again others find that libraries should just stop subscribing to journals and use the saved money for a modern publishing system.

Who’s responsible for the lack of action?

Since cOAlition S is asking for recommendations from the community for the implementation of their Plan S, I have also chipped in. In their feedback form, they ask two questions, to which I have answered with the replies below.

Providing recommendations for Plan S implementation

It’s now been 24 years since Stevan Harnad sparked the open access movement by suggesting in his “subversive proposal” in 1994 that scholars ought to just publish their scholarly articles on the internet:  Since then, we have been waiting on the behavior of scholars to change, such that all our works indeed become accessible.

After 24 years, when will academic culture finally shift?

In his fantastic Peters Memorial Lecture on occasion of receiving CNI‘s Paul Evan Peters award, Herbert Van de Sompel of Los Alamos National Laboratory described my calls to drop subscriptions as “radical” and “extremist” (starting at about minute 58):    Regardless of what Herbert called my views, this is a must-see presentation in which Herbert essentially presents the technology and standards behind the functionalities I have been asking for

Why academic journals need to go

These days, many academic publishers can be considered mere Pinos: ‘Publishers in name only’. Instead of making scholarly work, commonly paid for by the public, public, as the moniker ‘publisher’ would imply, in about 80% of the cases, they put them behind a paywall.

The scholarly commons: from profiteering to servicing

Academic publishers in general and Elsevier in particular have a reputation for their ruthless profiteering, using professional negotiators pitting hapless librarians against their own faculty during journal subscription negotiations.

Why can Elsevier keep insulting scholars without consequences?

Few insect behaviors are more iconic than the proverbial moths circling the lamps at night. Artist: Dave McKean  These observations are prime examples of the supposedly stereotypic insect responses to external stimuli. In contrast, in our new paper that just appeared today, we describe experiments suggesting that insects appear to make a value-based decision before approaching the light.

Why did the moth fly into the flame?

Why our Open Data project worked, (and how Decorum can allay our fears of Open Data).  I am honored to Guest Post on Björn’s blog and excited about  the interest in our work from Björn’s response to Dorothy Bishop’s first post. As corresponding author on our paper, I will provide more context to our successful Open Data experience with Björn’s and Casey’s labs.

Guest post: Why our Open Data project worked

With the start of the new year 2017, about 60 universities and other research institutions in Germany are set to lose subscription access to one of the main STEM publishers, Elsevier. The reason being negotiations of the DEAL consortium (600 institutions in total) with the publisher.

So your institute went cold turkey on publisher X. What now?

A recurrent topic among faculty and librarians interested in infrastructure reform is the question of whose turn it is to make the next move. Researchers rightfully argue that they cannot submit their work exclusively to modern, open access journals because that would risk their and their employees’ jobs. Librarians, equally correctly, argue that they would cancel subscriptions if faculty wouldn’t complain about ensuing access issues.

Practical roads to infrastructure reform

Around 2005, German politicians decided on a plan to circumvent a newly created amendment to the German constitution that prevents federal funds from supporting state-owned institutions such as universities.

Data show “excellence initiative” was a massive failure – help stop it

Three years ago, representatives of libraries, publishers and scholars all agreed that academic publishers don’t really add any value to scholarly articles. Last week, I interpreted Sci-Hub potentially being a consequence of scholars having become tired after 20 years of trying to wrestle their literature from the publishers’ stranglehold by small baby-steps and through negotiations and campaigning alone.

Academic publishers: stop access negotiations

tl;dr:
 
 Data from thousands of non-retracted articles indicate that experiments published in higher-ranking journals are less reliable than those reported in ‘lesser’ journals.

Vox health reporter Julia Belluz has recently covered the reliability of peer-review.

Even without retractions, ‘top’ journals publish the least reliable science

Last week, Elizabeth Pennisi asked me to comment on the recent paper from Schreiweis

 et al.

entitled “Humanized FoxP2 accelerates learning by enhancing transitions from declarative to procedural performance”. Since I don’t know how much, if anything, of my answers to her questions will end up in her article, I thought I might expand my answer into a post about this very interesting work.

Humanized FoxP2 and the timing of habits

The data clearly show that publications in

 Cell

,

 Nature

or

 Science

(

 CNS

for short), on average, cannot be distinguished from other publications, be it by methodology, reproducibility or other measures of quality. Even their citation advantage, while statistically significant, is so small that it is practically negligible.

No need to only send your best work to Science Magazine

By now, everybody reading this obscure blog knows about the so-called sting operation by John Bohannon in

 Science Magazine

last week. As virtually everybody has pointed out, the outcome of this stunt is entirely meaningless.

How embarrassing was the ‘journal sting’ for Science Magazine?

During my flyfishing vacation last year, pretty much nothing was happening on this blog. Now that I’ve migrated the blog to WordPress, I can actually schedule posts to appear when in fact I’m not even at the computer. I’m using this functionality to re-blog a few posts from the archives during the month of august while I’m away.

Unquestioning dogma: the gatekeepers of science

Flashback: The brain creates something out of nothing

Scientists as social parasites?

During my flyfishing vacation last year, pretty much nothing was happening on this blog. Now that I’ve migrated the blog to WordPress, I can actually schedule posts to appear when in fact I’m not even at the computer. I’m using this functionality to re-blog a few posts from the archives during the month of august while I’m away. This post is from April 19, 2011:

Flashback: Creationists, this is the evidence you have to beat!

As part of my scheduled re-posts during the summer break, I’ll also post some of the science videos from the archives. I originally posted these two on February 24, 2013:

The first one is a TED talk by Michael Dickinson on how flies fly: and the second one is on recording from fly visual neurons during flight and non-flight.

SummerScienceVideo: fruit fly research

Flashback: ‘stimulus-response’ concept based on artifacts?

This post was originally published on the London School of Economics “Impact of Social Sciences” blog, on July 30, 2013:

In various fields of scholarship, scholars accrue reputation via the proxy of the containers they publish their articles in. In most if not all fields, scholarly journals are ranked in a hierarchy of prestige.

Solutions to the looming crisis in science

During my flyfishing vacation last year, pretty much nothing was happening on this blog. Now that I’ve migrated the blog to WordPress, I can actually schedule posts to appear when in fact I’m not even at the computer. I want to use this functionality to re-blog a few posts from the archives during the month of august while I’m away. This is the first post in this series, just to see if it works and what needs to be tweaked.

Flashback: The neurobiology of self-learning

This morning I was reminded of the age of some of the technology we’re using. Hyperlinks were developed at Stanford University and first demonstrated by their inventor Douglas Engelbart (using the first mouse) in 1968:  On Tuesday, Douglas Engelbart died, even before the scholarly literature was able to fully implement the technology he invented, 45 years and counting.

The dysfunctionality of the scholarly literature: hyperlinks

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

One more reason to publish negative results

I have now posted the job ads for the PostDoc position in our lab at

 Nature

,

 Science

, SfN and FENS.

PostDoc opportunity in our lab now advertized

Trial and error is a successful problem-solving strategy not only in humans but throughout evolution. How do nervous systems generate novel, creative trials and how are errors incorporated into already existing experiences in order to improve future trials?

Come and do research with us!

This is our first poster at this year’s SfN meeting in San Diego. It’s about decision-making in fruit flies. We find a probabilistic form of decision-making that suggests that without understanding the mechanisms behind this fundamental uncertainty, we will never fully understand decision-making. Clicking on the image will let you download the PDF Version of the poster.

Do flies in groups make individual choices?

Notwithstanding the barrage of criticisms and warnings from every corner of the scholarly community, various initiatives, mainly in the Netherlands, Finland, Germany, France and the UK, continue their efforts for a smooth transition from subscriptions to open access without any further disruptions.

Why open access Big Deals are worse than subscriptions

Scholarly journals, on the face of it, emerged in the 17

 th

century as a medium to facilitate communication of scientific discoveries among interested scholars. In the 21

 st

century, it’s not all that different: researchers form communities around topics in which they share a common interest: Journal of Neuroscience, Pediatrics and Neonatology, Journal of Economics or the British Educational Research Journal.

Academic publishers and competition

This anecdote made my day today. On a

 Drosophila

researcher mailinglist, someone asked if anybody on the list had access to the Landes Bioscience journal ‘Fly‘. I replied by wondering that if #icanhazpdf on Twitter didn’t work, the days of ‘Fly’ are probably counted, with nobody subscribing.

#icanhazpdf more public than a publication?

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.

Official call for an end to journal rank

Tomorrow we travel to the annual meeting of the Society for Neuroscience and our diligent scientists have already printed their posters! Ottavia Palazzo will present her work on genome editing the

 FoxP

locus of

 Drosophila

with anatomical and behavioral characterizations of the various transgenic lines she has created.

With CRISPRed FoxP and habit formation to #SfN19

The recent publication of the “Ten Principles of Plan S” has sparked numerous discussions among which one of several recurring themes was academic freedom. The cause for these discussions is the insistence of the funders supporting Plan S that their grant recipients only publish in certain venues under certain liberal licensing schemes.

Does academic freedom entail exemption from spending rules?

Over the last ten years, scientific funding agencies across the globe have implemented policies which force their grant recipients to behave in a compliant way. For instance, the NIH OA policy mandates that research articles describing research they funded must be available via PubMedCentral within 12 months of publication. Other funders and also some institutions have implemented various policies with similar mandates.

Maybe try another kind of mandate?

Arguably, there is little that could be more decisive for the career of a scientist than publishing a paper in one of the most high-profile journals such as

 Nature

or

 Science

. After all, in this competitive and highly specialized days, where a scientist is published all too often is more important than what they have published.

How Nature Magazine consistently prefers anecdote over data

The recent call for a GlamMag boycott by Nobel laureate Randy Shekman made a lot of headlines, but will likely have no effect whatsoever. For one, the call for boycott isn’t even close in scale to “the cost of knowledge” boycott against Elsevier and even that drew less than 15,000 measly signatures, a drop in the bucket with 970,000 board members, reviewers and authors working for Elsevier largely for free.

In support of subscripton cancellations

In the last “Science Weekly” podcast from the Guardian, the topic was retractions.  At about 20:29 into the episode, Hannah Devlin asked, whether the reason ‘top’ journals retract more articles may be because of increased scrutiny there. The underlying assumption is very reasonable, as many more eyes see each paper in such journals and the motivation to shoot down such high-profile papers might also be higher.

Are more retractions due to more scrutiny?

Currently, our libraries are paying about US$5000 per peer-reviewed subscription article. What is more difficult to find out is where all that money goes. Which steps are required to make an accepted manuscript public?

What goes into making a scientific manuscript public?

This is the story behind our work on the function of the FoxP gene in the fruit fly

 Drosophila

(more background info). As so many good things, it started with beer. Troy Zars and I were having a beer on one of the ICN evenings, I think it was in Vancouver in 2007. I had recently learned about the conserved role of FoxP2 in songbirds, out of one of the labs in Berlin, where I was based at the time.

Why use fruit flies to study a gene involved in language?

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

Cut out the parasitic middle men!

This year’s Winter Conference on Animal Learning and Behavior (WCALB) will be on one of my oldest and most central research projects, the commonalities and differences between operant and classical conditioning.

Almost 80 years on, progress on operant and classical conditioning

In which potatoes in France are like high-ranking journals in science

This is the tweetlog covering July 3-5: Interesting! We find something similar in flies: Live fast, die young: Long-lived mice are less active https://feedly.com/k/16RDz21 It smells fishy: Copper prevents fish from avoiding danger https://feedly.com/k/12gw14F @

 biocs

@

 google

Yes!

Tweetlog: neuroscience and #openaccess

After almost 25 years since Stevan Harnad’s “subversive proposal“, now, finally, scholars and the public have a range of avenues at their disposal to access nearly every scholarly article. Public access, while not the default, has finally arrived. Granted, while all of the current options are considered legal for the

 reader

, not all

 providers

of scholarly literature conform to every law in every country.

With the access issue temporarily solved, what now?

Amazing bead chain experiment

Random Science Video: The value of fly research

There are those who demand journal peer-review be paid extra on top of academic salaries. Let’s have a look at the financials of that proposal. The article linked above confirms common rates of academic consulting fees, i.e., anything between US$100 per hour for graduate students and US$350 per hour for faculty. Taking a conservative US$200 as an easy, lower-bound estimate for, say, a post-doc hour seems to cover most cases.

How about paying extra for peer-review?

No matter how well-intended (and we all know to which place the road leads that is paved with good intentions!), transformative agreements (such as DEAL in Germany) are generally the wrong tool at the wrong time for making publicly funded science accessible to the public.

No Evilsevier DEAL!

The DFG is a very progressive and modern funding agency. More than two years ago, the main German science funding agency signed the “Declaration on Research Assessment” DORA.

German funder DFG: Why the sudden inconsistency?

tl;dr:


 Evidence suggests that the prestige signal in our current journals is noisy, expensive and flags unreliable science. There is a lack of evidence that the supposed filter function of prestigious journals is not just a biased random selection of already self-selected input material.

Replacing the prestige signal

Last week’s podium on the commodification of open science entitled “If you are not paying for the product, you are the product?” was surprisingly unanimous on the need to radically modernize academic publishing and abolish the current publishing system relying mainly on corporate publishers with monopoly status.

Academic publishing – market or collectivization?

There have been repeated online discussions about my suggestion to libraries that now would be an excellent time to start cancelling subscriptions. Prime counter-argument is that librarians risked their jobs or at least face faculty backlash if they did that. Personally, I have witnessed many such cancellations and there has never been a riot or even a librarian reprimanded, let alone fired.

How to convince faculty to support subscription cancellations

Stevan Harnad’s “Subversive Proposal” came of age last year. I’m now teaching students younger than Stevan’s proposal, and yet, very little has actually changed in these 21 years.

Sci-Hub as necessary, effective civil disobedience

Over the last decade or two, there have been multiple accounts of how publishers have negotiated the impact factors of their journals with the “Institute for Scientific Information” (ISI), both before it was bought by Thomson Reuters and after. This is commonly done by negotiating the articles in the denominator.

Just how widespread are impact factor negotiations?

tl;dr:
 
 It is a waste to spend more than the equivalent of US$100 in tax funds on a scholarly article.

Collectively, the world’s public purse currently spends the equivalent of US$~10b every year on scholarly journal publishing. Dividing that by the roughly two million articles published annually, you arrive at an average cost per scholarly journal article of about US$5,000.

How much should a scholarly article cost the taxpayer?

Posting my reply to a review of our most recent grant proposal has sparked an online discussion both on Twitter and on Drugmonkey’s blog. The main direction the discussion took was what level of expertise to expect from the reviewers deciding over your grant proposal. This, of course, is highly dependent on the procedure by which the funding agency chooses the reviewers.

How to write your grant proposal?

Update, Dec. 4, 2015: With the online discussion moving towards grantsmanship and the decision of what level of expertise to expect from a reviewer, I have written down some thoughts on this angle of the discussion.

With more and more evaluations, assessments and quality control, the peer-review burden has skyrocketed in recent years.

Why cutting down on peer-review will improve it

This is a post written jointly by Nelson Lau from Brandeis and me, Björn Brembs. In contrast to Nelson’s guest post, which focused on the open data aspect of our collaboration, this one describes the science behind our paper and a second one by Nelson, which just appeared in PLoS Genetics.

Laboratories around the world are generating a tsunami of deep-sequencing data from nearly every organism, past and present.

Data Diving for Genomics Treasure

When I finished my PhD 15 years ago, the neurosciences defined the main function of brains in terms of processing input to compute output: “brain function is ultimately best understood in terms of input/output transformations and how they are produced” wrote Mike Mauk in 2000 (DOI: 10.1038/76606). Since then, a lot of things have been discovered that make this stimulus-response concept untenable and potentially based largely on laboratory

Watching a paradigm shift in neuroscience

This is a post loosely based on an article appearing today in the German newspaper “Frankfurter Allgemeine Zeitung” by Axel Brennicke and me. The raw data for our analysis is available. Please do let us know if you find a mistake.


 UPDATE


 , 09/01/2015: A commenter made me aware of data rows in the raw data we had overlooked before.

Booming university administrations

I really loathe reviewing for GlamMagz for two main reasons. For one, it’s hard to remain neutral: publication of a paper in my field in such a journal is beneficial both for the field and for the young people who are authors on this paper. Second, the demands of some of my colleagues so often make my blood boil. At that point I’m very happy these reviews are anonymous and I really don’t want to know the names of these colleagues.

Why this GlamMag will likely not ask for my review again

See this post with the associated press releases on brembs.net.

The

 F

orkhead B

 ox

P2 (FOXP2) gene is well-known for its involvement in language disorders. We have discovered that a relative of this gene in fruit flies,

 dFoxP

, is necessary for a type of learning called operant self-learning, which resembles some aspects of language learning.

The Drosophila FoxP gene is necessary for operant self-learning

UPDATE
 
 , 10-02-2015: After a hint from a user on Twitter, I now know that it is possible to open a PDF document in several windows, one for text, one for legends and one for figures. Figures and legends occupy one virtual desktop and the text another. In this way, I can actually review on-screen, but it is one heck of a work-around and by no means convenient.

I cannot take it any more.

Publishers, stop torturing your reviewers!

Today, our most recent paper got published, before traditional peer-review, at

 F1000 Research

. The research is about how nominally identical fly stocks can behave completely differently even if tested by the same person in the same lab in the same test.

The way academic publishing should be

There is an interesting study out in the journal PNAS: “Evaluating big deal journal bundles“. The study details the disparity in negotiation skills between different US institutions when haggling with publishers about subscription pricing.

Your university is definitely paying too much for journals

Yesterday,

 Science Magazine

published a news story (not a peer-reviewed paper) by Gonzo-Scientist John Bohannon on a sting operation in which a journalist submitted a bogus manuscript to 304 open access journals (observe that no toll access control group was used).

 Science Magazine

reports that 157 journals accepted and 98 rejected the manuscript.

Science Magazine rejects data, publishes anecdote

I just got the nicest decline to review ever: That’s how you retire from science: you get to work like normal people. Awesome!

Retiring from science?

The cost of knowledge – in 2003?

Since the birth of our daughter, we spend our summers in Sweden, just like I used to, when I was little. This not only allows her to get more practice in Swedish then she gets talking with just me or her grandmother, but we also get to really recharge our batteries in the fabulous wilderness up there.

How to recharge in Sweden

Flashback: Noise in the brain?

As part of my scheduled re-posts during the summer break, I’ll also post some of the science videos from the archives. I originally posted this one on Agust 31, 2011:

SummerScienceVideo: science is real

This is a slightly edited (amended, essentially) version of

my article published today at The Conversation. In cases where a problem within a community is detected and collective action is required to address the problem. one needs to strike a fine line or any efforts to convince the community that action is required will fail.

The Conversation: The looming crisis in science

Following the example of Glyn Moody, I thought I’d start a log on the tweets I send around. One never knows what’ll happen to Twitter and besides, this provides a neat place to store and find everything. So here are the tweets for July first and second: Where are we, what still needs to be done?

Trying a new feature: Tweetlog

You may have seen a neutered version of this post over at the LSE blog. This post below, however, puts the tiger in the tank, as it was enhanced by CatGPT:  Maybe scholarly societies have taken “the instruction“follow the money!” a tad too literally?

Scholarly societies: like a cat chasing the laser dot

Yesterday, cOAlition S published their updated principles and implementation guidelines for #PlanS, together with the rationale behind the update. This constitutes a very much welcome effort, as evidence of the increasing awareness among funders as to their potential leverage in infrastructure modernization, at a time when institutions have apparently abandoned their faculty completely.

Improved Plan S principles raise hope of more effective policies soon

Due to ongoing discussions on various (social) media, this is a mash-up of several previous posts on the strategy of ‘flipping’ our current &gt;30k subscription journals to an author-financed open access corporate business model. I consider this article processing charge (APC)-based version of ‘gold’ OA a looming threat that may deteriorate the situation even beyond the abysmal state scholarly publishing is already in right now.

How gold open access may make things worse

Public institutions the world over are required to spend their funds responsibly. Commonly, this is done by requiring them to host bids for purchases or services above a certain threshold. If you work at a public institution and have wondered, e.g., why you are only allowed to buy a computer from your computing facility which only sells one particular brand, then the answer likely is that this brand won the bidding contest.

Should public institutions not be choosing the lowest responsible bidder?

Earning credibility in post-factual science?

For our course this year I was planning a standard neurogenetic experiment. I hadn’t ever done this experiment in a course, yet, just two weeks ago I tried it once myself, with an N=1. The students would get two groups of

 Drosophila

fruit fly larvae, rovers and sitters (they wouldn’t know which was which). About ten larvae from each group would be placed on one of two yeast patches on an agar plate.

If only all science were this reproducible

The recently discussed scenario of universal gold open access brought about by simply switching the subscriptions funds at libraries to have the libraries pay for author processing charges instead, seemed like a ghoulish nightmare. One of the few scenarios worse than the desolate state we call the

 status quo

today.

Whither now, Open Access?

On May 23, the Council of the EU adopted a set of conclusions on scholarly publishing that, if followed through, would spell the end for academic publishers and scholarly journals as we know them. On the same day, the adoption was followed by a joint statement of support by the largest and most influential research organizations in Europe.

The beginning of the end for academic publishers?

For ages I have been planning to collect some of the main aspects I would like to see improved in an upgrade to the disaster we so euphemistically call an academic publishing system. In this post I’ll try to briefly sketch some of the main issues, from several different perspectives.

 As a reader:

I’d like to get a newspaper each morning that tells me about the latest developments, both in terms of general science news (aka.

What should a modern scientific infrastructure look like?

The debate over how publishers use the large “non-publication costs” (Fig. 1) that they incur and academic libraries, mainly, are funding has been going on for some time now. Above and beyond the cost items we discuss in our paper on publication costs, it has been established that investments in surveillance technology are also part of the publisher spending academic libraries are financing.

Prioritizing academic publishers

Barely a fortnight has passed since

 Science Magazine

published the outcomes of a hoax perpetrated by one of their reporters, John Bohannon. Not surprisingly, the news article was widely criticized, not the least on this obscure blog. The content was simple enough: Bohannon picked a swath of largely fake journals, submitted fake manuscripts and boasted that more than 60% of his submissions were accepted.

Not to be outdone, Nature Magazine rejects data, publishes opinion

It is one of these rare events when I can post a video of one of my own talks. This one was in Berlin earlier this year, organized by The Lost Lectures in a very unusual venue, the Stattbad Wedding:    I’m planning to work more closely together with our computing center here to be able to record at least the lectures I give in English here at the university. So maybe there will be some more videos here, soon.

Video: Free will as an evolved brain function

Flashback: What can the spine teach us about learning?

Flashback: The neurobiology of operant conditioning

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.

A wonderful example of Open Science

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.

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

Our lab is looking for a PhD student interested in the molecular mechanisms of operant self-learning, a form of motor learning.

Looking for a PhD student

There have been many discussions about the march for science, pro and con. Some of them have made me doubt the utility of the march, some have made me fear unintended consequences, again others seemed tangential and petty. In these past months, I have struggled to articulate my own reasons why I feel the urge to march for science. Today, I start to see two main reasons to march for science.

Why I march

“an academic career, in which a person is forced to produce scientific writings in great amounts, creates a danger of intellectual superficiality”

Albert Einstein Isaacson W (2008) Einstein (His Life and Universe) (Simon and Schuster, New York), 1st Ed, p 79

On the productivity of scientists

This is an easy calculation: for each subscription article, we pay on average US$5000. A publicly accessible article in one of SciELO’s 900 journals costs only US$90 on average. Subtracting about 35% in publisher profits, the remaining difference between legacy and SciELO costs amount to US$3160 per article.

Are we paying US$3000 per article just for paywalls?

Over the last few months, there has been a lot of talk about so-called “predatory publishers”, i.e., those corporations which publish journals, some or all of  which purport to peer-review submitted articles, but publish articles for a fee without actual peer-review. The origin of the discussion can be traced to a list of such publishers hosted by librarian Jeffrey Beall.

Predatory Priorities

This year marks the 12th anniversary of the publication of this legendary letter to the editor in the Journal of systems and Software:  Nothing really has changed in a dozen years, it seems

12 year anniversary of angry letter to scientific journal editor

bjoern.brembs.blog

For the last few years, we have been working on the development of new
[*Drosophila* flight
simulators](http://brembs.net/learning/drosophila/simulator.html). Now,
finally, we are reaching a stage where we are starting to think about
how to store the data we'll be capturing both with Open Science in mind,
but particularly keeping in mind that this will likely be the final
major overhaul of this kind of data until I retire in 20 years. The plan
is to have about 3-5 such machines here and potentially others in other
labs, if these machines remain as 'popular' as they have been over the
last almost 60 years. So I really want to get it right this time (if
there is such a thing as 'right' in this question).

Such an experiment essentially captures time series with around 70-120k
data points per session, where about 3-6 variables are stored, i.e., a
total of at most \~500-800k table cells per session, each with 8-12bit
resolution. There will be at most about 8-16 such sessions per day and
machine, so we're really talking small/tiny data here.

Historically (i.e., from the early 1990s on), these data were saved in a
custom, compressed format (they needed to fit on floppy disks) with
separate meta-data and data files. We kept this concept of separated
meta-data from data also in other, more modern set-ups such as our
[Buridan experiments](http://brembs.net/buridan/). For these
experiments, we use XML for the meta-data files ([example
data](https://github.com/jcolomb/CeTrAn/tree/master/CeTrAn/example_data/schmale_streifen)).
One of our experiments also uses data files where the meta-data are
contained as a header at the beginning of the file with the actual
time-series data below ([example
data](https://figshare.com/account/home#/projects/3434)). That of course
makes for easy understanding of the data and makes sure the meta-data
are never separated from the raw data, i.e., less potential for
mistakes. In another, newer, experiment we are following some of the
standards from the [Data Documentation
Initiative](https://www.ddialliance.org) (no example data, yet).

With all of these different approaches over the last two decades, I
thought I ought to get myself updated on by now surely generally agreed
on conventions for data structure, meta-data vocabularies, naming
conventions, etc. I started looking around and got the impression that
the different approaches we have used over time are still being used and
then some new ones, of course. I then asked on
[Twitter](https://twitter.com/brembs/status/829689387013308418) and the
varying responses confirmed my impression that there isn't really a
"best-practice" kind of rule.

Given that there was quite a lively discussion on Twitter, I'm hoping to
continue this discussion here, with maybe an outcome that can serve as
an example use case someday.

What do we want to use these data for?

Each recording session will be one animal experiment with different
phases ("periods") during the experiment, for instance some "training"
sessions and some "test" sessions with experimental conditions differing
between training and test. The data will be saved as time series data
continuously throughout the experiment, so the minimal data would be a
timestamp, the behavior of the animal and a variable (stimulus) that the
animal is controlling with its behavior. Thus, in the simplest case,
three columns of integers.

The meta-data for each experiment has to contain a description of the
columns, of course, as well as date and time at the start of the
experiment, genotype of the animal, text description of the experiment,
DOI of the code used to generate the data, sequence and duration of
periods, temperature, and other variables to be recorded or set on a per
session or per period level.

A dataset or small project can consist of maybe three to four groups of
experiments, let's say one experimental genotype and two control groups.
Traditionally the way we handled this grouping in most of our
experiments, is to keep a text file in which the experimenter lists
which file belongs to which group. That way, anybody can read the text
file and get an understanding of the experimental design. The file also
contains comments and notes about user observations during the
experiment and a text description of the project. In a way, this text
file is like a meta-data file for a data-set, rather than an individual
experiment and thus should probably also contain some minimal mark-up.
This text file is then read by either custom software or an R script to
compile summary data for each group, e.g. means and standard errors of
some variables we extract on a per period basis, plotted and compared
between groups. As there are numerous ways to evaluate an animal's
behavior if we have the full time series, there is any number of
different parameters one can want to extract from the data and
plot/compare.

This is where the open science part would come in. Whenever the user
runs the script that evaluates, plots and compares the data, the entire
dataset is automatically made publicly accessible. Along with the
dataset (raw data, meta-data and grouping text file), all the
evaluations should also be deposited. Currently, we do this as a PDF
file, but that is all but useless -- only for human use. Ideally, I'd
like this evaluation file to contain all the content of the grouping
text file, as well as the DOI of the script that generated it and
(semantic?) markup that structures the evaluation document. Such an
evaluation document would be both machine and human (with a reader,
which is why we started by using the PDF format) readable and provide an
overview of exactly what was done to what data.

One eventual goal is to also use these evaluation documents during
manuscript authoring. Instead of copying the figures, pasting them into
a manuscript and then trying to describe the statistics, I'd like to
just link the different evaluations from inside the manuscript. Each
figure in a manuscript would then just be a link to one of the
evaluations in the evaluation document, the one I want readers to see so
they can follow my line of arguments. Any reader who wants to see other
aspects of the data has single-click access to the entire evaluation
document, with all our evaluations for this data-set, as well as access
to all the code used to generate and evaluate the data, if they so wish.
For this, all the data and meta-data in each dataset has to be linked to
both each other, and the code and the text. Of course, all the data in a
manuscript should also be linked together, even though they likely come
from different datasets/projects.

With the data and code solutions we're currently developing, this should
allow us to just write code, collect data and link both into our
manuscripts. Everything else (data management, DOI assignment, data
deposition, etc.) would be completely automatic. Starting at the
undergraduate student level, users would simply have to follow one
protocol for their experiments and have all their lab-notebooks
essentially written and published for them -- they'd have a collection
of these evaluation documents, ready to either be used by their
supervisor, or to be linked in a thesis or manuscript.

So, what would be the best data structure and meta-data format with
these goals in mind?


For the last few years, we have been working on the development of new

 Drosophila

flight simulators. Now, finally, we are reaching a stage where we are starting to think about how to store the data we’ll be capturing both with Open Science in mind, but particularly keeping in mind that this will likely be the final major overhaul of this kind of data until I retire in 20 years.

bjoern.brembs.blog

Data structures for Open Science