Björn Brembs

So this is essentially what happened instead of us sitting down and thinking how we could spend our money in the most technologically savvy way to the benefit of science, scholars and society. A generation later, roughly US$300 billion poorer and none the wiser, it seems.

The ultimate Open Access timeline

tl;dr: So far, I can’t see any principal difference between our three kinds of intellectual output: software, data and texts.   I admit I’m somewhat surprised that there appears to be a need to write this post in 2014. After all, this is not really the dawn of the digital age any more.

What is the difference between text, data and code?

Lately, there has been some public dreaming going on about how one could just switch to open access publishing by converting subscription funds to author processing charges (APCs) and we’d have universal open access and the whole world would rejoice. Given that current average APCs have been found to be somewhat lower than current subscription costs (approx.

What happens to publishers that don’t maximize their profit?

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!

While the first day (day 2, day 3) was dominated by philosophy, mathematics and other abstract discussions of chance, this day of our symposium started with a distinct biological focus.

 Martin Heisenberg, Chance in brain and behavior

First speaker for this second day on the symposium on the role of chance in the living world was my thesis supervisor and mentor, Martin Heisenberg.

Chance in animate nature, day 2

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

*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.

Flashback: Programming Free Will – creative robots

For 14 years, the main research funding agency in Germany, the German Research Foundation (DFG) has stated in its guidelines that submitted grant proposals will be assessed primarily on the basis of their

 content

, rather than counting the applicants’ previous publications. However, not all of DFG’s panels seem to be on board.

Research assessment: new panels, new luck?

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

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

Over the weekend, I received the following short message from a Hotmail account:  This email is full of signs that the student may not have been all that interested in any information or discourse, but instead trying to make some sort of ‘gotcha’ statement. Curiously, the author first states that their scientific training is lacking and then they disagree with a scientific position.

How not to contact faculty as student

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?

In what area of scholarship are repeated replications of always the same experiment every time published and then received with surprise, only to immediately be completely ignored until the next study? Point in case from an area that ought to be relevant to almost every single scientist on the planet: research evaluation.

How scientific are scientists, really?

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

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

Yesterday, Alex Kacelnik published yet another fascinating discovery – one of many over the years out of his lab. This time, they show how birds can pick even five consecutive locks to get to a food reward:  According to the authors, the birds solve this problem by trial and error, i.e., in the operant, goal-directed way, which is the learning mechanism we study in our lab.

…and now for some lock-picking cockatoos

There can be little doubt that the defunding of public academic institutions is a main staple of populist movements today. Whether it is Trump’s budget director directly asking if one really needs publicly funded science at all, or the planned defunding of the endowments of arts and humanities or the initiatives to completely abolish the EPA and other science agencies.

Are we inadvertently supporting the defunding of public science?

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?

I usually don’t write about politics, but there has been one or the other exception to this rule in the last 12 years of this blog. This time, I’ve been missing one particular response to the various terrorist attacks in recent times, perhaps one of the few readers of this obscure blog has found it somewhere and can point me in this direction?

Have you seen this response to terrorism anywhere?

UPDATE

: I’m still not completely sure I understood Churchland accurately, but there are comments suggesting I may just have completely misunderstood her replies to the interviewer. Read the interview and judge for yourself! I really like Patricia Churchland.

[updated]Churchland: “Ignore science and live a make-believe life!”

In the process of migrating content from the old site to WordPress, I’m also moving some articles from there and re-publishing them here as posts. This one is such a case, originally published on December 7, 2006.

Brains as output/input systems

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 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

Rejection is one of the unpleasant but inevitable components of life. There are positive components to rejection: they build character, they force you to deal with negativity and sometimes they force you to change your life to avoid future rejections.

The cost of the rejection-resubmission cycle

At seemingly every possibility in a discussion on peer-review, people apparently feel the need to emphasize that in the current model reviewers (or most academic editors handling peer-review) are not being paid.

Peer-review is not free – it’s a subsidy for publishers

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?

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

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

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

Just before Christmas 2019, the Washington Post reported, based on “people familiar with the matter”, that the US Justice Department were investigating the Sci-Hub founder Alexandra Elbakyan for potentially “working with Russian intelligence to steal U.S. military secrets from defense contractors”. Besides such a highly unusual connection, the article also reiterated unsubstantiated (but mainly circulated by publishers) allegations that access

Is the SNSI the new PRISM?

Jeffrey “predatory journals” Beall famously catapulted himself out of any serious debate with an article in the journal TripleC, entitled “The Open-Access Movement is Not Really about Open Access”. In it, Beall claimed that OA proponents don’t care about access, but that they form an “anti-corporatist movement that wants to deny the freedom of the press to companies it disagrees with”. The article is so replete with similarly unhinged fairy

Is this Smits’ tripleC moment?

Open Access (OA) pioneer and OA journal eLife founding member and sponsor, the Max Planck Society just released a white paper (PDF) analyzing open access costs in various countries and institutions and comparing them to subscription costs. Such studies are fundamental prerequisites for evidence-based policies and informed decisions on how to proceed with bitterly needed reforms.

A study justifying waste of tax-funds?

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 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

In her recent editorial on Sci-Hub (an initiative I support), editor-in-chief of

 Science Magazine

Marcia McNutt wrote: The editorial is essentially trying to make the somewhat tenuous but not implausible case that using sci-hub may lead to subscription cancellations which, in turn, may lead to scholarly societies (like those of Dr. McNutts employer, AAAS) to miss revenue they need in order to pay for important services (such as paying

In which a Science editorial demonstrates the ineffectiveness of OA activism

Over the years, publishers have left some astonishingly frank remarks over how they see their role in serving the scholarly community with their communication and dissemination needs. This morning, I decided to cherry-pick some of them, take them out of context to create a completely unrealistic caricature of publishers that couldn’t be further from the truth.

How do academic publishers see their role?

You’d be forgiven if after reading the title of this post, you thought scholars have started to revolt against journal rank. Unfortunately, while there is DORA and of course the evidence that journal rank is like homeopathy, most researchers are still fine with ex-scientists rejecting 92% of all submitted articles and charging a grand sum of more than US$30,000 per article that they select on a whim.

Publisher selects the best open access science – authors complain

Earning credibility in post-factual science?

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

Scientists as social parasites?

Time and time again, academic publishers have managed to create the impression that publishing incurs a lot of costs which justify the outrageous prices they charge, be that US$11M p.a. for an

 Elsevier

Big Deal subscription or an article processing charge (APC) of US$5,200 for a

 Nature Communications

article.

How publishers keep fooling academics

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

As a regular user of the scholarly literature since before the internet (I started reading primary scientific literature for a high-school project around 1989), I have closely followed its digitization.

7 functionalities the scholarly literature should have

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

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?

The cost of knowledge – in 2003?

It’s the time of the year again where 30,000 neuroscientists head to the US to talk neuroscience. This year the big annual conference is in Washington, DC, one of the three cities able to host this large event. Our first poster will be up on Tuesday morning and shows results from operant self-stimulation experiments using optogenetics and dopaminergic neurons.

Heading for #SfN23 with two posters

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?

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

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?

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

“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 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

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?

Until today, I was quite proud of myself for not caving in to SIWOTI syndrome like Mike Taylor did. And then I read his post and caved in as well. What gets us so riled up is Elsevier’s latest in a long list of demonstration of what they think of the intellectual capacities of their customers. It’s precisely because it is only one in a long row that I initially didn’t feel like commenting.

Is this supposed to be the best Elsevier can muster?

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?

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

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

Random Science Video: The value of fly research

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

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?

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

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

The other day I was alerted to an interesting evaluation of international citation data. The author, Curt Rice, mentions a particular aspect of the data:  The context here is that the “bottom” refers to scientific articles that aren’t cited, assuming that no citations mean low scientific quality of that article.

Citation inflation and incompetent scientists

Genetically Separable" href="https://www.slideshare.net/brembs/wcalb14" target="_blank"&gt;Pavlovian and Skinnerian Processes are Genetically Separable

Two evolutionary conserved, fundamental learning mechanisms

Sven Fund, CEO of the German publishing house de Gruyter was recently interviewed by Richard Poynder in his widely read interview series on open access. In the interview, he first avoided answering the question if de Gruyter had ever lobbied against open access.

Is de Gruyter’s lobby-by-proxy not lobbyism?

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?

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

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

A fistful of dollars: why corporate publishers have no place in scholarly communication

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

Flashback: All brains possess free will because there is no design in biology

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.

Science, red in tooth and claw

*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 February 9, 2011: *     In this week’s journal club, we talked about an old paper from 1918!

Flashback: Nothing new 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’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 this one on Agust 31, 2011: *

SummerScienceVideo: science is real

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

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.

SHARE: Library-based publishing becoming a reality?

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

Amazing bead chain experiment

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:
 
 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?

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

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!

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

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

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

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?

Talk about egg on face!

 Nature

“the world’s best science”

 Magazine

sets out to publish back-to-back papers on – of all topics – stem cell science.

Even the most thorough peer-review at the ‘best’ journals not up to snuff?

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?

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?

Flashback: What can the spine teach us about learning?

Flashback: The neurobiology of operant conditioning

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

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.

A new home for bjoern.brembs.blog

I recently was sent a report from a university-wide working group on the publishing habits within the Freie Universität Berlin. I don’t think this document is available online, but I think I’m not doing anything illegal if I publish some of the survey results here. The working group polled all faculty members of the university on various questions concerning scholarly publishing.

How important is the Impact Factor?

Think, check, submit: who hasn’t heard of this mantra to help researchers navigate the jungle of commercial publishers? Who isn’t under obligation to publish in certain venues, be it because employers ask for a particular set of journals for hiring, tenure or promotion, or because of funders’ open access mandates?

How academic institutions neglect their duty

The academic journal publishing system sure feels all too often a bit like a sinking boat: we have a reproducibility leak an affordability leak a functionality leak a data leak a code leak an interoperability leak a discoverability leak a peer-review leak a long-term preservation leak a link rot leak an evaluation/assessment leak a data visualization leak … … … and even a tiny access leak still remains even after 30 years of trying to fix it.

Scholarly publishing in three cartoons

bjoern.brembs.blog

Last week, I spent two days at a symposium entitled "[Governance,
Performance & Leadership of Research and Public
Organizations](https://www.faces.wi.tum.de/index.php?id=121)". The
meeting gathered professionals from all walks of science and research:
economists, psychologists, biologists, epidemiologists, engineers,
jurists as well as politicians, university presidents and other leaders
of the most respected research organizations in Germany. It was
organized by [Isabell
Welpe](https://www.professoren.tum.de/en/welpe-isabell-m/), an economist
specializing in incentive systems, broadly speaking. She managed to
bring some major figures to this meeting, not only from Germany, but
notably also [John
Ioannidis](https://med.stanford.edu/profiles/john-ioannidis) from the
USA or [Margit Osterloh](https://www.voxeu.org/person/margit-osterloh)
from Switzerland. The German participants included former DFG president
and now Leibniz president [Matthias
Kleiner](https://www.leibniz-gemeinschaft.de/en/about-us/organisation/president/matthias-kleiner/)
(the DFG being the largest funder in Germany and the Leibniz Association
consisting of 89 non-university federal research institutes), president
of the [German Council for Science and the
Humanities](https://en.wikipedia.org/wiki/German_Council_of_Science_and_Humanities),
[Manfred Prenzel](https://www.professoren.tum.de/en/prenzel-manfred/),
Secretary General of the Max-Planck Society [Ludwig
Kronthaler](https://www.mpg.de/619162/new-secretary-general-2010), or
the president of Munich's Technical University, [Wolfgang
Herrmann](https://portal.mytum.de/tum/praesident/index_html), only to
mention some of them. Essentially, all major research organizations in
Germany were represented with at least one of their leading positions,
supplemented with expertise from abroad.

All of these people shape the way science will be done in the future
either at their universities and institutions, or in Germany or around
the world. They are decision-makers with the power to control the work
and job situation for tens of thousands of current and future
scientists. Hence, they ought to be the most problem-solving oriented,
evidence-based individuals we can find. I was shocked to learn that this
was an embarrassingly naive assumption.

In my defense, I was not alone in my incredulity, but maybe that only
goes to show how insulated scientists are from the political realities.
As usual, there were of course gradations between the individuals, but
at the same time there seemed to be a discernible grouping in what could
be termed the evidence-based camp (scientists and other professionals)
and the ideology-based camp (the institutional leaders). With one
exception I won't attribute any of the instances I will recount to any
particular individual, as we better focus on the solutions to the more
general prohibitive  attitude, rather than on a debate about the
individuals' qualifications.

On the scientific side, the meeting brought together a number of thought
leaders detailing how different components of the scientific community
perform. For instance, we learned that peer-review is quite capable of
weeding out obviously weak research proposals, but in establishing a
ranking order among the non-flawed proposals, it is rarely better than
chance. We learned that gender and institution biases are rampant in
reviewers and that many rankings are devoid of any empirical basis.
Essentially, neither peer-review nor metrics perform at the level we
expect from them. It became clear that we need to find solutions to the
lock-in effect, the Matthew effect and the performance paradox and to
some extent what some potential solutions may be. Reassuringly,
different people from different fields using data from different
disciplines arrived at quite similar conclusions. The emerging picture
was clear: we have quite a good empirical grasp of which approaches are
and in particular which are not working. Importantly, as a community we
have plenty of reasonable and realistic ideas of how to remedy the
non-working components. However, whenever a particular piece of evidence
was presented, one of the science leaders got up and proclaimed "In my
experience, this does not happen" or "I cannot see this bias", or "I
have overseen a good 600 grant reviews in my career and these reviews
worked just fine". Looking back, an all too common scheme of this
meeting for me was one of scientists presenting data and evidence, only
to be countered by a prominent ex-scientist with a "I disagree without
evidence". It appeared quite obvious that we do not seem to suffer from
a lack of insight, but rather from a lack of implementation.

Perhaps the most egregious and hence illustrative example was the
behavior of the longest serving university president in Germany,
Wolfgang Herrmann, during the final panel discussion (see
[\#gplr](https://twitter.com/search?q=%23gplr&src=typd&vertical=default&f=tweets)
on Twitter for pictures and live comments). This will be the one
exception to the rule of not mentioning individuals. Herrmann was the
first to talk and literally his first sentence was to emphasize that the
most important objective for a university must be to get rid of the
mediocre, incompetent and ignorant staff. He obviously did not include
himself in that group, but made clear that he knew how to tell who
should be classified as such. When asked which advice he would give
university presidents, he replied by saying that they ought to rule
autocratically, ideally by using 'participation' as a means of appeasing
the underlings (he mentioned students and faculty), as most faculty were
unfit for democracy anyway. Throughout the panel, Herrmann continually
commended the German [Excellence
Initiative](https://www.excellence-initiative.com/), in particular for a
'raised international visibility' (whatever that means), or 'breaking up
old structures' (no idea). When I confronted him with the [cold hard
data](https://bjoern.brembs.net/2015/01/booming-university-administrations)
that the only aspects of universities that showed any advantage from the
initiative were their administrations and then asked why that didn't
show that the initiative had, in fact, failed spectacularly, his reply
was: "I don't think I need to answer that question". In essence, this
reply in particular and the repeated evidence-resistant attitude in
general dismissed the entire symposium as a futile exercise of the
'[reality-based
community](https://en.wikipedia.org/wiki/Reality-based_community)',
while the big leaders were out there creating the reality for the
underlings to evaluate, study and measure.

Such behaviors are not surprising when we hear them from politicians,
but from (ex-)scientists? At the first incidence or two, I still thought
I had misheard or misunderstood -- after all, there was little
discernible reaction from the audience. Later I found out that not only
I was shocked. After the conference, some attendees discussed several
questions: Can years of leading a scientific institution really make you
so completely impervious to evidence? Do such positions of power
necessarily wipe out all scientific thinking, or wasn't all that much of
it there to begin with? Do we select for evidence-resistant science
leaders or is being/becoming evidence-resistant in some way a
prerequisite for striving for such a position? What if these
ex-scientists have always had this nonchalant attitude towards data?
Should we scrutinize their old work more closely for questionable
research practices?

While for me personally such behavior would clearly and unambiguously
disqualify the individual from any leading position, relieving these
individuals from their responsibilities is probably not the best
solution. Judging from the meeting last week, there are simply too many
of them. Instead, it emerged from an informal discussion after the end
of the symposium, that a more promising approach may be a different
meeting format: one where the leaders aren't propped up for target
practice, but included in a cooperative format, where admitting that
some things are in need of improvement does not lead to any loss of
face. Clearly, the evidence and the data need to instruct policy. If
decision-makers will be ignoring the outcomes of empirical research on
the way we do science, we might as well drop all efforts to collect the
evidence.

Apparently, this was the first such conference on a national level in
Germany. If we can't find a way for the data presented there to have a
tangible consequence on science policy, it may well have been the last.
Is this a phenomenon people observe in other countries as well, and if
so, how are they trying to solve it?


Last week, I spent two days at a symposium entitled “Governance, Performance &amp; Leadership of Research and Public Organizations”. The meeting gathered professionals from all walks of science and research: economists, psychologists, biologists, epidemiologists, engineers, jurists as well as politicians, university presidents and other leaders of the most respected research organizations in Germany.

Evidence-resistant science leaders?

tl;dr: So far, I can't see any principal difference between our three
kinds of intellectual output: software, data and texts.

 

I admit I'm somewhat surprised that there appears to be a need to write
this post in 2014. After all, this is not really the dawn of the digital
age any more. Be that as it may, it is now March 6, 2014, six days since
PLoS's 'revolutionary' [data sharing
policy](https://www.plos.org/data-access-for-the-open-access-literature-ploss-data-policy/)
was revealed and only few people seem to observe the irony of avid
social media participants pretending it's still 1982. For the
uninitiated, just skim Twitter's
[\#PLoSfail](https://twitter.com/search?q=%23PLOSfail&src=tyah), read
[Edmund Hart's post](https://emhart.info/blog/2014/03/04/data-sharing/)
or see [Terry McGlynn's
post](https://smallpondscience.com/2014/03/03/i-own-my-data-until-i-dont/)
for some examples. I'll try to refrain from reiterating any arguments
made there already.

Colloquially speaking, one could describe the scientific method somewhat
shoddily as making an observation, making sense of the observation and
presenting the outcomes to interested audiences in some version of
language. Since the development of the scientific method somewhere
between the 16th century and now, this is roughly  how science has
progressed. Before the digital age,it was relatively difficult to let
everybody who was interested participate in the observations. Today,
this is much easier. It still varies tremendously between fields,
obviously, but compared to before, it's a world's difference. Today, you
could say that scientists collect data, evaluate the data and then
present the result in a scientific paper.

Data collection can either be done by hand or more or less
automatically. It may take years to sample wildlife in the rainforest
and minutes to evaluate the data on a spreadsheet. It may take decades
to develop a method and then seconds to collect the data. It may take a
few hours to generate the data first by hand and then by automated
processing, but decades before someone else comes up with the right way
to analyze and evaluate the data. What all scientific processes today
have in common is that at some point, the data becomes digitized, either
by commercial software or by code written precisely or that purpose.
Perhaps not in all, but surely in the vast majority of quantitative
sciences, the data is then evaluated using either commercial or
hand-coded software, be it for statistical testing, visualization,
modeling or parameter/feature extraction, etc. Only after all this is
done and understood does someone sit down and attempts to put the
outcome of this process into words that scientists not involved in the
work can make sense of.

Until about a quarter of a century ago, essentially all that was left of
the scientific process above were some instruments used to make the
observations and the text accounts of them. Ok, maybe some paper records
and later photographs. With a delay of about 25 years, the scientific
community is now slowly awakening to the realization that the
digitization of science would actually allow us to preserve the
scientific process much more comprehensively. Besides being a boon for
historians, reviewers, committees investigating scientific misconduct or
the critical public, preserving this process promises the added benefit
of being able to reward not only those few whose marketing skills
surpass the average enough to manage publishing their texts in glamorous
magazines, but also those who excel at scientific coding or data
collection. For the first time in human history, we may even have a shot
at starting to think about developing software agents that can trawl
data for testable hypotheses no human could ever come up with -- proofs
of concepts already exist. There is even the potential to [alert
colleagues](https://bjoern.brembs.net/2013/05/a-wonderful-example-of-open-science/)
to problems with their data, use the code for purposes the original
author did not dream of or extract parameters from data the
experimentalist had not the skill to do. In short, the advantages are
too many to list and reach far beyond science itself.

Much like the after the previous [hypothetical requirement of proofs for
mathematical
theorems](https://proteinsandwavefunctions.blogspot.dk/2014/03/top-10-reasons-to-not-share-your-data.html),
or the [equally hypothetical requirement of statistics and sound
methods](https://www.nature.com/news/announcement-reducing-our-irreproducibility-1.12852),
there is again resistance from the more conservative sections of the
scientific community for largely the [same 10
reasons](https://proteinsandwavefunctions.blogspot.dk/2014/03/top-10-reasons-to-not-share-your-data.html),
subsumed by: "it's too much work and it's against my own interests".

I can sympathize with this general objection as making code and data
available is more work and does facilitate scooping. However, the same
can be said of publishing traditional texts: it is a lot of work that
takes time away from experiments and opens all the flood gates of others
making a career on the back of your work. Thus, any consequential
proponent of "it's too much work and it's against my own interests"
ought to resist text publications with just as much fervor as they
resist publishing data and code. The same arguments apply.

Such principles aside, in practice, of course our general infrastructure
makes it much too difficult to publish either text, data or software,
which is so many of us now spend so much time and effort on publishing
reform and why our lab in particular is [developing ways to improve this
infrastructure](https://www.slideshare.net/brembs/making-science-open-by-default).
But that, as well, does also not differ between software, data and
science: our digital infrastructure is dysfunctional, period.

Neither does making your data and software available make you
particularly more liable to scooping or exploitation than the
publication of your texts does. The risks vary dramatically from field
to field and from person to person and are impossible to quantify.
Obviously, just as with text publications, data and code must be cited
appropriately.

There may be instances where the person writing the code or collecting
the data already knows what they want to do with the code/data next, but
this will of course take time and someone less gifted with ideas may be
on the hunt for an easy text publication. In such (rare?) cases, I think
it would be a practical solution to implement a limited provision on the
published data/code stating the precise nature of the planned research
and the time-frame within which it must be concluded. Because of its
digital nature, any violation of said provisions would be easily
detectable. The careers of our junior colleagues need to be protected
and any publishing policy on text, data or software ought to strive
towards maximizing such protections without hazarding the entire
scientific enterprise. Also here no difference between text,data and
software.

Finally, one might make a reasonable case that the rewards are stacked
disproportionately in favor of text publications, in particular with
regard to publications in certain journals. However, it
[almost](https://twitter.com/DNLee5/status/441511863122018304) goes
without saying that it is also unrealistic to expect tenure committees
and grant evaluators to assess software and data contributions before
anybody even is contributing and sharing data or code. Obviously, in
order to be able to reward coders and experimentalists just as we reward
the Glam hunters, we first need something to reward them for. That being
said, in today's antiquated system it is certainly a wise strategy to
prioritize Glam publications over code and data publications -- but
without preventing change for the better in the process. This is
obviously a chicken-and-egg situation which is not solved by the
involved parties waiting for each other. Change needs to happen on both
sides if any change is to happen.

To sum it up: our intellectual output today manifests itself in code,
data and text. All three are complementary and contribute equally to
science. All three expose our innermost thoughts and ideas to the
public, all three make us vulnerable to exploitation. All three require
diligence, time, work and frustration tolerance. All three constitute
the fruits of our labor, often our most cherished outcome of passion and
dedication. It is almost an insult to the coders and experimentalists
out there that these fruits should remain locked up and decay any
longer. At the very least, any opponent to code and data sharing ought
to consequentially also oppose text publications for exactly the same
reasons. We are already 25 years late to making our CVs contain code,
data and text sections under the "original research" heading. I see no
reason why we should be rewarding Glam-hunting marketers any longer.

**UPDATE**: I was just alerted to an important and relevant distinction
between text, data and code: [file
extension](https://twitter.com/IanMulvany/status/441651497257156608).
Herewith duly noted.


The recently released [development
draft](https://www.arl.org/storage/documents/publications/share-proposal-07june13.pdf)
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](https://www.whitehouse.gov/sites/default/files/microsites/ostp/ostp_public_access_memo_2013.pdf)
to federally funded research in the US sounds a lot like the
library-based publishing system I've
[been](https://bjoern.brembs.net/2013/06/cut-out-the-parasitic-middlemen/)
[perpetually](http://blogarchive.brembs.net/comment-n856.html)
[arguing](http://blogarchive.brembs.net/comment-n841.html)
[for](http://blogarchive.brembs.net/comment-n835.html). It's even in our
[paper on the pernicious consequences of journal
rank](https://www.frontiersin.org/Human_Neuroscience/10.3389/fnhum.2013.00291/abstract){target="_blank"}.
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](https://bjoern.brembs.net/2013/06/cut-out-the-parasitic-middlemen/),
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.


In our [new lab here in
Regensburg](http://blogarchive.brembs.net/comment-n875.html), we are
currently re-establishing the method of [confocal
microscopy](https://en.wikipedia.org/wiki/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](https://lab.brembs.net/biofoo_project/the-neurobiology-of-spontaneous-flight-behavior-in-drosophila/)).
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](https://youtube.com/brembs){target="_blank"}:

::: {.youtube style="width: 450; height: 400;"}
:::

Only an hour or so after I posted the video, [Douglas
Armstrong](https://homepages.inf.ed.ac.uk/jda/){target="_blank"} sent me
an email:

> <div>
>
> 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/>
>
> </div>

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!

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.

bjoern.brembs.blog

Evidence-resistant science leaders?

What is the difference between text, data and code?

SHARE: Library-based publishing becoming a reality?

A wonderful example of Open Science