Showing posts with label Open Access. Show all posts
Showing posts with label Open Access. Show all posts

December 22, 2017

The nightmare a couple of days before Christmas

by Daniel S. Margulies

'Twas two nights before Christmas
and throughout the net
a faint murmur was heard
that foretold great regret...[1]

From inbox to inbox
and web dissemination [2]
all soon heard of social neurosciences'
voodoo correlations.
source

But what's in a name?
How could all understand
what statistical nuances of criticism
were at hand? [3]

While some thusly retorted,
it all came too late,
as the mighty blogosphere
had decided its fate.

When a voice from within cried:
``But this is not fair!
Science can't be debated
out in open air!

When complex ideas
and thoughts are at play
behind tightly closed doors
must the dialogue stay.

Until resolutions within
the community are decided,
we're too vulnerable to
sensationalistic media bias.''[4]

``We know,'' said Vul et al,
"that you all are good-hearted.
We know that only needed
to finish what you started--
source

That statistics are tricky
That the tools are quite new;
But running biased
secondary analyses is voodoo.

There are ways to correct
the scientific lit
Just reanalyze your data
and we shall acquit." [5]

``But we did nothing wrong!
You misunderstand!
Using secondary correlations is NOT
some brilliant scam!

To bedazzle you
with brain-behavior relations!
It's just another way of doing
data presentation.''

``But do you really believe
Without correlation values so high
You could publish in Science,
Nature, and Nature Neurosci?''

``The question,'' they responded,
``is not how strong but where
such social function is processed
right under your hair.''

source
But with the tables turned,
None really cared.
Bloggers kept blogging,
And social neuroscience got scared:

``What will we do
when no one wants to fund us?
To publish our papers
or with brain scanners entrust us? [6,7]

Why were those voodoo
critics so mean?!
Naming our names,
and crushing our dreams?

All we ever wanted
was to help understand
Why people need people--
And how our brains lend a hand.

Why are we moral?
And why do we hate?
And how does the love or pain
of another translate?

Why does being alone
sometimes cause us such pain,
If all is controlled
by our solitary brains?
source

But most of all
how could we be to blame
For asking such questions
in the social realm's name?''

Over months the debate dwindled
'Till summer arrived at last
And a salmon was scanned
During a perspective taking task.

The point, the authors told us
Was not that dead salmons feel
But rather that the importance
Of statistical correction was real.

With uproarious laughter
The conference hall replied:
``Multiple comparison correction
Cannot be denied!''



The moral:

When finger pointing begins
You'll get everyone's attention
But surely before long
you'll be buried in dissention.

To say something critical,
Try to say it in jest--
And those who can follow
Might just heed your request.


1.    Vul, E. Ed Vul - Voodoo correlations. (2010).at <http://www.edvul.com/voodoocorr.php>
2.    Begley, S. The 'Voodoo' Science of Brain Imaging. Lab Notes  (2008).at <http://blog.newsweek.com/blogs/labnotes/archive/2009/01/09/the-voodoo-science-of-brain-imaging.aspx>
3.    Abbott, A. Brain imaging studies under fire. Nature News 457,  (2009).
4.    Jabbi, M., Keysers, C., Singer, T. \& Stephan, K.E. Voodoo Correlations in Social Neuroscience" by Vul et al. - summary information for the press. at <www.bcn-nic.nl/replyVul.pdf>
5.    Vul, E. Ed Vul - Voodoo rebuttal.  (2010).at <http://www.edvul.com/voodoorebuttal.php>
6.    Bardin, J. Voodoo That Scientists Do. Seed Magazine  (2009).at <http://seedmagazine.com/content/article/that_voodoo_that_scientists_do/>
7.    Lehrer, J. In Defense of the Value of Social Neuroscience. Mind Matters  (2009).at <http://www.scientificamerican.com/article.cfm?id=defense-social-neuroscience>

July 03, 2017

Piracy Ahoy: Hackers Get (Neuro)scientific

Working at a large, wealthy institution like the Charité, we are mostly insulated from the frustrations of academic paywalls. Multi-million euro academic subscription fees assure that works published in most large biomedical databases are easily within reach, and not being able to access a publication is the exception. However, in other places, a publisher paywall can literally make or break an academic career. A single paper typically costs around 20-30 euros to purchase, while some websites cheekily offer “rentals”. Imagine yourself considering what you can afford to read. In science, information is power, and corralling this information behind paywalls means a steep imbalance in who gets to set the tone of the cutting-edge research.

Introducing Sci-Hub
If the digitization of scientific knowledge is feeding an ever-growing problem, could it also provide some solutions? Some self-proclaimed scientific data pirates are using big data to beat online scientific publishing at its own game. Enter Sci-Hub [1], the “Pirate Bay of Scientific Publishing”. On this site, not unlike PubMed, anyone can search and download texts pertaining to their scientific field. It’s free, simple, and incredibly popular worldwide. Understandably, the publishers hate it.
A few quick facts and figures [2]: Sci-Hub handles about 200,000 paper requests per day, coming from all over the world and most academic disciplines. The heaviest use of the site is in Iran, but other nations aren’t far behind. The publisher arguably being hit hardest by these illegal downloads is Elsevier, though analysis found that Sci-Hub was only diverting about 5% of its legal traffic. Thus far, more than 6 million papers have been accessed through the site, and these numbers continue to grow. The number one downloaded paper so far was a piece on wind turbine testing [3], followed by a paper on glioma [4].
Sci-Hub was the brainchild of 22-year old Kazakh computer science and neuroscience student Alexandra Elbakyan. Frustrated by the lack of availability of scientific resources in her home country and with a knack for hacking, she created the site in the hopes of leveling the playing field for academics worldwide [5]. She’s widely been celebrated as a game-changer in the field of digital media, but her whereabouts are currently unknown… Due to ongoing legal proceedings, being found could mean imprisonment.

via Wikimedia Commons


The Publishers Strike Back
In 2015, the publication group Elsevier sued the website for unlawful use of copyrighted material [1]. Despite Elbakyan invoking the Universal Declaration of Human Rights, which calls on signatory parties to "to share in scientific advancement and its benefits", Sci-Hub lost, and the website was promptly taken down. However, thanks to a sophisticated team of hackers and administrators involved in the project, it was up again in no time, and has since appeared under several different domain names. In the age of Big Data, Sci-Hub is not disappearing anytime soon.
Recently, Science magazine undertook an official study on the use of Sci-Hub, and the results were surprising. Whereas the study authors expected that use of the site would be most popular in less developed countries, it seems that the site was also being heavily used in Europe and North America [2]. Site critics seized on this point, claiming that for most, data piracy was an issue of convenience, rather than necessity. In some sense, they’re right: Science’s analysis of the site found that a large number of open-access articles (which theoretically anyone, anywhere can access) were being pulled from the site.

Leverage and Loopholes
There are other reasons why some are skeptical of Sci-Hub. One argument is that official publishers often keep track of downloads and usage statistics for individual works – something that Sci-Hub doesn't do. These statistics are increasingly being used as career metrics for researchers. Without facts and figures about journal readership/downloads, institutions or smaller publishers may cut ties with periodicals that are immensely popular and useful to the community [6].
A final argument from the publishing industry is that many large companies already have lots of ways to get free access to articles in their collections. For example, after users register with the journal Science, they can access all articles that were published more than a year ago for free [6]. However, not all journals are as generous with their materials, and the loopholes that researchers have to jump through make the process cumbersome, and still occasionally expensive. The heavy use of Sci-Hub in less wealthy countries suggests that (a) most researchers don’t know about these special channels to access manuscripts behind paywalls, or (b) they don’t work as advertised [2,6]. Whether a matter of education or logistics, it’s clear that there is still significant work to be done on the part of the journals.

Piracy or Cooperative Change?
However, one point remains a fact: publishing companies are not immune to change. Ten years ago, open access publishing for scientific articles was still in its infancy, and today represents a major step forward in the democratization of scientific knowledge. This happened through public pressure together with cooperation of the companies. But will publishing companies ever be able to deal with scientific data piracy in a productive manner? Peter Suber from the Office of Scholarly Communications at Harvard put it succinctly when interviewed in Science: “Lawful open access forces publishers to adapt […], unlawful open access invites them to sue instead.” [2].

by Constance Holman, PhD Student AG Schmitz


[1] http://bit.ly/1UI574H
[2] http://bit.ly/1STnFAv
[3] Osgood et al. Proceedings of the IMAC-XXVIII, 2010
[4] Cancer Genome Atlas Research Network, NEJM 2015
[5] http://bit.ly/1SIgci8
[6] http://bit.ly/1NO7qSS

June 28, 2017

From Clay Tablets to eReaders: How Digitalization Changed Scientific Publishing

Creating knowledge is a researcher's primary goal, with publications being the vehicle for dissemination. However, manuscripts are no invention of modern times. The earliest evidence  of written records comes from clay tablets in Mesopotamia, and didn't change much until Johannes Gutenberg's revolutionary printing press in1450. This new technique brought us a huge step closer to mass-produced scientific publishing as we know it today. In 1665, the first scientific journal was founded: Philosophical Transactions of the Royal Society. Big titles of today, i.e. Nature and Science, only started in the 19th century [1].

In the very beginning, scholarly publishing was rather an expensive investment than a source of money, however, more recently publishers' business models were based on subscriptions and fees to finance processing, printing and shipping of their paper-based products [2,3].
The current process of scientific publishing works by selling access to journals that feature articles that have been submitted by authors for free and have been reviewed by peers for free as well. In contrast, open access journals and platforms, such as PLoS (Public Library of Science), levy a publication fee from authors, but make their articles available to everyone.

via Wikipedia


The Rise of Open Access
Despite an increasing variety of open access online journals classical publisher-controlled academic journals are not in decline. The (hotly debated) impact factor of a published paper still determines a good part of the reputation of scientists, tempting many to still prefer established classical journals over new open-access channels argues Michael Eisen, geneticist at Berkeley and one of the PLoS' founders [3]. However, nowadays several open-access titles are already high ranked, like Translational Psychiatry or PLoS One Medicine, rendering these concerns increasingly obsolete.
Only since 2008, when the NIH implemented open access rules in its funding policy [4], has the general attitude of the scientific community towards alternative journals changed. Consequently, the online journal PLoS One avoided producing classical print publications altogether and therefore rejection or delay in publication of articles due to space limitation of their (print) issue. The online only open access journal selects manuscripts only for their scientific quality, possibly ending the cherry-picking by the journal and subsequent delay of otherwise accepted work. Such a simple, but fundamental change in publishing policy has dramatically shortened the time until novel research enters public knowledge [3,5].
This is very important as only free access to research conclusions allows objectively informed and thus truly democratic processes. The control of knowledge via pay walls by very few publishing companies has inevitably led to formation of resistance: see an article on page 11 detailing the rise of data piracy in academic publishing.

Even Hotter Than Off The Presses
Another new approach to disseminate research independently from the publisher companies is provided by platforms like arXiv.org. They allow researchers to publish their work as preprints and have it critically reviewed by colleagues long before being submitted to classical scientific journals, a route of publishing common for mathematicians and physicists [6]. A similar approach was taken by the Registered Reports of the Journal of European Psychology Students, which allows publishing the work before any data was collected. Based on the scientific quality of the proposal, but independently of the results to be achieved, the submissions might be accepted to peer-review and publication afterwards [1].



DIGITALIZATION PERMITS FREE ACCESS TO KNOWLEDGE


Digitalization also changed the medium of publication from printed journal "papers", over to PDF files to alternative formats like ReadCube. Also, not only do publication databases enable fast searches for relevant literature, but newly established scientific social networks (like ResearchGate, Academia.edu or Mendeley by Elsevier) allow easy access to individual researchers and their work. Nowadays, this often includes "non-traditional" formats such as blogs or podcasts [7,3].
New technologies and digital tools have also influenced the kind of published data itself: Original studies can now easily include raw experimental data as supplemental files or freely available databases for other researchers to inspect. Web-based journals also allow easy embedding of various multimedia files as realized in the Journal of Visualized Experiments, a methodology-oriented online journal which publishes video files with accompanying manuscripts. Digital tools have generally sped up the generation of data and graphics, but made the publishing process prone to manipulation of images and data, thus contributing to the “irreproducibility crisis” [8].
In summary, digitalization made our primary goal of creation and distribution of knowledge faster, more flexible and versatile.

[1] http://bit.ly/2pkm4GY
[2] http://bit.ly/2qv8wNo
[3] http://bit.ly/2q5YZuK
[4] http://bit.ly/2r5lVZA
[5] http://tcrn.ch/2qLVmIA
[6] http://bit.ly/2pQuV6w
[7] http://bit.ly/2pR8Jah
[8] http://go.nature.com/2qNHzAh

by Bettina Schmerl, PhD Student AG Shoichet
this article originally appeared June 2017 in CNS Volume 10, Issue 2, Digital Health and Big Data

January 30, 2017

Why is it again that we yawn?

This question is probably as old as yawning itself and still remains to be answered, although there are a lot of interesting hypotheses out there:

1. Respiratory and circulatory hypothesis
The most widely believed and oldest hypothesis that yawning functions to regulate levels of oxygen and carbon dioxide. However, studies by Provine and colleagues showed that when measured in a controlled environment, yawning frequency was not affected by manipulating levels of oxygen and carbon dioxide [1].

2. Mental attribution hypothesis and social/communication hypothesis
This hypothesis claims that just thinking about yawning makes you yawn [2] and is closely linked to the social/communication hypothesis. Yawning is understood across cultures and frequently occurs in social contexts. Moreover, everyone has experienced a yawn being "contagious". Interestingly, the susceptibility to contagious yawning correlates with empathic skills. This is reduced, for example, in patients with autism or schizophrenia. However, experimental data are lacking and highly debated [3,4].

3. Arousal hypothesis
This hypothesis proposes that yawning facilitates arousal. The experimental data suggest that yawning indeed occurs during progressive drowsiness or sleepiness, which would be compatible with the hypothesis. However, EEG data could not show specific arousing effects of yawning on the brain or the autonomic nervous system [4].

Macaca fuscata juvenile yawning via Wikimedia Commons
4. Thermoregulation hypothesis
This is one of the most recent hypotheses and puts forward that yawning functions as a brain cooling mechanism. The mechanism proposed being an increase in brain temperature triggers a yawn and the physiological reactions following promote a return to brain thermal homeostasis. However, again, experimental data remain sparse and highly debated [3,4].
Nevertheless, here are a few facts that we know for sure: Yawning is a phylogenically old property and occurs in four vertebrates classes: mammals, reptiles, birds and fish. A yawn is characterized by a standard cascade of movements over a 5- to 10-second period. The mouth opens widely for 4 to 6 seconds with simultaneous retraction of the tongue, and is usually combined with retroflexion of the head and sometimes elevation of the arms. Numerous neurotransmitters, neuropeptides, and hormones have been found to be implicated in the control of yawning; amongst others, dopamine, acetylcholine, glutamate, serotonin, nitric oxide, adrenocorticotropic hormone related peptides, oxytocin, and steroid hormones facilitate yawning, whereas opioid peptides have an inhibitory effect [4].

What is there to be concluded? 
Ladies and gentlemen, there's research to be done!
Do you also sometimes wonder about the simple neuroscientific questions in everyday life, but don't really feel like looking them up right away?

Do you also sometimes wonder about the simple neuroscientific questions in everyday life, but don't really feel like looking them up right away? For questions like this, just mail us your question (cns-newsletter@charite.de) and Dr. Harebrained will give us his explanation!


[1] Provine et al., Behav Neural Biol, 1987
[2] Provine, Ethology, 1986
[3] Gallup, Neurosci Biobehav Rev, 2011
[4] Guggisberg et al., Neurosci Biobehav Rev, 2010


By Veronika Lang, originally published June 2012 – Volume 05, Issue 2, "Open Access"