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Aug05

SummerScienceVideo: fruit fly research

In: blogarchives • Tags: behavior, dickinson, Drosophila, neuroscience, TED, video

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:

Michael Dickinson: How a fly flies
Michael Dickinson: How a fly flies

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and the second one is on recording from fly visual neurons during flight and non-flight. This one was done in CalTech where Michael Dickinson used to work:

Brain recording from flying fruit fly
Brain recording from flying fruit fly

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Posted on August 5, 2013 at 09:17 Comments Off on SummerScienceVideo: fruit fly research
Aug02

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

In: blogarchives • Tags: impact factor, journal rank, open access, publishing

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 26, 2010:

There are about 1.5 million scholarly articles published in all the sciences, spread over about 24,000 journals. Even if there were a single database or entry-point providing access to all the literature, nobody would be able to keep up with everything that is being published in their field of work any more. Desperately looking for some clue as to which publications to select for in-depth reading and which to ignore, scientists began to rank the journals according to how often the articles in these journals were cited. This ranking got started around the 1960s, when the number of journals started to proliferate. Fast-forward to today: What began as a last-ditch effort to handle an overwhelming flood of scientific information is now a full blown business. Journal ranking by citations is now done commercially by a multi-billion Dollar media corporation, Thomson Reuters. The journal rankings are sold to research institutions on a subscription basis ranging anywhere between approx. 30,000-300,000€ (US$40,000-400,000) annually.

With increased visibility for the high-ranking journals came an increase in submitted contributions. The higher ranking the journal, the more readers and contributors, so the more income for the publisher. And so the vicious cycle of scientific publishing evolved: more and more scientists want to publish in and read the high-ranking journals. Due to the high volume of submissions, the publishers of these journals are in a position to pick about 2-5% of the submitted articles for publication and reject the rest, increasing the prestige of these journals even more. Sometimes these rejections are accompanied by a recommendation to submit the work to one of the lower-rank journals of the same publisher. Clearly, something has to be exceptionally ‘good’ to make it into a high-ranking journal (or, as some claim, have the potential to increase the journal’s rank). After a few cycles, it became difficult to distinguish if a scientific finding was so ‘good’ that it made it into the high-ranking journals or if it had to be good because it was published there. Indeed, for some aspects of scientific life such as promotions, hiring, grant proposals or other sorts of evaluations, this question wasn’t even asked anymore. Publication quality became synonymous with journal rank. Today, where a scientist has published is often more important than what was published. In all human life, scarcity and branding are two powerful factors for determining value, as I’m sure any economist can tell a story or two about. Scientists are human beings and journal rank is but one example of just how prevalent the human factor is in the scientific enterprise. Today, the future of a professional scientist is all too often dominated more by the economics of scarcity and branding, rather than science.

What does all that have to do with potatoes in France?

After a discussion about potatoes over lunch the other day, I stumbled across this beautiful tale, published in 1956 in the American Potato Journal on how the potato arrived in France in the 18th century:

This endorsement of the potato and that of the various potato dishes served at the King’s table were enhanced by placing a uniformed guard on Parmentier’s potato plot. Parmentier’s considerate removal of the guard at night during the harvest season is reported to have furthered the success of the potato with the King’s subjects.

This story so reminded me of scientific publishing. Wikipedia puts the story a little more bluntly:

Parmentier therefore began a series of publicity stunts for which he remains notable today, hosting dinners at which potato dishes featured prominently and guests included luminaries such as Benjamin Franklin and Antoine Lavoisier, giving bouquets of potato blossoms to the King and Queen, and surrounding his potato patch at Sablons with armed guards to suggest valuable goods — then instructed them to accept any and all bribes from civilians and withdrawing them at night so the greedy crowd could “steal” the potatoes.

Now I wouldn’t know anything about bribes, but the part about creating artificial scarcity and a brand name to increase value for an ordinary object rang familiar.

In a recent ‘Opinion’ article in one of the journals at the very top of the rank, Nature, the author correctly points out that this system of journal rank has many flaws and should be replaced by a more scientific system for the metric evaluation of science. She specifically calls for social social scientists and economists to be involved in developing this new system, underscoring the points above. Indeed, it is remarkable that our current journal rank system is still in place. After all, not only does the author and many scientists agree, but also the originators of the journal rank system, the high-ranking journals themselves and even some evaluators all have long realized that using journal rank to evaluate individual researchers is both “unfair and unscholarly“. I have lamented this absurd state of affairs plenty of times right here and elsewhere.

However, artificial scarcity and brand name have, by now, developed such a powerful dynamic, fueled by billions in taxpayer money and a rich history of great scientific traditions, that it seems unstoppable, even if all participating parties agree that putting an end to it would be better for science.

It is with these powerful dynamics (and some analogous evolutionary dynamics) in mind that I posted an off-hand comment to the ‘Opinion’ article mentioned above. The comment stated that any, even the most complex and scientifically tested system will eventually succumb to social dynamics adapting the scientific community to the system and maximizing the individual participant’s benefit while minimizing their costs. The only system that would be immune to such dynamics is one where the rules change more quickly than the social dynamics can follow:

Wouldn’t it be nice if metrics weren’t needed? However, despite all the justified objections tobibliometrics, unless we do something drastic to reduce research output to an amount manageable in the traditional way, we will not have any other choice than to use them.However, as the commenters before already mentioned, no matter how complex and sophisticated, any system is liable to gaming. Therefore, even in an ideal world where we had the most comprehensive and advanced system for reputation building and automated assessment of the huge scientific enterprise in all its diversity, wouldn’t the evolutionary dynamics engaged by the selection pressures within such systems demand that we keep randomly shuffling the weights and rules of these future metrics faster than the population can adapt?

This comment was published as a ‘Correspondence’ piece in the printed version of Nature. Coincidentally, the current LaborJournal contains a letter from me, which states pretty much the same thing, with some additional information.


Hougas, R. (1956). Foreign potatoes, their introduction and importance American Potato Journal, 33 (6), 190-198 DOI: 10.1007/BF02879217
Lane, J. (2010). Let’s make science metrics more scientific Nature, 464 (7288), 488-489 DOI: 10.1038/464488a

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Posted on August 2, 2013 at 18:21 Comments Off on In which potatoes in France are like high-ranking journals in science
Aug01

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

In: blogarchives • Tags: action, brain, response, spontaneity

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 June 13, 2011:

Most neuroscientists would subscribe to the sensorimotor hypothesis, according to which brains mainly evaluate sensory input to compute motor output. For instance, Mike Mauk wrote now over ten years ago: “brain function is ultimately best understood in terms of input/output transformations and how they are produced” [1]. Tony Dickinson recognized already in 1985 that “Indeed, so pervasive is the basic assumption of this model that it is common to refer to any behaviour as a ‘response’ and thus by implication […] assume that there must be an eliciting stimulus.” [2]. Textbooks to this day mostly begin with a graph showing sensory input entering the brain (usually via the eyes) and then motor-output leaving it.However, more and more information is now accumulating that to the extent that these stimulus-response relationships actually exist, they may be the exception, rather then the rule of what brains are doing when they’re not in a laboratory experiment. Perhaps most recently, in the area of human brain research this change in perception has also begun. Marcus Raichle’s “Two views of brain function” [3] provides plenty of evidence against the sensorimotor hypothesis. There are many more examples of this kind of evidence. For me personally, the most eye-opening one was this famous video by Ken Catania:
Tentacled snake in action
Tentacled snake in action

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If all behavior were always organized according to stimulus-response schemes such as the C-start response in fish, animals would be extremely vulnerable not only to predators (or prey), but of course also to competitors. Evolution is a competitive business: if you’re too predictable, you lose.

In our labs, reproducibility is key to success. This is precisely the reason why escape responses are so well-studied: these are the exceptions where animals have specialized in speed and sacrificed unpredictability in an evolutionary trade-off. I would hypothesize that no species would survive for long if all other behaviors sacrificed unpredictability in this way,

More likely, brains need to balance input-output processing with output-input processing, with the latter probably being both the more prevalent and the ancestral form of behavioral control. It is this delicate balance that brains must constantly strike to survive, procreate and be successful. If we want to understand what the brains we study are really doing when they are not in the lab, we need to take a step back and design more experiments that don’t require a response, but an action. This process has already started, but the realization that we have been heading down the stimulus-response direction for too long has not widely set in yet, IMHO.

The stimulus-response approach has been hugely successful for the most derived and simplified forms of behavior – and we’re still far from done with the task. Now comes the vastly more complex task of understanding how brains decide which action to take next, when there is no simple stimulus providing unambiguous information. Many labs have already started to embark on this task. In our lab, we study animals in the complete absence of discrete sensory stimulation, in order to find out how brains create “something out of nothing”. Which actions are you studying?

This post was originally written for the launch of the new social network for neuroscientists, NeurOnline (@SfN).


[1] Mauk, M. (2000). The potential effectiveness of simulations versus phenomenological models Nature Neuroscience, 3 (7), 649-651 DOI: 10.1038/76606
[2] Dickinson, A. (1985). Actions and Habits: The Development of Behavioural Autonomy Philosophical Transactions of the Royal Society B: Biological Sciences, 308 (1135), 67-78 DOI: 10.1098/rstb.1985.0010
[3] Raichle, M. (2010). Two views of brain function Trends in Cognitive Sciences, 14 (4), 180-190 DOI: 10.1016/j.tics.2010.01.008

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Posted on August 1, 2013 at 15:50 Comments Off on Flashback: ‘stimulus-response’ concept based on artifacts?
Jul31

Solutions to the looming crisis in science

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

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. This prestige is reflected in the rejection rates of the individual journals: the more prestigious a journal, the more authors desire publishing in it, the higher the rejection rate.

However, much like the potential patrons lining up in front of a new – but perhaps empty – club, or the peasants stealing potatoes from Parmentier’s fields at Sablon, only few scholars are asking if there are any other indicators of quality that correlate with journal rank, besides perceived or manufactured exclusivity. A recent overview of the work of these few scholars revealed that very few measures showed any correlation at all: neither was the methodology any more sound in higher ranking journals, nor do they fare better at replication tests. A few measures, such as crystallographic quality, effect size accuracy or sample size have been reported to correlate negatively with journal rank, while the literature does not contain a single measure related to quality that correlates positively with journal rank.

In the light of such data, it is perhaps not surprising, that one of the strongest correlations of journal rank is that with retractions: high-ranking journals publish research that is a lot less reliable than that in other journals: the combination of prestige attracting surprising and counterintuitive discoveries, combined with not only average (perhaps even sub-par) quality, but also increased readership and hence scrutiny is a recipe for disaster. The data in plain words: scientific top journals are like tabloids: widely read, but not necessarily trustworthy.

These data provide empirical evidence to support the hypothesis that the incentive structure in science can be blamed for much of the alarming trends of the past decades, such as the exponentially increasing retraction rates, ever larger and more frequent cases of fraud and the replicability crisis. Apparently, the current system of journal prestige favors scientists who are effective at marketing their research to prestigious journals, but not those whose research is reliable. In addition, the prestige bestowed by journal rank is what prevents authors from seeking alternative publishing venues (or they would risk their careers), contributing to the serials crisis of legacy publishers charging exorbitantly for subscriptions.

Figure 1: Current Trends in the Reliability of Science

bjoern figure 1
(A) Exponential fit for PubMed retraction notices (data from pmretract.heroku.com). (B) Relationship between year of publication and individual study effect size. Data are taken from Munafò et al. (2007), and represent candidate gene studies of the association between DRD2 genotype and alcoholism. The effect size (y-axis) represents the individual study effect size (odds ratio; OR), on a log-scale. This is plotted against the year of publication of the study (x-axis). The size of the circle is proportional to the IF of the journal the individual study was published in. Effect size is significantly negatively correlated with year of publication. (C) Relationship between IF and extent to which an individual study overestimates the likely true effect. Data are taken from Munafò et al. (2009), and represent candidate gene studies of a number of gene-phenotype associations of psychiatric phenotypes. The bias score (y-axis) represents the effect size of the individual study divided by the pooled effect size estimated indicated by meta-analysis, on a log-scale. Therefore, a value greater than zero indicates that the study provided an over-estimate of the likely true effect size. This is plotted against the IF of the journal the study was published in (x-axis), on a log-scale. The size of the circle is proportional to the sample size of the individual study. Bias score is significantly positively correlated with IF, sample size significantly negatively. (D) Linear regression with confidence intervals between IF and Fang and Casadevall’s Retraction Index (data provided by Fang and Casadevall, 2011).


Thus, the picture emerges that by reforming the scholarly publishing structure, we can solve several current issues at once:

  1. We can reward reproducible discoveries, rather than publications, increasing scientific reliability.
  2. We can save lives and boost the world’s economies by providing universal open access to all of the scholarly literature
  3. We can save billions every year in subscription costs

What do we need to do to accomplish this? One solution is to use the already existing infrastructure and know-how in our scholarly institutions: collectively, our libraries and computing centers have all it takes to serve the world not only the two million new publications every year, but also all the literature from the past. There is no reason why publishers should be required for this task any more – libraries around the world are already publishing the works of their faculty. The SciELO (Scientific Electronic Library Online), originally from Brazil, but now used in most Latin American countries and South Africa, is a cooperative electronic publishing system which now publishes over 900 open access journals at a cost of just US$90 per article. Compare these US$90 to the US$4000 per article we currently pay on average for legacy publishing or with the US$30,000-40,000 for articles in the most prestigious journals. As mentioned above, the evidence suggests that this gigantic surplus is not buying any added value. With a total yearly revenue of legacy publishing around US$10 billion, the scholars are wasting approximately US$9.8 billion every year, compared to an institution-based publishing system like SciELO, and even more if we would use preprint systems such as Arxiv.

The success of SciELO demonstrates that such an alternative is technically feasible, scalable, significantly cheaper than our current model, and would provide universal open access to the whole planet if the rest of the world would adopt it. Thus, universal adoption of SciELO alone would cover points 2 and 3. Obviously, this is not only one of several solutions, but also an example of how easy it is technically to effectively reform scholarly publishing.

The remaining first point can be addressed by identifying alternative metrics to accrue reputation. Once we have full access to all the literature, we can use the scientific method not only for the identification of such metrics, but we can also use this method to test how to ideally design a reputation system that aligns the incentives for each individual researcher with science and the public. Once we have taken back the control over the fruits of our labor: literature, data and software, we can reward scientists who excel at designing software that evaluates data, who are unsurpassed at collecting and curating large amounts of data, who shine with their talent for experimental design and consequently generate reproducible research, but who are not necessarily the best salesmen. We can reward the crucial personnel without which the scientific enterprise could not exist, but who currently fall through the cracks.

These ideas demonstrate that by overcoming journal rank and replacing it with a scientific reputation system as part of an institution-based publishing service for scholarly literature, software and data, we could collectively free more than US$9b every year for science and innovation. By further delaying publishing reform, we not only keep wasting tax-payer money, we also continue to reward salesmen who may possibly also be great scientists (if we are lucky) and to punish excellent scientists who are not extraordinary marketers. It does not take an evolutionary biologist to predict what this sort of selection will do to the scientific community within only a few generations.

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Posted on July 31, 2013 at 10:48 Comments Off on Solutions to the looming crisis in science
Jul24

Publisher selects the best open access science – authors complain

In: science politics • Tags: impact factor, journal rank, libraries, open access, publishing

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. Never mind the unnecessary delay of science and the agony not only of the rejected authors but also of the reviewers who need to re-review the papers as they trickle down the hierarchy. No, hardly anybody thinks 30k per article is too much, just because some ex-scientist is selecting the work. Regular journals publish at costs of “a few hundred dollars“, so the only justification for the 30k price tag is the selection.

Essentially, almost everybody’s fine with paying 30k per article for a selection process devoid of any evidence that it actually improves anything.

What some authors and colleagues are upset about, is that a new publisher, Apple Academic Press, is selling selected open access papers as books – for around US$100 a pop. Granted, there is a lot to criticize about this particular publisher’s stunt: they repackaged a selection of open access (CC-BY licensed) articles without the knowledge of the authors, they changed some titles and hid the original publisher in the acknowledgment section of the papers and obviously didn’t send the authors complimentary copies. There is no question that this is some really horrible style. However, compared to $30k an article or several hundred each year for a subscription, $100 for a whole book seems like a fair deal. Given that these books seem to cover highly specialized areas, featuring articles that are available for free, one wouldn’t expect they will sell much, so the actual cost per article in each book is miniscule. So essentially, the $100 are only for someone to do the selecting, which is precisely what the ex-scientists at the GlamMagz do to the detriment of science as well as researchers and at much, much higher financial costs to boot.

Balancing what ‘traditional’ publishers do to science and scientists on a daily basis with the listed shortcomings of this new strategy by Apple AP, I can’t help but wonder what people get so upset about? Of course, authors ought to be notified, but if we got upset about everything publishers ought to do, nobody would be able to calm down ever again. Of course, the publisher should show that the papers have been published before, but that info is in the acknowledgments. Moreover, the price is a real bargain, compared to other ‘selection services’ and you don’t even have to pay it as long as you get the list of titles. Anybody who gets upset about such bad style, ought to be ragingly mad at what GlamMag publishers do.

Clearly, to emphasize it again, this new procedure leaves much room for improvement. However, in principle, this is exactly what we want: someone serving as a filter for selecting the most relevant discoveries – but after the publication, not before, when it slows everything down and clogs the system. With more and more of these services, they can compete with each other and develop track records that can be compared. There will be some that cater to the public, others to clinicians or other professional sections of the public, again others will cater to scientists. This is precisely the kind of re-use CC-BY had in mind. Apple AP obviously didn’t win a prize for the most innovative post-publication review system, but it’s a beginning of what open access advocates have been proposing for almost two decades now: open access and wide commercial re-use of publicly funded research to the benefit of the public. Imagine if some whiz kid picked up one of these books from a public library or some other place where it was lying around and developed a new cancer diagnostic!

For sure, nobody needs to be enthusiastic about this particular instance, but every open access proponent should embrace, not condemn these developments, if just for the potential they carry.

UPDATE: after some Twitter discussion, here’s a suggestion for how the execution of this service might be improved: the publisher could just offer the list of titles for sale with a print-on-demand option. If their selection if worth anything, they should find customers willing to pay for it.

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Posted on July 24, 2013 at 21:50 6 Comments
Jul18

Tweetlog: fruit flies, evolution and #openaccess

In: Tweetlog • Tags: aplysia, evolution, fruit flies, open access

This third installment of my tweetlog covers July 10-18:

  • Cytoskeletal Determinants of Stimulus-Response Habits https://feedly.com/k/15OdS3q
  • Wow! 7340 full-text and PDF downloads, and only 5510 abstract views for our journal rank paper: https://www.frontiersin.org/Human_Neuroscience/10.3389/fnhum.2013.00291/full
  • In Science We Trust: Poll Results on How You Feel about Science: https://www.scientificamerican.com/article.cfm?id=in-science-we-trust-poll …
  • “Doubt is our product” – how the tobacco industry misrepresented our research: https://targ.blogs.ilrt.org/2013/07/16/doubt-is-our-product/ … by @MarcusMunafo
  • Motor Circuit-Specific Burst Patterns Drive Different Muscle and Behavior Patterns https://feedly.com/k/1atMeKc
  • Interestingly: the sentence adverbs of PubMed Central https://nsaunders.wordpress.com/2013/07/16/interestingly-the-sentence-adverbs-of-pubmed-central/ …
  • Further Fell Fallout From Finch Folly: The Royal Society Relapse https://openaccess.eprints.org/index.php?/archives/1021-Further-Fell-Fallout-From-Finch-Folly-The-Royal-Society-Relapse.html …
  • Joseph Esposito on the state of Open Access: Where are we, what still needs to be done? https://poynder.blogspot.com/2013/07/joseph-esposito-on-state-of-open-access.html …
  • Misconceptions about evolution video has its own misconceptions https://feedproxy.google.com/~r/Neurodojo/~3/vOoyPoLrCHk/misconceptions-about-evolution-video.html …
  • Science and the public: Promotional tactics corrupt research https://feedly.com/k/15Ogi29
  • Reproducibility: Two more red flags for suspect work https://feedly.com/k/15OfZ7w
  • Sending a message https://wp.me/p4g7f-nU  via @researchremix
  • Why librarians are needed more than ever in the 21st century https://boingboing.net/2013/07/16/why-librarians-are-needed-more.html …
  • Congratulations! @ivanoransky leaves Reuters for MedPage Today. https://shar.es/k3t16
  • Open Access DOI Resolver:give it a DOI it gives back OA full-text institutional repository URL! https://doi2oa.erambler.co.uk/  via @HSSOpenAccess
  • “surprisingly readable for something so depressingly stupid.” – ‘Positivity Ratio’ Criticized In New Sokal Affair https://bit.ly/17k78JV
  • Animal studies produce many false positives https://www.nature.com/news/animal-studies-produce-many-false-positives-1.13385 …
  • “we should not make the author field of papers a proxy for all scientific output credit…” – https://bit.ly/1bFzyRZ
  • Anybody with first-hand experience with Primo ScholarRank? https://www.youtube.com/watch?v=YDly9qPpPYQ …
  • @Protohedgehog @bioSimonUoB @brembs Judging a paper on journal IF like judging photography contest on presence of celebrity in background.
  • Recombineering Homologous Recombination Constructs in Drosophila https://feedly.com/k/12PrjvY
  • The Molecular Basis of Sugar Sensing in Drosophila Larvae https://feedly.com/k/13JXhQH
  • Heather Joseph on the state of Open Access: Where are we, what still needs to be done? https://poynder.blogspot.de/2013/07/heather-joseph-on-state-of-open-access.html …
  • It’s plain and simple: transparency is good for science and in the public interest https://www.trialsjournal.com/content/14/1/215/abstract … #trials
  • Of the 10k downloads, ~6k full-text views: https://www.frontiersin.org/Journal/AbstractImpact.aspx?ART_DOI=10.3389/fnhum.2013.00291&name=human_neuroscience&utm_source=newsletter&utm_medium=email&utm_campaign=Psychology-w28-2013&type=1 …
  • Today, 10k+ downloads for our paper on the lack of evidence for journal rank: https://www.frontiersin.org/Human_Neuroscience/10.3389/fnhum.2013.00291/full …
  • iPhylo: Learning from eLife: GitHub as an article repository https://iphylo.blogspot.com/2013/07/learning-from-elife-github-as-article.html?spref=tw …
  • The cat frog came back, the very next day https://feedly.com/k/1btBayl
  • An astonishingly shallow treatment of a very real problem: Risk https://feedly.com/k/10PiLHV
  • The Evolution of Drosophila melanogaster as a Model for Alcohol Research https://feedly.com/k/1bty5OA
  • @Technixer Exactly. To get around this issue, we wrote this instead: https://www.frontiersin.org/Human_Neuroscience/10.3389/fnhum.2013.00291/full …
  • The Selected Papers Network (Part 3) https://feedly.com/k/1btxlch
  • Fruit Flies Seek Mates Leggingly: Scientific American Podcast https://www.scientificamerican.com/podcast/episode.cfm?id=fruit-flies-seek-mates-leggingly-13-07-11&WT.mc_id=SA_sharetool_Twitter … via @sciam
  • Want good reasons to be a Creationist? You won’t find them here. https://blogs.scientificamerican.com/doing-good-science/2013/07/11/want-good-reasons-to-be-a-creationist-you-wont-find-them-here/?WT.mc_id=SA_sharetool_Twitter … via @sciam
  • Brains don’t respond to stimuli – brains act and then evaluate the response of the environment: https://bjoern.brembs.net/2013/07/brains-as-outputinput-systems/ …
  • Unhelpful Research Advice #2 https://wp.me/pP1Q8-JZ
  • Brains as output/input systems https://wp.me/p3walV-4R
  • “Why Has the Number of Scientific Retractions Increased?” New study tries to answer https://buff.ly/1dmB7Cx
  • A call for open access to all data used in AJ and ApJ articles https://buff.ly/1dmzZPn
  • The Cost of Scientific Publishing https://disq.us/8e1c8n
  • Open is a state of mind https://feedly.com/k/13ONY0u
  • On the Training of Future Neuroscientists: Insights from the Grass Laboratory https://feedly.com/k/10O65Rz
  • How Did the Chicken Cross the Road? With Her Striatal Cholinergic Interneurons, Of Course https://feedly.com/k/10O5b7B
  • Olfaction and Vision Meet in the Retina https://feedly.com/k/10O4FGt
  • Busting the top five myths about open access publishing https://theconversation.com/busting-the-top-five-myths-about-open-access-publishing-14792 … via @ConversationUK
  • Isolation of Sensory Neurons of Aplysia californica for Patch Clamp Recordings of Glutamatergic Currents https://feedly.com/k/10O3Tti
  • #Open Access and the looming crisis in #science #OA #scientific papers #biomedical journal #publication | @scoopit https://sco.lt/5Oa6uP
  • Open access on the conference circuit https://buff.ly/12lnORq  via @stephen_curry
  • The challenge of semantically marking up articles (more thoughts on PLoS Hubs) https://iphylo.blogspot.co.uk/2013/07/the-challenge-of-semantically-marking.html …
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Jul11

Brains as output/input systems

In: science • Tags: brain, classical, conditioning, free will, operant, self-learning
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. Unfortunately, I never found the time to submit it to a peer-reviewed journal.
Neuroscience is predominantly interested in elucidating the effects environmental stimuli cause in our brains and how the brain transforms these stimuli into meaningful behavior. Animals including humans are thought to react with a complex combination of innate and learned “responses” to one or a set of external stimuli. However, a series of recent advances in modern behavioral neuroscience and neuroethology reminds us that freely behaving animals treat self-generated stimuli differently from other stimuli. We are always both cause and effect in the closed feedback loop between our behavior and the environment we live in. This operant loop renders the linear input/output view one-sided. The renewed interest in the biological mechanisms of operant conditioning is the result of many years of research towards a more sophisticated view of the main function of brains.
The concept of causality is so central to the human thought process that Kant concluded it must precede all experience [1]. Our constant search for causes eventually led to the development of religion, science and technology. In science, we look for the underlying causes of natural phenomena. Humans are also subjected to this scrutiny. The neurosciences try to understand the underlying causes for perception, disease, aging or development. In this very successful approach it is often overlooked that humans are not only responding mechanically in a cause-and-effect (stimulus-response) fashion to everything that happens to them. Humans are active agents as well and as such just as much cause as they are effect. Where does this spontaneous activity come from in a cause-and-effect world? Why is there spontaneity? Or is it just an illusion?
Early, often overlooked psychological conjecture emphasizes that spontaneous behavioral variability is a useful, as one would say today “adaptive” trait. In this article I will cite neurobiological evidence to strengthen this view. I will use a number of examples to argue that the variability measured in the behavioral performance of animals is exactly the kind of output that is required to effectively detect which of the stimuli in the incoming stream of sensory input can be controlled by the animal and which cannot. I will deliver an account as to how and why, despite its importance, this essential output-input feature of brains has largely been overlooked in recent decades. This forgotten feature is associated with a number of psychiatric disorders and only recently a new and growing trend has emerged which now provides steadily increasing understanding about the mechanisms underlying it.

Behavioral Variability: the output

We all feel the very basic notion that we possess a certain degree of freedom of choice. Bereaving humans of such freedom is frequently used as punishment and the bereft do in-variably perceive this limited freedom as undesirable. This experience of freedom is an important characteristic of what it is like to be human. It stems in part from our ability to behave variably. Voltaire expressed this intuition in saying “Liberty then is only and can be only the power to do what one will” [2]. But the concept that we can decide to behave differently even under identical circumstances underlies not only our justice systems. Electoral systems, our educational systems, parenting and basically all other social systems also presuppose behavioral variability and at least a certain degree of freedom of choice. Games and sports would be predictable and boring without our ability of constantly changing our behavior in always the same settings. Faced with novel situations, humans and most animals spontaneously increase their behavioral variability [3-5]. Inasmuch as behavioral variability between individuals has genetic components, it is a crucial factor of niche exploitation in evolution. Moreover, behavioral variability within individuals has been shown to be ecologically advantageous in game theoretical studies [6-11], in pursuit-evasion contests such as predator/prey interactions (“Protean Strategy”) [12-15], in exploration/foraging [16], in mobbing attack patterns by birds and in the variation of male songbirds’ songs [17]. Clearly, invariable behavior will be exploited [14,18] and leaves an organism helpless in unpredictable situations [19,20].

Controlling external events: the input

Thus, competitive success and evolutionary fitness of all ambulatory organisms rely critically on intact behavioral variability as an adaptive brain function. But relative freedom from environmental contingencies is a necessary, but most often not a sufficient criterion for such accomplishments. Tightly connected to the ability to produce variable behavior is the ability to use the effects of these behaviors to control the environment. The incoming stream of sensory information is noisy and fluctuates for any number of reasons. Any covariance between the behavioral variations and those of sensory input indicates that the latter are con-sequences of the behavior and can thus be controlled be the animal [21,22]. It is the on-line detection system for when the animal itself is the reason for any environmental fluctuation. This function is so paramount, that we humans express our delight over control of our environment (including other people) already as children, by e.g., shrieking in excitement when Daddy jumps after a “boo” or proudly presenting Mom with “look what I can do!”. Later, children find pleasure in building airplane models, become carpenters with a delight for shaping wood, artists feeling gratified creating art out of the simplest materials, musicians enjoying mastering their instrument to perfection, athletes, scientists, engineers or managers. Using trial and error, we have shaped our world from caves to skyscrapers, from horses to jet-planes, from spears to hydrogen bombs. Cultural or religious rituals (e.g., rain dance) and superstition may have evolved as means to create a feeling of control where ultimately there is none. Obviously, behaving flexibly in order to control our environment is at the heart of human nature and probably affects more aspects of our daily lives than any other cognitive brain function. So essential is such functioning that even very simple brains possess it. The modest fruit fly prefers a situation in which it controls its environment over one where it does not. If certain flight directions are experimentally superimposed with uncontrollable visual movements, flies quickly avoid such directions and fly only in areas of full control [23]. This experiment demonstrates that control over environmental stimuli is inherently rewarding already for simple, but more likely for all brains.

The main function of brains

The first experiments into the mechanistic basis of this basic brain function was initiated already early in the 20th century by eminent scientists like Thorndike [24], Watson [25] and Skinner [26]. Of course, the primary process by which all animals, including humans learn to control their environment is operant (or instrumental) conditioning (Box 1). Ultimately, this comparatively simple process forms one of the fundamental cornerstones not only for all of our human nature, but also for our social coherence: human nature as described in planning, willing and controlling our behavior [22,27-30] and our social coherence as based on cooperation [6,31,32]. Modern neuroscience, however, with the success of research into the mechanisms of the even simpler process of Pavlovian or classical conditioning (Box 1), has understandably shifted the focus away from the central role operant learning plays in our daily lives.

Box 1: Predictive learning
Classical (Pavlovian) conditioning is the process by which we learn the relationship between events in our environment, e.g., that lightning always precedes thunder. The most famous classical conditioning experiment involves Pavlov’s dog: The physiologist I.P. Pavlov trained dogs to salivate in anticipation of food by repeatedly ringing a bell (conditioned stimulus, CS) before giving the animals food (unconditioned stimulus, US). Dogs naturally salivate to food. After a number of such presentations, the animals would salivate to the tone alone, indicating that they were expecting the food.
Operant (instrumental) conditioning is the process by which we learn about the consequences of our actions, e.g. not to touch a hot plate. The most famous operant conditioning experiment involves the ‘Skinner-Box’ in which the psychologist B.F. Skinner (and colleagues – he mainly used pigeons himself)  trained rats to press a lever for a food reward. The animals were placed in the box and after some exploring would also press the lever, which would lead to food pellets being dispensed into the box. The animals quickly learned that they could control food delivery by pressing the lever.
Both operant and classical conditioning serve to be able to predict the occurrence of important events (such as food). However, one of a number of important differences in particular suggests that completely different brain functions underlie the two processes. In classical conditioning external stimuli control the behavior by triggering certain responses. In operant conditioning the behavior controls the external events.

This shift is signified by a steady decrease in the fraction of biomedical publications with operant topics, despite an absolute increase of publications over the last 25 years (Fig. 1). It is an understandable shift, because nearly every learning situation seems to involve a dominant classical component anyway [33,34] and classical conditioning offers the unique advantage to quickly and easily get at the biological processes underlying learning and memory: the animals are usually restrained, leaving only few degrees of freedom and the stimuli can be traced to the points of convergence where the learning has to take place. The neurobiological study of classical conditioning, pioneered by Nobel laureate Eric Kandel, was the first avenue into some of the biological mechanisms of general brain function. Today, overwhelmed by the amazing progress in the past three decades, some neuroscientists even ponder reducing general brain function almost exclusively (“95%”) to classical stimulus-response relationships, with profound implications for society, in particular for the law [35,36]. The Dana Foundation, the American Association for the Advancement of Science and the American Civil Liberties Union have already sponsored meetings on these implications [37,38]. Stretching the generality of such awesome classical conditioning paradigms as fear conditioning in rats and mice [39], rabbit eyeblink conditioning [40] or classical conditioning of the Aplysia gill withdrawal reflex [41], the current neuroscientific standard implies that they are all-encompassing paradigms for general cognitive brain function: “brain function is ultimately best understood in terms of input/output transformations and how they are produced” [42].


Fig.1: Publishing development of publications on operant conditioning. The graph shows a steady decline in the fraction of publications dealing with operant conditioning (blue) despite an increase in absolute number of publications over the last 25 years (red). Note the increase in the last four years. Absolute numbers were gathered by running an NCBI PubMed query “((operant OR instrumental) AND (conditioning OR learning))” (red). This number was divided by the number of publications containing only “conditioning”, to derive a percentage (blue). Notice the sharp jump in the absolute number for the last five years. This jump is even noticeable in the relative contributions.

It is rarely recognized that, at an adaptive level, cognitive capacities, such as those involved in encoding the predictive relations between stimuli, can be of little functional value to a hypothetical, purely Pavlovian organism. For instance, one can imagine any number of situations which require the animal to modify, even to withhold or reverse, the direction of some behavior in order to solve the situation. Such situations demand greater behavioral flexibility than the system mediating classical conditioning provides. Moreover, using the re-afference principle [43-45], operant behavior underlies the distinction between observing and doing, i.e. differentiating between self and non-self. We compare our behavioral output (efference) with incoming sensory input (afference) to detect when we are the ones authoring environmental change [21,22]. One almost iconographic example of such behavior is to per-form various spontaneous movements in front of a mirror to detect whether it is us we are perceiving [46,47]. This automatic detection-mechanism explains why we cannot tickle our-selves [21], why we perceive a stable visual world despite our frequent quick, or saccadic, eye movements [48] and is reflected in different brain activation patterns between self-generated and exogenous visual stimulation [49]. It is thought that the detection is accomplished via an efference copy (or corollary discharge) of the motor command which is compared to incoming afferent signals to distinguish re-afference from ex-afference. Such a differentiation has been implied to demonstrate causal reasoning in rats [50,51]. Even robots can use such “self-modeling” to generate a continuously updated model of themselves and their environment [52]. Conspicuously, the organization of the brain also raises doubts about the input/output mainstream image. Less than 10% of all synapses in the brain carry incoming sensory information and as little as 0.5-1% of the brain’s total energy budget are sufficient to handle the momentary demands of the environment [53]. In other words, input/output transformations may only account for a small fraction of what brains are doing. Maybe a much more significant portion of the brain is occupied with the ongoing modeling of the world and how it might react to our actions? Recent evidence suggests that the brain predicts the sensory consequences of motor commands because it integrates its prediction with the actual sensory information to produce an estimate of sensory space that is enhanced over predictions from either source alone [54]. This effect of operant enhancement of sensory cues can be observed also in fruit fly learning [23,34] and may explain why starlings, but not tamarin monkeys can recognize patterns defined by so-called recursive grammar [55]. Such control of sensory input has often been termed “goal-directed” behavior. This perspective provides an intuitive under-standing of the rewarding properties of being in control of the environment. Setting and obtaining goals is inherently rewarding [56]. This reward ensures that individuals always actively strive to control.

At the same time, by controlling the environmental input using operant feedback loops, individuals exert their effect not only on themselves, but their survival and procreation in the environment they create for themselves directly affects evolution. This has been shown in the field, e.g., for western bluebirds, which dissociate into different niches ac-cording to their level of aggression [57]. Another example are small-brained prey being more likely to be caught by predators, presumably because their capacity for behavioral variability is also smaller [15]. In humans such mechanisms have been proposed to explain otherwise hard to understand phenomena such as high IQ heritability estimates and associated paradoxes (i.e., increasing IQ heritability with age/experience and the “Flynn-Effect” of increasing IQ over generations) [58,59]. Expecting sensory feedback signals can go so far that willing to move a limb can lead to the illusion of limb movement, even if none occurred [60]. One may say that we so want our actions to have an effect that we sometimes even develop a bad con-science even though we have not done anything wrong. Considering the operant feedback loop between initiating behavioral variability and the continuous prediction/evaluation of the environmental stimuli under behavioral control, it becomes clear that brain function can probably be understood just as well in terms of output/input transformations as the other way around. Deciding which output to produce in the next moment in order to control sensory input is the central organizing principle of brains [61]. Only through developing an understanding of the neural bases of operant learning, will we come to a full biological understanding of this principle.

Far-reaching implications

This evidence indicates that our behavior consists at least as much of goal-directed actions as it consists of responses elicited by external stimuli. But not all stimulus-response contingencies are acquired by classical conditioning. Goal-directed actions can become partially independent of their environmental feedback and develop into habits controlled mainly by antecedent stimuli [62-64]. Everybody has experienced such ‘slip of action’ instances, when we take the wrong bus home days after we have moved, when we keep reaching for the wrong buttons or levers in our new car, when we try to open our home door with the work keys or when we take the freeway-exit to our workplace, even though we were heading for the family retreat. William James [65] is often quoted as claiming that “very absent-minded persons in going in their bedroom to dress for dinner have been known to take of one garment after an-other and finally to get into bed, merely because that was the habitual issue of the first few movements when performed at a late hour”.

Habits or rituals are important for efficiently carrying out often-repeated behaviors by limiting the amount of behavioral variability. The degree to which classical responses or operant habits/rituals limit the behavioral variability can also be used to gauge mental health. A range of psychiatric disorders share the symptoms of reduced behavioral variability, in severe cases even behavioral rituals or stereotypies (e.g., autism spectrum disorder, obsessive com-pulsive disorder, depression [17]). Functional magnetic resonance imaging studies provide a potential mechanistic basis for these cases: Negative behavioral consequences mimic depression in that they tend to inhibit cortical premotor-areas. This inhibition is sensitive to psycho-logical therapy [66]. On the other hand, individuals diagnosed with attention deficit/hyperactivity disorder are reported to have increased behavioral variability. Being able to flexibly produce the right amount of behavioral variability under any given circumstance is not only a prerequisite for controlling our environment, but appears to also be a key marker for psychological health. It fits very well into the concept of producing behavioral variability to control our environment that patients with psychiatric depression also often report a lack of control of their lives. The dysfunctional behaviors of animals and people deprived of the opportunity to control their environments are common knowledge, e.g., the self-injury and cage stereotypies of solitary animals, and the depressing, dispiriting effects of living on welfare. “Learned helplessness” is a standard animal model for depression in which animals become depressed by exposure to uncontrollable shocks [67]. The degree of control over such stress-ors is critical for the development of depression. In rats, the infralimbic and prelimbic regions of the ventral medial prefrontal cortex detect whether the stressor is under operant control and suppress the depression-inducing effects the stressor would have without operant control [68]. The ventral medial prefrontal cortex is part of a prefrontal-basal ganglia-cortical feedback system thought to be involved in motor selection and control [62]. In humans, control of painful stimuli exerts an analgesic effect which appears to rely on the anterolateral prefrontal cortex [69]. Operant control is even said to slow the cognitive decay occurring in patients when they enter the late stage of Amyotrophic Lateral Sclerosis (ALS, Lou Gehrig’s disease), a degenerative motorneuron disorder [70]. Anorexic patients often report that controlling their eating and hunger is the only means of control left in their lives. Often these patients, when they eat, always cut the food into the same number of pieces and chew them for the same number of times. Anorexia nervosa and obsessive compulsive disorder share this symptom of rituals/stereotypies and show a high degree of comorbidity [71]. Patients with obsessive compulsive disorder show hyperactivity in the rostral anterior cingulate cortex, a region involved in on-line behavioral evaluation and detection of negative behavioral consequences [72-74]. The anterior cingulate is also part of the prefrontal-basal ganglia-cortical feedback system.
Apart from overt behavior, the degree to which we feel in control also influences cognitive performance [75]. The need to feel in control drives some people to seek excessively to master novel situations. These “novelty seekers” are known for their vulnerability to develop an addiction to drugs of abuse [76]. It appears that the same midbrain dopamine neurons which are thought to mediate reward [77-80] also mediate the stimulating effects of novelty [5]. This aspect has received particular attention with the majority of studies involving oper-ant conditioning being concerned with the mechanisms of addiction. In these paradigms, ad-diction is modeled by training animals to perform actions in order to obtain drugs until the actions have become habits, i.e. independent of their consequences. This situation mimics the failure of the negative consequences of addiction to exert any significant effect on the drug-taking habit.
But operant conditioning is also the paradigm of choice to model the production of flexible behavior often compromised in a number of other medical conditions. Complementing the deficits in behavioral variability and control cited above, other symptoms particularly in neuropathologies involving higher-order cognitive or executive functions as well as, more generally, the impact of emotional and motivational dysfunction in a range of syndromes, indicate the widespread relevance of operant mechanisms. For example, neuropsychological studies have established a connection between various compromised prefrontal-subcortical circuits and deficits associated with executive function in humans [27-29,81]. Deficits in ex-ecutive function have been generally described as comprising multiple components usually including volition, planning, purposive action and effective performance [30] and so signifi-cant operant involvement can be expected. Over and above specific deficits in behavioral choice and motor control, executive dysfunction has also been found in a range of neurode-generative disorders, including Alzheimer’s disease, Pick’s disease, progressive supranuclear palsy, Parkinson’s and Huntington’s disease. The early onset of many of the executive dysfunctions associated with these disorders suggests that even motor deficits involving tremor and choreic symptoms may partially reflect a disorder in the sustained functioning of the pre-frontal-basal ganglia-cortical feedback system during planning, decision making and behavior initiation [82]. In contrast, patients with Tourette’s syndrome show enhanced executive control, dissociating cognitive (frontal, medio-frontal) from non-cognitive control (subcortical, where the tics are assumed to be initiated) [81]. Interestingly, bilingual children also show enhanced cognitive control.
The experience of willing to do something and then successfully doing it is absolutely central to developing a sense of who we are (and who we are not) and that we are in control (and not being controlled). This sense is compromised in patients with dissociative identity disorder, alien hand syndrome, or schizophrenic delusions [21]. In some of these disorders the abovementioned midbrain dopamine neurons appear to play a central role, tying, e.g., Parkinson and schizophrenia tightly to operant models. Parkinson’s patients are administered the dopamine precursor L-DOPA, while schizophrenics are treated with a group of antipsychotics, most of which target and inhibit the D2 dopamine receptor. Some of these antipsychotic drugs have Parkinson-like side-effects. Recent research shows that L-DOPA and the antipsychotic haloperidol have opposite effects on operant decision-making in humans [83]. One is tempted to interpret these data as evidence for the hypothesis that the overlapping and interacting dopaminergic systems mediating primary rewards such as food, water or sex and those mediating behavior initiation and control are so tightly inter-connected precisely because of the rewarding properties of controlling the environment with behavior. As information such as the above accumulates, elucidating the mechanisms of operant conditioning becomes more and more promising as an avenue into understanding the causality underlying disorders such as those described above and their treatment.
There may even be a wider prospect of the study of operant conditioning. Many of the abovementioned disorders show a gender-specific pattern of occurrence. For example, depression, anorexia and obsessive compulsive disorder show a higher prevalence in women than in men, while autism, addiction and Tourette’s syndrome are more common in men then in women. A recent study has shown the male striatum to release up to 3 times more dopamine when stimulated by amphetamine, than in females [84]. It is conceivable that such a gender-difference in the processing of appetitive and aversive stimuli may be the underlying factor influencing the gender-specificity of many psychiatric disorders, which can be modeled by operant conditioning paradigms.

Scarce but converging biological data

Compared to its significance, our understanding of the biological mechanisms underlying operant conditioning is rather vague. The more important is a recent swell of ground-breaking studies (see also Fig. 1). A number of different model systems have contributed to this progress on various levels of operant conditioning. I will try to integrate the knowledge gained from such disparate sources to describe the general picture as it is currently emerging.

Conceptually, the mechanism underlying operant conditioning appears to consist of two modules: one is concerned with generating variable behavior and another predicts and evaluates the consequences of this behavior and feeds back onto the initiation stage [85-87]. Evidence from imaging humans suggests that dorsal and ventral striatum, respectively, may represent circuits involved each in one of the modules [87]. There is only very poor biological knowledge about the first module. Behavioral variability could be generated actively by dedicated circuits in the brain [12,14,88] or simply arise as a by-product of accumulated errors in an imperfectly wired brain (“neural noise” [89-92]). Despite recent evidence supporting the neural control of behavioral variability [9,17,93], the question remains controversial. Only little more is known about the neurobiology of the second module. Promising potential mechanisms have recently been reported from humans [21], rats [94], crickets [95] and Aplysia [96]. These studies describe neural pathways for re-afferent evaluation of behavioral output (via efference copies) and potential cellular mechanisms for the storage of the results of such evaluations. However, to this date, a general unifying principle such as that of synaptic plasticity in classical conditioning is still lacking. But with Eric Kandel joining the swell with new operant conditioning paradigm for Aplysia gill withdrawal [97], one can speculate that we may well be on the verge of a genuine paradigm shift in the neurosciences.
From a larger perspective, there is early evidence suggesting that the traditional distinction into operant and classical conditioning needs to be reconsidered. It appears that an experimental separation of classical and operant components is essential for the study of associative learning. Most associative learning situations comprise components of both behavioral (operant) and sensory (classical) predictors (composite conditioning). For example, if we touch a hot plate, we learn both about the plate and about our touch. If a frog attempts to catch a bee with its tongue, it can learn both about the striped insect and about extending its tongue towards it. If a rat in a Skinner-Box presses the lever for a food reward, it learns both about pressing the lever and about a depressed lever indicating food.
Research primarily from Drosophila and Aplysia has succeeded in eliminating much if not all of the classical component in ‘pure’ operant conditioning experiments [34,98-101]. This type of operant conditioning appears more akin to habit formation and seems to lack an extended goal-directed phase. The same studies also revealed that such pure operant conditioning (maybe better termed “self-learning”) differs from classical conditioning (more parsimoniously called “world-learning”) on the molecular level. While world-learning acts via a type I adenylyl cyclase that is regulated by Ca2+/Calmodulin and G protein, the evidence points towards self-learning as being based on a dopamine receptor-coupled type II adenylyl cyclase which eventually leads to the activation of dopamine and cyclic adenosine 3′,5′-monophosphate-regulated phosphoprotein, 32 kDa – DARPP-32, which is involved in a variety of processes and disorders associated with operant functioning in vertebrates [102-104]. The research implies that the acquisition of skills and habits, such as writing, driving a car, tying laces or our going to bed rituals is not only processed by different brain structures than our explicit memories, the neurons also use different biochemical processes to store these memories. If these early results were substantiated, classical conditioning paradigms cannot serve as the general tools for all learning and memory research as they do today.
The realization that composite conditioning consists of separable self-learning and world-learning components opens the possibility to observe the interactions between them [23,34]. For instance, the early, goal-directed phase is dominated by world-learning which is facilitated by allowing a behavior to control the stimulus about which the animal learns. Self-learning in this phase is suppressed by the world-learning mechanism. If training is extended, this suppression can be overcome and a habit can be formed. Organizing these processes in such a hierarchical way safeguards the organism against premature stereotypization of its behavioral repertoire and allows such behavioral stereotypes only if they provide a significant advantage. This insight supports early hypotheses about dominant classical components in operant conditioning [33], but only for the early, goal-directed phase.
These results may have drastic implications for all learning experiments: as soon as the behavior of the experimental subject has an effect on its subsequent stimulus situation, different processes seem to be at work than in experiments where the animal’s behavior has no such consequences, even if the subject in both cases is required to only learn about external stimuli. The hierarchical organization of fact- and skill-learning processes also explains why we sometimes have to train so hard to master certain skills and why it sometimes helps to shut out dominant visual stimuli by closing our eyes when we learn them. Gene expression analysis in vertebrates supports the separation of these two components: goal-directed phases of learning are characterized by immediate-early gene expression in the frontal and cingulate cortices, whereas later, habitual phases are characterized by gene expression in the ventrolateral striatum [63,64].
As mentioned above, midbrain dopamine neurons are considered to be the main mediators of reward in vertebrates[77-80]. Given the prominent status of input/output transformations in the brain, it is not surprising that the role of dopamine signaling has always been described in the context of prediction errors triggered by external stimuli. Only now has a re-thinking begun and a new hypothesis has emerged which challenges this view and instead suggests a prominent role of the short latency dopamine signal in output/input computations [105]. Recent brain imaging evidence points towards the medial orbitofrontal cortex as a component downstream of this dopamine signal. When controlling the environment with behavior, this brain area shows activation both to obtained rewards and to successfully avoided punishments [56].

Another case for multiple model systems

Our relative lack of knowledge stems in part from research into operant conditioning being conceptually much more challenging than classical conditioning. However, recent progress in invertebrate neuroscience suggests that the now classic Kandelian approach of relying heavily on simpler brains while developing tools and models for vertebrate research is even more promising today in the age of advanced molecular, genetic, imaging and physiological repertoires in invertebrates than 30 years ago [20,106]. Even in the post-genomic era, invertebrate models offer the possibility to rapidly and effectively learn about important principles and molecules which can then be used to reduce the complexity of the vast vertebrate brain [107]. Besides offering a more effective avenue into studying the neural basis of operant conditioning, such an integrative approach will provide us with insights into the exciting question of why invertebrate and vertebrate brains are structurally so very different even though the basic demands of life are quite similar in both groups. Moreover, a multi-faceted approach will allow us to distinguish general mechanisms from species-specific adaptations. Coincidentally, using multiple model systems effectively reduces the number of vertebrate experimental animals, working towards the ‘3R’ goals — refinement, reduction and replacement [108]. Combining the rapid technical advancements also in vertebrate physiology, imaging and behavior [109] with modern computational power, neuroscience is now more than ready to finally tackle operant conditioning on a broad scale. The recent swell of publications on operant conditioning is the logical consequence of 20 years of meticulous research during the dominant input/output mainstream [62]. The most important questions to be answered in future research are:

  • What are the brain-circuits generating spontaneous behavior?
  • How is sensory feedback integrated into these circuits?
  • Which are the ‘operant’ genes?
  • What are the mechanisms by which fact-learning suppresses skill-learning?
  • How can repetition overcome this suppression?

Acknowledgments: I am grateful to Bernd Grünewald, Bernhard Komischke, Gérard Leboulle, Diana Pauly, John Caulfield, Peter Wolbert, Martin Heisenberg and Randolf Menzel for critically reading an earlier version of the manuscript. I am especially indebted to Bernard Balleine and Charles Beck for providing encouragement, stimulating information and some key references.

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Jul09

The Conversation: The looming crisis in science

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

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. If one describes the problem too cautiously, the message will be ineffective in rallying the community and collective action will not happen. Describe the problem too drastically, and the community will not be convinced by the alarmist rhetoric and also fail to take action.

Here are some data, together with a computed trend that indicates what I think would be best described as a looming crisis for the scientific community: not yet urgent, but if no action is taken, the trend will threaten the entire scientific enterprise within the coming 30 years.

Currently, the number of scientific papers retracted from PubMed is a mere 0.05%, an astonishingly low rate, given the vagaries of the job and the common .05 statistical significance level in biomedicine. However, recently this rate has been rising. The rise is exponential such that, if the trend were to continue, by about 2045 almost all scientific publications will have to be retracted. Apart from high-profile fraud cases which since recently also make it into the general news media, the numbers themselves are not yet alarming. Extrapolating the current trend, we will not reach the .05-level, i.e. 5% of all published articles in a given year will be retracted, before 2033 – it will take almost twenty years for this hundredfold increase, i.e. doubling about every three years. If the current trend were to continue that far into the future, 10% would be reached about 2036, 20% in 2039, 40% in 2042, 80% in 2045 and soon thereafter, for every new publication in PubMed, at least one older one would have to be retracted.

Causes

Usually, any problem at this scale will have a number of underlying causes. Science, like any enterprise, is a complex affair. In this special case, however, a large part of these causes can be traced to the reward structure that scientists have built around them to make this enterprise work. They are related to how scientists choose to publish their results and how fellow scientists reward this publishing behavior.

Unfortunately, even with a clearly identifiable cause, in this case there is no easy fix.

History

Starting in the 1960s, the rising number of scholarly journals increased subscription costs for libraries too quickly. Institutional libraries and university faculty were faced with the problem of deciding which journals to read and subscribe, keeping their budgets in mind. One solution, it seemed, was to rank journals according to how many citations each of its publication garnered on average.

Back then only a few realized that a generation later their future colleagues would not only adjust their reading habits to journal rank, but that those reading habits will translate into new publishing habits. After all, every one wants their work to be read by as many as possible.

Today, where you publish matters more than what you publish. This behavior may vary from country to country and field to field, but it is quite widely known that tenure, promotion, grant funding, etc. all depends on where in the hierarchy of journals one’s research results have been published.

What makes it worse is this feedback loop: more citations means more attention. More attention more citations. As long as space is scarce, more manuscript submissions mean higher rejection rates, for some journals the rejection rates can be as high as 90%. Like long lines in front of hip clubs, higher rejection rates mean more validation for the few researchers that actually manage to get published in these journals and hence more citations.

Publishers

Not surprisingly, as researchers adjusted their behavior, so did publishers. The top journals did not increase space for the increased demand. Instead, they spawned ever more lower ranking offspring to reinforce the ratchet and keep the demand high.

With the arrival of the internet, publishers went through a complete reversal of their role in knowledge dissemination. Before the internet, publishers would heed their profession, investing in printing presses and delivery systems for a wide and efficient system of dissemination to the public. Today, academic publishers have become the opposite. These corporations are now “hiders”: they invest in paywalls, hiding the research from the public that paid for it.

But perhaps this is all fine and well? After all, publishers select the very best science using professional editors and need to protect their investment.

Rankings

Superficially, one may assume that such strong selection would only enable the most groundbreaking, methodologically sound research to clear such monumental hurdles. However, the data speak a different language. While indeed quantifications of ‘novelty’ and ‘importance’ have been found to correlate significantly with journal rank, the correlation is so weak, that for every publication correctly published in a high-ranking journal, there is one that should not have been published there. Conversely, such a large percentage of research findings that did not manage to get published in a top journal end up being recognized as deserving after being published in a lower journal, that the practical value of journal rank as an evaluation signal is negligible, despite the statistics. Even more damaging, however, quality-related metrics such as technical quality, methodological soundness, reproducibility and so on either failed to show any correlation with journal rank, or correlate negatively. These data support the observation of decreasing intervals between prominent scientific fraud scandals and the increasing range and scope of each case, mostly based on fraudulent work published in top journals.

Marketing

Apparently, as the pressure mounts to publish in top journals, authors race to find a way to present their work as important and groundbreaking, no matter the actual content and quality. Science today has become a rat race between authors marketing their research and professional editors struggling to see through the fluff. It is the perfect arrangement to bring our the worst in all participants: scientists fear for their livelihoods and do what is necessary to survive, with little regard to science. Publishers fear their business model and do what is necessary to survive, with little regard to science. And librarians are caught in the middle.

Multiplicators

This straightforward, evidence-based analysis of the current state of affairs suggests a slightly more alarmist suspicion. Exponential effects are typical for social phenomena, where feedback is driving much of the dynamics of the system. The already described, relatively fast feedback loop propped up by journal rank supports a second, slower loop: after a generation of increasing pressure to publish in top journals, many of the now leading scientists are excellent at marketing their research to top journals. After all, this is how they were selected. It may of course happen that these researchers are also excellent scientists, but this was often enough not the selection criterion. These scientists are now training the next generation of scientists in how to be successful in science. The anecdotal evidence suggests that – intentional or not – marketing one’s research to top journals may play a dominant role in this training. If this were indeed the case, it would help explain the exponentially increasing retraction rates in the scientific literature and constitute cause for grave concern with respect to the looming crisis in science.

Reform

Of course, laziness, vanity, ambition, desperation, hubris, self-aggrandizement, sleep deprivation or bad time management are not going to disappear any time soon. Scientists are human too. The realistic task can thus not be to altogether eliminate shoddy, unreliable science, but to reform our infrastructure which currently almost appears to be purposefully designed to exacerbate aforementioned traits and bring out the worst in scientists, thereby wasting resources and threatening lives. Scientific discoveries are unreliable enough even under the best of circumstances, given the complexity of the matter, there surely is no need to worsen the situation. Instead, we must design an infrastructure that brings out the best in scientists and aligns their incentives with that of science and the public.

Technicalities

Given the current status quo, this is technically rather straightforward: one has to remove the incentives for scientists that encourage and reward marketing at the expense of science and instead encourage and reward actions of scientists that benefit both science and scientists. Given that scholarly communication is at the heart of the scientific endeavor, this is where we should place most emphasis in our infrastructure reform. What we need is to abandon the traditional idea of journal publishing altogether, in favor of an institution-based platform that allows every tax-payer, scientist or not, to access all the literature, data and software that is being paid for out of the public purse. For the past two decades, corporate publishers have proven to have become exceedingly poor custodians of the public good that is research results. From their continued and often shamefully backstabbing and cunning resistance to change their business model to provide even simple read-only access to the scientific literature to those who paid for the research in the first place, to the current prohibition of text- and data-mining access for scientists to their own literature, corporate publishers have proven beyond the shadow of a doubt that they have forfeited every right to be perceived as partners of scientists. Instead, the evidence weighs heavy that many if not most of these corporations are now enemies of science.

Solutions

Small versions of such open access platforms exist in many university libraries today, in various forms. They need to be combined and made interoperable using common standards. In less fortunate parts of the world, where research billions are not as abundant, governments felt forced, long before us, to realize how wastefully corporate academic publishing treats tax-funds. These countries have very successfully been running a multi-national platform, SciELO, which, if implemented on a global scale and funded with only a single digit fraction of what corporate publishing costs today, would eliminate the pernicious incentives currently in place and provide full open access to the public. Recent initiatives like SHARE, the DPLA or the LPC could serve as nucleation points for such developments in the rich countries. Provided that the reputation system built into this platform is guided by the same evidence-based reasoning and tested with the same scientific rigor we commonly apply to our experiments, this kind of reform would not only come for free, it would save billions in tax-funds every year and, by virtue of its public accessibility, literally save countless lives.

It is a collective disgrace for the entire scientific community that saved money and saved lives are apparently not sufficient incentives to drive forceful and rationally designed reform right now. Instead, as in many other communities, vested, not exclusively corporate, interests are still keeping an upper hand.
This must change.

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Jul08

Flashback: The neurobiology of self-learning

In: blogarchives • Tags: classical, conditioning, Drosophila, mice, operant, self-learning, transgenic

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. This post is from October 31, 2011:

 

It’s been a while since I’ve last been so excited about a new finding by someone else And until today, this paper from last week even flew completely under my radar. I had seen the title and decided it’s not relevant. A collaborator of mine sent it to me after she found it searching for a current affiliation of a former postdoc of hers – which was how she realized how pertinent this work was to our research and sent it to me (which says something about the way scientists are able to stay on top of the literature. Note to self: write separate post!).

This paper detailing experiments in transgenic mice joins a pair of papers in invertebrate model systems ( Aplysia and Drosophila), suggesting that brains have two distinct molecular learning mechanisms, one to learn about relationships among events in the world around them and one to learn about the effects of their own behavior on the world. This distinction shares several conceptual features with the distinctions that have been made between operant conditioning and classical conditioning or between declarative and procedural memory, and several other related dichotomies, but is yet slightly different.

Here’s a drastically simplified diagram of what the current canonical pathway looks like for ‘synaptic plasticity’, the kind of physiological process that modifies the connections between neurons in order to store memories (screenshot from one of my talks):

canonical_small.png

Briefly, the to-be-remembered information is translated into neuronal signals which are eventually translocated into the memory-storing neuron, where an adenylyl cyclase (encoded by the rutabaga gene in flies) generates cAMP, which activates Protein Kinase A (PKA), which in turn eventually activates a protein with the acronym CREB. CREB is a transcription-factor switching on genes which modify the neuron, storing the memory. Not shown is how PKA can itself also modify the neuron to allow memories to form almost instantaneously, without the need for protein synthesis (which takes a while). OK, this is really extremely simplified, but the important point here is that there is no Protein Kinase C (PKC) involved. In fact, PKC has been shown to either not be involved at all, or only to maintain the memory, long after it’s been formed. The cool thing about this learning mechanism (and why its discovery got the Nobel Prize in 2000) is that you find it in all bilaterian animals, e.g. flies, snails and mice.

In 2008 I wrote here about one of our publications that we had discovered a ‘Skinnerian‘ learning mechanism, which did not require the rutabaga gene, but PKC. Back then we couched the discovery in terms of the 70-something year-old debate about whether operant and classical conditioning share a common learning mechanism or not. The idea was that operant conditioning involves learning about the consequences of one’s behavior while classical conditioning involves learning about the ring of a bell being followed by food For this experiment, we used the genetic toolkit of Drosophila to express an inhibitor of PKC (PKCi) in all cells of the fly only during the experiment. These flies had trouble learning an operant task in which all external cues had been removed, but as soon as ‘classical’ cues were added, they learned just fine.

This discovery was followed in the same year by a paper from my postdoctoral lab that showed basically the analogous outcomes in the marine snail Aplysia. This got me very excited: flies and snails? What about the chordates?

conservation_small.png

In their new paper, Rochefort et al. express the same PKCi peptide that we had used in our fly study in the cerebellum of mice. They use these mice to perform orientation and navigation experiments in which the animals either have to rely on self-motion cues (procedural learning) or on the position and identity of external cues (declarative learning) to find a particular location. It turned out that in all three of their experiments, whenever the animals could rely on external cues, they learned to find the location just fine. However, when the cues either were removed or arranged in a way to conflict with each other, the mice showed a severe decrement in performance. In other words, also these colleagues found a PKC-dependent form of learning which is mainly concerned with the behavior of the animal itself and less with learning about events in its environment.

Are these experiments in three model systems enough to make a strong claim there we are in the process of opening up a new field of research, the study of ‘self-learning‘? I wouldn’t think so if we wouldn’t have yet another piece of evidence up our sleeves: we are currently in the process of submitting a manuscript that details our results on the fly gene most closely related to the ‘language gene‘ (that wasn’t), FOXP2. Briefly, language acquisition can be thought of as an operant process: babies babble and use the auditory feedback of what it sounded like when they babbled to change their babbling – eventually into language. Songbirds learn their songs in a quite similar way. Both humans and songbirds have trouble learning their respective vocalizations if the gene FoxP2 is not intact. So we went and looked for a homologous gene in Drosophila, found it (dFoxP), manipulated it and found that the manipulations had the same effect as the PKCi expression: self-learning was affected and world-learning wasn’t.

Thus, we (several different labs independently) now appear to have discovered not one, but two components of this new self-learning mechanism, PKC and FoxP:

nuplast_small.png

In fact, evidence from Aplysia suggests that this mechanism also includes cAMP, but form a different cyclase and activating a different sort of PKA. However, this has not been tested in the other systems, so far.
Thus, I think there now are too many converging results from very disparate experiments to just be chance. I now have the very strong suspicion that we are on the cusp of the birth of a new research field: the neurobiology of self-learning.


Rochefort, C., Arabo, A., Andre, M., Poucet, B., Save, E., & Rondi-Reig, L. (2011). Cerebellum Shapes Hippocampal Spatial Code Science, 334 (6054), 385-389 DOI: 10.1126/science.1207403

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Jul05

Tweetlog: neuroscience and #openaccess

In: Tweetlog • Tags: neuroscience, open access, Twitter

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! I hated to receive the message that Google essentially tries to kill RSS technology https://img.ly/vE3J
  • A Selfish Genetic Element Influencing Longevity Correlates with Reactive Behavioural Traits in Female House Mouse. https://dx.plos.org/10.1371/journal.pone.0067130
  • June 30, 2013 Dramatic Growth of Open Access https://feedly.com/k/18znPVA
  • Optogenetic Perturbation of Neural Activity with Laser Illumination in Semi-intact Drosophila Larvae in Motion https://feedly.com/k/13oKSBs
  • The causes of variation in learning and behavior: why individual differences matter https://shar.es/A5o4M
  • Joint statement on Europe’s Open Data Pilot from OpenAIRE, LIBER, and COAR “The European… https://goo.gl/fb/qjdTU
  • Horizon 2020 – Outline of a Pilot for Open Research Data: Joint statement by OpenAIRE, LIBER and COAR https://ow.ly/mFEpW  #opendata
  • Martin Paul Eve considers how open access might influence quality control and the future of peer review – https://www.socialsciencespace.com/2013/07/martin-paul-eve-considers-how-open-access-might-influence-quality-control-and-the-future-of-peer-review
  • Automated High-throughput Behavioral Analyses in Zebrafish Larvae https://www.jove.com/video/50622/automated-high-throughput-behavioral-analyses-in-zebrafish-larvae
  • When will we get proper hyperlinks in scholarly communication? https://buff.ly/12fctgN
  • Operant trial and error learning: Cockatoo cracks lock with no prior training https://buff.ly/1aFyKO9
  • Waiting for the lame excuses as to why Nature fails to round 38.597 to 39… pic.twitter.com/qm052J2KgQ
  • How Beliefs in Extraterrestrials and Intelligent Design Are Similar https://buff.ly/15hqX52
  • Science standards in US classrooms: Evolution makes the grade https://feedly.com/k/1cTC312
  • #devbio #wnt Home truths and ugly facts about Wingless in #drosophila https://bit.ly/16QLjBu
  • Plasticity in the Drosophila larval visual system https://feedly.com/k/12IBm4t
  • Retraction of 19-year-old Nature paper reveals hidden cameras, lab break-in, evidence tampering https://wp.me/pYKlt-3Rx
  • Delighted to have 11 really strong postdoc applications out of a total of 32 complete applications. How to narrow down to a short-list?
  • No, the whole planet should rid themselves of this disgrace: “Latin America should ditch impact factors” https://feedly.com/k/1cTCeJA
  • Operant behavior: Explorative Learning and Functional Inferences on a Five-Step Means-Means-End Problem in Cockatoos https://buff.ly/1aFyY7V
  • Operant learning: Cockatoos show technical intelligence on a 5-lock problem https://www.eurekalert.org/pub_releases/2013-07/uov-amc070313.php#.UdVaarcgihM.twitter
  • Call to libraries: Biology must develop its own big-data systems https://feedly.com/k/1cTBLHf
  • Awesome, more evidence: Long-Range Correlations in Resting-State Oscillations Predict Timing-Error Dynamics https://feedly.com/k/1cTzxro
  • Short summary of a smart experiment: Opening the black box: dopamine, predictions, and learning https://feedly.com/k/1cTy9oW
  • “your government does not trust you. Why therefore should you trust it?” https://gu.com/p/3h3m9/tw
  • Hmmm? “Yawning manifests a process of increasing clearance of somnogenic factors in CSF” https://feedly.com/k/1cTwUWE
  • The dysfunctionality of the scholarly literature: hyperlinks https://wp.me/p3walV-4y
  • ArduiPod Box: A low-cost and open-source Skinner box using an iPod Touch and an Arduino microcontroller. https://feedly.com/k/1cTwlfp
  • I liked a @YouTube video https://youtu.be/e_44G-kE8lE?a  Michael Dickinson: How a fly flies
  • Glühwürmchen und die Frage nach dem Sinn allen Forschens https://feedly.com/k/1cTB5So
  • Scaling-Laws of Human Broadcast Communication Enable Distinction between Human, Corporate and Robot Twitter Users https://dx.plos.org/10.1371/journal.pone.0065774
  • Libertarianism and Human Agency. Alfred Mele 2011 https://onlinelibrary.wiley.com/doi/10.1111/j.1933-1592.2011.00529.x/abstract
  • Science metrics, LitRoost, and the networked era https://www.theunstudent.com/2013/07/science-metrics-litroost-and-the-networked-era/ via @@mikhailklassen
  • Drosophila pseudoobscura: a model fruit fly for the real world https://blogs.scientificamerican.com/compound-eye/2013/07/03/drosophila-pseudoobscura-a-model-fruit-fly-for-the-real-world/?WT.mc_id=SA_sharetool_Twitter … via @sciam
  • If publishers would only let us: “A text-mining system for extracting metabolic reactions from full-text articles.” https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475109/?report=reader
  • Nice article: MT @WiringTheBrain Compulsivity and Free Will – nice, short overview by Damiaan Denys https://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8947414
  • NIH sees surge in open-access manuscripts https://blogs.nature.com/news/2013/07/nih-sees-surge-in-open-access-manuscripts.html

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