bjoern.brembs.blog

Aug16

Scientific discoveries are like orgasms: you can’t have any bad ones

In: blogarchives • Tags: dunning-kruger, incompetence, 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 June 24, 2010:

What is it with non-scientists trying to go and save science from the scientists? First, there’s an English major at Scholarly Kitchen trying to tell us we should stick with a 400 year-old publishing system despite more modern systems being widely and readily available. Then the same blog sports a post wondering why their 400 year-old system they just touted doesn’t seem to operate as they imagine. So first these guys write a post to make sure every scientist who reads it understands that they have no clue and then they wonder why their clueless and hence baseless predictions don’t materialize? WTF? I have an answer for The Scholarly Kitchen: because what you imagine how science works has nothing to do with reality!

Then there is a completely weird article in The Chronicle of Higher Education on how we need to get rid of all ‘low-quality’ science. This piece, probably not unexpected by now, was written by English, management, mechanical engineering and geography professors. The lone medical researcher in the group does have a fair amount of PubMed articles, but none of them are in one of the supposedly high-quality journals mentioned in the article, so he basically just called himself ‘low-quality’ and thus should be struck from the public record, Moreover, the articles where he was single author or one of two authors are all on clinical practice and testing, raising the tentative suspicion that medical practice is really his strong area of expertise, rather than science. Which means that, again, none of these guys is actually a scientist, i.e., working in physics, chemistry, biology and regularly publishing scientific, experimental papers, which makes up the bulk of the scientific literature. If they were, they would know that there isn’t such a thing as a ‘low-quality’ scientific discovery. Scientific discoveries are like orgasms: you can’t have any bad ones. Now, I agree that there are badly conducted experiments, missing control procedures and outright fraud. None of these examples are eliminated by reducing scientific output, obviously. The authors make sure that this is not what they mean, as they refer to ‘low-quality’ science as journals or papers that aren’t cited. Obviously, hi-profile fraud cases are cited a lot. One reason for low citation counts is that very few scientists understand the topic and/or are interested in it. Clearly, this can change in a heartbeat and what was boring one day can be all the rage tomorrow. Only someone not steeped in scientific research would not be aware of that. Not surprisingly, this article has received a thorough smackdown in the comment section over there and in the blogosphere.

And then finally, to cap it all off, this completely inane post, riddled with factual errors, ludicrous assumptions and outright slander. The author characterizes himself as the person who trademarked the term “Science 2.0”. Moreover, in the comments, he gives it away: “I’m not a researcher” (as if that wasn’t already blatantly obvious from the post). I wonder why he’s even touching his keyboard such that it generates these nonsensical sentences? This post contains about as much valuable and accurate information as if a monkey had sat on the keyboard. By his own admission, he has about as much competence in this topic as a monkey’s rear end. This guy could probably just go and give it a shot trying out for the LA Lakers – at least he couldn’t be any less qualified than for his chosen topic.

I’m a biologist. Do I go to engineers and tell them how to build bridges? Do I try to play in the NBA? Do I tell BP to just put a lid on it? Sheesh, why are so many people trying to outcompete each other to exemplify the Dunning-Kruger effect these days? These guys are even more pathetic than Rupert Pupkin in The King of Comedy. What’s with this current slate of ignorant imbeciles trying to grandstand as if they had any relevant competence whatsoever and address an international group of hundreds of thousands of professionals with the actual expertise and experience? Where do these guys get the idea they have anything meaningful and worthwhile to contribute? What’s gotten into them? A different collusion of delusion?

claimtoken-520f68e90ad03

Posted on August 16, 2013 at 09:15 Comments Off

Aug15

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

In: blogarchives • Tags: archeology, creationism, evolution, genetics, language

The last decades of research on human evolution have provided an astounding body of converging evidence for an African origin of the human lineage just under about 200k years ago, with a subsequent migration across the globe starting around 60k years ago until all the main regions of this planet were inhabited by humans at around 15k years ago. Compare this scenario to the creationist story, where humans were shaped by a magic man out of clay about 6k years ago, which means it happened just after the Sumerians have invented glue.What is the converging evidence telling the “Out of Africa” story?It all started with fossils and artifacts. Archeology, with its own dating techniques and collection methods, suggested a route that looks something like this:

(Image source)

Later, genetic evidence came along. Geneticists, with their own dating techniques and experimental methods suggested migration routes that looked something like this:

(Image source)

After the genetic evidence, came evidence from a bacterium associated with humans: Helicobacter pylori. It lives in our guts and can cause stomach ulcers. It’s been associated with our digestive tract for many thousands of years. Looking at the different strains of these bacteria, microbiologists, using their own dating techniques and experimental protocols, deduced that this bacterium in our guts must have traveled roughly along these routes:

(Image source)

Most recently, linguists came along and studied the phonemes that make up 504 of the different human languages around the globe. These linguists adopted the analysis tools from the geneticists to their own dating techniques and sampling methods and came up with a map that suggested the following main routes along which the human languages seem to have developed:

(Image source)

Clearly, getting the dates correct using phonemes will prove a lot harder than the previously used dating techniques. Nevertheless, these are four independent lines of evidence, collected over many decades by scientists with vastly different backgrounds and training. Yet, the results agree to an astonishing extent.

However, this doesn’t mean it’s ‘true’ or ‘scientifically proven’. It only means that this is the best humans can currently possibly do and anything new that comes along must not only explain the current congruence of disparate data, but also explain more data, than the current ‘Out of Africa’ theory can explain. A few self-contradictory passages in an ancient text do not even begin to come close to being a contender.

Given this sort of evidence, it becomes rather obvious that creationists are either uninformed or unpersuadable. For the former, information like the one in this post should be more than sufficient to falsify the creationist dogma. For the latter, ridicule and derision is the best response.

This post was inspired by Lapidarium Notes.

Pertinent peer-reviewed literature:

Green, R., Krause, J., Ptak, S., Briggs, A., Ronan, M., Simons, J., Du, L., Egholm, M., Rothberg, J., Paunovic, M., & Pääbo, S. (2006). Analysis of one million base pairs of Neanderthal DNA Nature, 444 (7117), 330-336 DOI: 10.1038/nature05336
Linz, B., Balloux, F., Moodley, Y., Manica, A., Liu, H., Roumagnac, P., Falush, D., Stamer, C., Prugnolle, F., van der Merwe, S., Yamaoka, Y., Graham, D., Perez-Trallero, E., Wadstrom, T., Suerbaum, S., & Achtman, M. (2007). An African origin for the intimate association between humans and Helicobacter pylori Nature, 445 (7130), 915-918 DOI: 10.1038/nature05562
Atkinson, Q. (2011). Phonemic Diversity Supports a Serial Founder Effect Model of Language Expansion from Africa Science, 332 (6027), 346-349 DOI: 10.1126/science.1199295

Posted on August 15, 2013 at 18:16 Comments Off

Aug13

Neither gold, nor green, nor hybrid are sustainable open access models

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

If you trust empirical evidence, science is currently heading for a cliff that makes dropping off the fiscal cliff look like a small step in comparison. As we detail in our review article currently under revision, retractions of scientific articles are increasing at an exponential rate, with the majority of retractions being caused by misconduct and fraud (but also the error-rate is increasing). The evidence suggests that journal rank (the hierarchy among the 31,000 scientific journals) contributes a pernicious incentive: because funds are tight and science is increasingly under pressure to justify its expenditure, people are rewarded for publishing in high-ranking journals. However, there is no empirical evidence that science published in these journals is any different from scientific discoveries published in other journals. If anything, high-ranking journals publish a much larger fraction of the fraudulent work than lower ranking journals and also a larger fraction of the unintentionally erroneous work. In other words, journal rank is like homeopathy, astrology or dowsing: one may have the subjective impression that there is something to it, but any such effects disappear under scientific scrutiny.

As journal rank has only been used as an instructor for the hire-and-fire policy and institutions world-wide for a few decades, the data also project some potentially catastrophic consequences of journal rank: science has been hiring those candidates who are especially good at marketing their science to top journals, but maybe not equally good at the science itself. Conversely, excellent scientists were fired who did not reach institutional requirements for marketing their research. If this is really what has been taking place, it has now been going on just long enough by now to replace an entire generation of scientists with researchers who are particularly good at marketing, providing one potential explanation of why the fraud and retraction rate is exploding just at this particular point in time. However, until a few years ago, this has been a trend that has only been observed by a few bibliometricians.

At the same time, a much more obvious trend has been receiving a lot of attention: the rising costs of acess to the scholarly literature. To counter this trend, three different publishing models have emerged, which only address the access problem, but not the parallel, and potentially underlying problem of journal rank. These models aim to provide unrestricted, open access to publicly funded research results either by charging the authors once for each article (gold), or by mandating them to place a copy not of the final PDF, but of the version approved by the referees (i.e., the version before the publishers format it) in institional repositories (green), or by providing an option for authors to make heir article accessible in a subscription journal by an additional article fee, i.e., if the authors pay the fee, their article becomes openly accessible, if not, it stays behind a paywall (hybrid). Importantly, the three models which are currently aimed at publishing reform are not sustainable in the long term:

Gold Open Access publishing without abolishment of journal rank (or heavy regulation) will lead to a luxury segment in the market, as evidenced not only of suggested author processing charges nearing 40,000€ (US$~50,000) for the highest-ranking journals, but also by the correlation of existing author processing charges with journal rank. Such a luxury segment would entail that only the most affluent institutions or author would be able to afford publishing their work in high-ranking journals, anathema to the meritocracy science ought to be. Hence, universal, unregulated Gold Open Access is one of the few situations I can imagine that would potentially be even worse than the status quo.
Green Open Access publishing entails twice the work on the part of the authors and needs to be mandated and enforced to be effective, thus necessitating an additional layer of bureaucracy, on top of the already unsustainable status quo.
Hybrid Open Access publishing inflates pricing and allows publishers to not only double-dip into the public purse, but to triple-dip. Thus, Hybrid Open Access publishing is probably the most expensive version overall for the public purse.

Thus, what we have now is a status quo that is a potential threat to the entire scientific endeavor both from an access perspective and from a content perspective, and the three models being pushed as potential solutions are not sustainable, either. The need for drastic reform has never been more pressing.

Posted on August 13, 2013 at 19:49 2 Comments

Aug12

Flashback: The neurobiology of operant conditioning

In: blogarchives • Tags: Drosophila, FoxP, neurogenetics, operant, PKC, rutabaga, self-learning

It turns out, operant conditioning is very different from other forms of learning, all the way from the genes up. When I started my research on operant conditioning in 1995, I did so with the opposite hypothesis, namely that the underlying mechanism of all learning processes was always synaptic plasticity with the well-known molecular pathway: Ca⁺⁺, cAMP, PKA, CamK, CREB and so on. After all, wasn’t that pathway conserved all the way from flies, snails and mice to humans? By the time I finished by PhD in 2000, Eric Kandel had received the Nobel prize for exactly these learning mechanisms – he wouldn’t have gotten the prize if the pathways had not been so conserved. In principle, changing the weight of the synapses is all you need to do to store whatever information you want. There is no a priori need to have several different mechanisms by which neural networks are modified.

A few years ago, I started getting data from fruit flies ( Drosophila) that were exactly the opposite of what my initial hypotheis was: the genes required for standard synaptic plasticity (such as the rutabaga adenylyl cyclase) were not required in our form of operant conditioning. In contrast, a gene which had previously been shown not to be involved in classical conditioning, protein kinase C (PKC) turned out to be crucial for operant conditioning. What made the whole story even more intriguing was that the same evidence started to show up in the lab where I did my postdoc, using the marine snail Aplysia as a model system: PKC was required, but the rut-cyclase was not.

Why had nobody discovered this dichotomy between the learning mechanisms before us? It turned out that the crucial experimental advance was to prevent the animals from learning about anything else besides their behavior. As soon as we let the animals learn about any external cues in addition to their behavior, the results go back to the expected canonical pathways being required and PKC not. Obviously, nobody had been able to completely isolate operant conditioning to the extent that was required. Because all our experiments were operant in nature, but only differed in whether or not the animals were able to learn about environmental cues or not, we called the PKC-dependent learning mechanism operant self-learning and the other, well-described form, operant world-learning.

How far is this new form of plasticity (in Aplysia it is a form of ‘intrinsic plasticity’ modifying the entire neuron and not just the synapse; in Drosophila we don’t know) conserved? We are currently in the process of writing up our experiments on the ‘language gene’ FoxP2. Drosophila has an orthologue of this gene and if we mutate it (or knock it down with RNAi), we find that it is required for operant self-learning, but not for operant world-learning, paralleling the results we had for PKC. This means we now have a new learning mechanism at hand that is clearly distinct from the well-known synaptic plasticity pathway, but is equally conserved among invertebrates and vertebrates. These results suggest an ancient evolutionary origin for operant self-learning, possibly at the root of the bilaterian branch, and a complementary role to world-learning.

I have summarized these results in an invited review on occasion of the 2010 conference of SQAB in the journal “Behavioural Processes”. Unfortunately, there are a few mistakes in the copy available from the publisher. Some spaces are missing between words and the references Brembs 2009a and Brembs 2009b are mixed up. I’ve notified the publisher, but they said it was too late to fix. I’ve now fixed the HTML version of my local copy, but I can’t fix my PDF copy as they use a font that is not freely avaliable. So if anybody knows how I can fix my own PDF copy, please let me know!

Brembs, B. (2011). Spontaneous decisions and operant conditioning in fruit flies Behavioural Processes DOI: 10.1016/j.beproc.2011.02.005

Posted on August 12, 2013 at 21:09 Comments Off

Aug11

SummerScienceVideo: science is real

In: blogarchives • Tags: fun, science, 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 this one on Agust 31, 2011:

A nice song with a really cool little video:

They Might Be Giants - Science is Real (official TMBG video)

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Posted on August 11, 2013 at 13:24 Comments Off

Aug08

12 year anniversary of angry letter to scientific journal editor

In: science politics • Tags: publishing

This year marks the 12th anniversary of the publication of this legendary letter to the editor in the Journal of systems and Software:

A letter from the frustrated author of a journal paper

R. L. Glass

Computing Trends, 1416 Sare Road, Bloomington, IN 47401, USA

Available online 28 September 2000.

Editor’s Note: It seems appropriate, in this issue of JSS containing the findings of our annual Top Scholars/Institutions study, to pay tribute to the persistent authors who make a journal like this, and a study like that, possible. In their honor, we dedicate the following humorous, anonymously-authored, letter!

—

Dear Sir, Madame, or Other:

Enclosed is our latest version of Ms. #1996-02-22-RRRRR, that is the re-re-re-revised revision of our paper. Choke on it. We have again rewritten the entire manuscript from start to finish. We even changed the g-d-running head! Hopefully, we have suffered enough now to satisfy even you and the bloodthirsty reviewers.

I shall skip the usual point-by-point description of every single change we made in response to the critiques. After all, it is fairly clear that your anonymous reviewers are less interested in the details of scientific procedure than in working out their personality problems and sexual frustrations by seeking some kind of demented glee in the sadistic and arbitrary exercise of tyrannical power over hapless authors like ourselves who happen to fall into their clutches. We do understand that, in view of the misanthropic psychopaths you have on your editorial board, you need to keep sending them papers, for if they were not reviewing manuscripts they would probably be out mugging little old ladies or clubbing baby seals to death. Still, from this batch of reviewers, C was clearly the most hostile, and we request that you not ask him to review this revision. Indeed, we have mailed letter bombs to four or five people we suspected of being reviewer C, so if you send the manuscript back to them, the review process could be unduly delayed.

Some of the reviewers’ comments we could not do anything about. For example, if (as C suggested) several of my recent ancestors were indeed drawn from other species, it is too late to change that. Other suggestions were implemented, however, and the paper has been improved and benefited. Plus, you suggested that we shorten the manuscript by five pages, and we were able to accomplish this very effectively by altering the margins and printing the paper in a different font with a smaller typeface. We agree with you that the paper is much better this way.

One perplexing problem was dealing with suggestions 13–28 by reviewer B. As you may recall (that is, if you even bother reading the reviews before sending your decision letter), that reviewer listed 16 works that he/she felt we should cite in this paper. These were on a variety of different topics, none of which had any relevance to our work that we could see. Indeed, one was an essay on the Spanish–American war from a high school literary magazine. The only common thread was that all 16 were by the same author, presumably someone whom reviewer B greatly admires and feels should be more widely cited. To handle this, we have modified the Introduction and added, after the review of the relevant literature, a subsection entitled “Review of Irrelevant Literature” that discusses these articles and also duly addresses some of the more asinine suggestions from other reviewers.

We hope you will be pleased with this revision and will finally recognize how urgently deserving of publication this work is. If not, then you are an unscrupulous, depraved monster with no shred of human decency. You ought to be in a cage. May whatever heritage you come from be the butt of the next round of ethnic jokes. If you do accept it, however, we wish to thank you for your patience and wisdom throughout this process, and to express our appreciation for your scholarly insights. To repay you, we would be happy to review some manuscripts for you; please send us the next manuscript that any of these reviewers submits to this journal.

Assuming you accept this paper, we would also like to add a footnote acknowledging your help with this manuscript and to point out that we liked the paper much better the way we originally submitted it, but you held the editorial shotgun to our heads and forced us to chop, reshuffle, hedge, expand, shorten, and in general convert a meaty paper into stir-fried vegetables. We could not – or would not – have done it without your input.

—

Journal of Systems and Software, Volume 54, Issue 1, 30 September 2000, Page 1

Nothing really has changed in a dozen years, it seems

Posted on August 8, 2013 at 16:09 Comments Off

Aug06

Flashback: What can the spine teach us about learning?

In: blogarchives • Tags: conditioning, operant, response, spine, spontaneity, wolpaw

Only very few laboratories in the world perform operant conditioning of spinal reflexes. In fact, a quick PubMed search reveals there is only a single lab which has published in this field in the last decade, the lab of Jonathan Wolpaw. Jonathan’s review “What Can the Spinal Cord Teach Us about Learning and Memory?” in The Neuroscientist shows what neuroscience is missing out on by not investing more in this fascinating field.Operant conditioning of spinal reflexes is probably the most controlled operant conditioning situation imaginable: reward the animal when it responds with a reflex magnitude above or below a certain threshold, respectively. This is done by triggering the reflex with a cuff electrode around the nerve and then measuring the amplitude of the reflex with electromyography (EMG):

The electrical stimulation via the cuff excites the muscle directly (the M signal in the EMG in the upper left corner) and, with a delay, indirectly via the H-reflex.

Below is an image of what that setup looks like when it’s implanted in a rat:

The rat is running around in its cage and receives a food reward whenever the H-reflex reaches the required amplitude.

Given that the textbook reflex (i.e., the spinal stretch reflex shown in the first image above) is monosynaptic, one would expect just this synapse to be modified after operant conditioning. However, this synaptic plasticity only contributes to one form of this learning, namely up-conditioning. Up-conditioning refers to the experiment where increased reflex amplitude was rewarded. In these experiments, the synaptic input from the primary 1a afferents (blue, in the first figure above) is increased, making the reflex amplitude larger. In down-conditioning, however, the synaptic input to the motor neuron is not altered, but the motor neuron itself (green) reveals an increased firing threshold and reduced postsynaptic potentials, making the motor neuron less likely to fire (and hence reflex amplitude smaller). In addition to these different forms of plasticity, correlates of the memory can be found throughout the spinal cord and even in the cortex. Some of these correlates appear to be compensatory modifications to other reflexes, preventing the increased amplitude of the conditioned reflex from making the animal limp. Again others are required for the maintenance of the memory, but do not seem to directly contribute to the memory trace itself. There are many more examples in the paper.

Taken together, the results presented in this review open up more questions than they answer and demonstrate that this is a promising research field, with still plenty of low-hanging fruit and a large variety of basic neuroscientific lessons which are hard, if not impossible to learn from other models.

What are you waiting for? Go and study operant conditioning of these reflexes already!

Wolpaw, J. (2010). What Can the Spinal Cord Teach Us about Learning and Memory? The Neuroscientist, 16 (5), 532-549 DOI: 10.1177/1073858410368314

Posted on August 6, 2013 at 18:01 Comments Off

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

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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

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Posted on August 5, 2013 at 09:17 Comments Off

Aug02

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

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

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

Posted on August 2, 2013 at 18:21 Comments Off

Aug01

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

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

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

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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