bjoern.brembs.blog

Aug26

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

In: blogarchives • Tags: Elsevier, open access, publishing, RWA, SOPA

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 January 10, 2012:

With roughly four billion US$ in profit every year, the corporate scholarly publishing industry is a lucrative business. One of the largest of these publishers is Anglo-Dutch Elsevier, part of Reed Elsevier. According to their website, their mission is to

publish trusted, leading-edge Scientific, Technical and Medical (STM) information – pushing the frontiers and fueling a continuous cycle of exploration, discovery and application.

However, Elsevier recently admitted to publishing a set of six fake journals, aimed to promote medical products and drugs by the company Merck, but with the appearance of peer-reviewed, scholarly literature. Clearly, trust is not Elsevier’s top priority.
What is Elsevier’s top priority, though, is making money. Like all scholarly publishers, Elsevier is thriving, despite global financial and economic crises in recent years:

How can a private company be so isolated from the general economy? The reason is that they’re largely funded by the tax payer and so far education and R&D budgets have been relatively spared. How do commercial publishers do their job? Here is a brief sketch of how a scholarly paper comes about:

Researchers generate data

Researchers write manuscript

Publisher’s editor sends manuscript to other researchers who peer-review the manuscript at no cost to the publisher

Researchers modify the manuscript

Researchers pay page charges

Publisher copy-edits manuscript and puts it online.

Library or researcher pays subscription fees to access article

Thus, according to their website, 7,000 paid journal editors are working for the approx. 2,000 journals of Elsevier, while 970,000 unpaid board members, reviewers and authors, largely funded by the tax payer, are donating their time, brains and other valuable resources to the corporation. With hardly any labor costs to speak of and great value provided from outside for free by tax-funded researchers, it is not surprising hat corporate publishers sport great profit margins:

Publisher	Revenue	Profit	Margin
Elsevier	£2b	£724m	36%
Springer’s Science + Business Media	€866m	€294m	33.9%
John Wiley & Sons	$253	$106	42%
Informa.plc	£145	£47	32.4%

On top of very small up front costs publishers increase subscription prices manifold beyond inflation:
Quite obviously, with low costs and an ever increasing stream of tax funds burning holes in your pocket, you wonder how all the money could be invested to protect your shareholder value for the future. Therefore, commercial publishers:

Buy access to elected representatives

Use this access to lobby for protective legislation

Pay full-time employees for government lobbying

Support SOPA

Discredit Open Access by hiring professional ‘pit-bull’ campaigners

Lobby against Open Access at the US White House

Comparing commercial with non-profit publishers shows how competition doesn’t bring the price down in scholarly communication: non-profit publishers are providing a publishing service that is consistently half or less of what commercial publishers provide (see also here). Therefore, I am very skeptical of suggestions to transform the scholarly communication ecosystem into a service business. Given that commercial publishers have a proven track record of untrustworthiness, price-gouging and political interference, what would keep them from increasing their prices for the services they provide, just as they have increased subscription prices?
No, the evidence is very clear, we need to rid the scholarly communication system from commercial publishers if we want to reduce or at least limit the burden on tax-payers:

Just eliminating profits will cut publishing costs by approx. US$4b annually

1.5 million papers will have to be published anyway, so no jobs will be lost, just transferred

per-publication costs will come down further as scholarly communication becomes completely online.

Any proponent of for-profit scholarly publishing first needs to explain why future commercial publishers’ behavior should dramatically change from current and past behavior, before any other arguments will even be considered.

Posted on August 26, 2013 at 16:30 Comments Off

Aug23

Scientists as social parasites?

In: blogarchives • Tags: career, contracts, unemployment

In a recent report on German public TV, a sad but tragically very commonplace procedure is being described as the latest, most extreme case of worker exploitation: scientists continuing to do science while being officially unemployed.

On the face of it, the report seems to be correct in claiming that people who are working despite being paid unemployment benefits are incriminating themselves – which is what people colloquially call social parasites. However, the idea of paying these benefits is to enable people to look for jobs, maybe even to go and learn a new, more promising trade. In short, to give the candidate the leeway to do everything possible to secure a new job as soon as possible. Now what is the best way to secure a job in science? To do more science, get more papers, get more teaching experience, etc.: whatever pads your CV is what will enhance your chances to get the next job in science.

Moreover, scientists are so highly specialized, unemployment agencies are not able to find adequate employment for them. This means that German unemployment offices who have experience with unemployed scientists are actually complicit: they will specifically allow you to keep working as a scientist while they pay you, because they know that this is the best thing in this situation. In fact, they realize that it would be counterproductive to force you to stop doing science. If you are a scientist in Germany and unemployed (pretty common species), go to your local unemployment agency and ask them if they’ll let you continue working and they’ll say yes, I promise. That’s how normal this situation has become, with 65% of all jobs in German science being on short-term contracts.

This doesn’t mean that it’s a good thing that the money for science in Germany comes partly from the social budget and not exclusively from the science and education budget. Far from it. It is despicable that in some departments, the majority of PhD students will write their dissertation on unemployment benefits. If it weren’t so sad, it would be laughable that so many of the ‘excellent elite’ PhD students who were able to secure a scholarship for their PhD, will not even get unemployment benefits, but have to finish their degrees on welfare. There’s nothing positive about scores of postdocs finishing their last experiments and writing their papers while simultaneously writing the grant for the next projects and being paid from the wrong government branch. But it is neither criminal nor some exploitation perpetrated by unscrupulous professors in some isolated departments at German universities. It’s just the deplorable standard situation in a totally messed up scientific career system and it’s not even the worst part, not by a long shot.

And here is another reason why this practice will be difficult to change: the German taxpayer saves a lot of money. Think of this one scientist in the report who worked on short-term contracts for 17 years. For four years he was on benefits, which in Germany is 60% of your last salary. This means that in this time, the German taxpayer, who would have been paying him a full salary, only paid 60% for the same service and part of that is even paid for by the scientist himself in the form of his unemployment insurance. That’s some major savings right there.

What would the rational reaction of German politicians be to this report? Certainly not to try and prevent this gigantic money saver! More likely, one would expect them to demand to cut the salaries of scientists by 40% because 60% seems to be sufficient to keep them going.

Posted on August 23, 2013 at 16:25 1 Comment

Aug21

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

In: blogarchives • Tags: evolution, free will, spontaneity

I have no idea when it started, but probably long before Darwin, the notion of ‘design’ kept creeping into descriptions of biological organisms or traits: Birds are designed to fly or the eye is designed to see. I’ve also been guilty of using the word ‘design’ for biological objects every now and then. However, after reading a fair bit and after thinking for some time now, I’ve come to the conclusion that the word ‘design’ is so misleading and not even wrong, that it should never be used in biology at all, ever.

I’m only partially saying this because of a prominent creationist movement in the US awfully dubbed ‘intelligent design’ (which couldn’t be further from biological reality). My main reason is that the use of ‘design’ is pernicious for biological research. ‘Design’ or engineering approaches have been used over and over in biology and many if not most of them have gone the way of Newtonian mechanics: extremely useful and successful initially (and to some extent still today), but scientifically falsified eventually. Take a rather recent, prominent example: Lee Hood‘s automobile paradigm, according to which systems biology is akin to finding car parts without a manual in the fog and then trying to assemble the car. Current research shows that genetic networks are, in contrast to car components, highly plastic and forgiving of errors (a phenomenon termed robustness, often due to degeneracy in evolved systems). Even though the car analogy might seem daunting, it is still grossly oversimplified and biologically misleading. Indeed, expecting genetic networks to behave as stably as car components will lead to the wrong experiments and the wrong conclusions. Nevertheless, systems biology was and still is a very successful branch of biology. I’m not a systems biologist, but I would be surprised if many systems biologists still bought into the car analogy these days any more, after what they have found out until today.

For the same reasons, there is no blind watchmaker, because there is no watch. The analogy may still be useful in a rule-of-thumb kind of way, but biologically it is completely false.

Another, much older engineering approach is that of brains as input-output systems in neuroscience (the ‘sensorimotor hypothesis’), which purports that brains passively wait for stimuli to occur in order to respond to them, much like radios, computers or other equipment that we have designed. In some fields of neuroscience (and psychology) this approach has been so pervasive that any behavior is referred to as a response, assuming that there always must be an underlying stimulus triggering the behavior. It is not only recent ecological and ethological research on predators specializing in exploiting stereotypic behaviors in prey species which shows that being responsive is not an evolutionary stable strategy: responding reliably to the same stimuli in the same predictable way will neither get you to the unexpected food patch nor prevent a predator or competitor from predicting your next move. “Nature red in tooth and claw” will make sure that any predictable species will not last for long. There is a very good ultimate cause for the Harvard Law of Animal Behavior: “Under carefully controlled experimental circumstances, an animal will behave as it damned well pleases”: species which didn’t obey the law have not survived. It thus appears that for the last 100 odd years, neuroscience has been studying the exceptions to the rule that brains are always active and are constantly producing output, on which sensory stimuli merely exert a modest, modulatory role. I think it is fair to assume that one reason for this research direction (apart from the relative experimental ease) is that there is no mechanism or object we have designed that works in such a way. Everything we have made responds to commands and so people thought this is how brains operate.

Given the success of this approach in biology and of Newtonian mechanics in physics, it is no surprise that some thinkers have come to see brains as deterministic Newtonian clockworks. Complicated, maybe, but deterministic and predictable none the less. Any observed behavioral variability was shrugged off as random noise, when indeed it was the one brain function that kept animals in the run for the next generation. It is high time that neuroscientists realize that Newtonian mechanics are as falsified in biology as they are in physics: the world is not deterministic and neither are brains. The fact that brains are not engineered, but evolved allows for freedom of choice without quasi-magical quantum computing in the brain. All the brain requires to be unpredictable is some source of variability from which it can generate spontaneity, and there is plenty of such variability in neurons and their components, with or without quantum effects. The selection pressure of predictable animals being outcompeted, eaten or left without a mate established early on that every brain is equipped with a function which allows for adaptive behavioral choice. In some animals, there was need for more of such capabilities. Those animals seem to have more freedom of choice. Other animals could get away with being more predictable, giving the impression of being less ‘free’ and more robot-like. I’m starting to get the impression that the model systems used in neuroscience are predominantly of the latter sort.

Be that as it may, all animals possess this trait to a larger or lesser degree and have been using it for survival and procreation since the very first brain evolved. I think it is time biology sheds the last remnants of classical thinking and starts to study ‘free will’ as the biological trait it is: the ability to behave differently in the same situations, the ability to chose from identical options, the mental coin toss. The centuries of philosophical thinking on this topic have provided us with a wonderful framework within which these empiricial findings can be embedded. Because brains are output-input systems (rather than the other way around), our lab has started to study the spontaneous choices of the fruit fly Drosophila and how the brain generates them. Currently, a graduate student in our lab is studying where in the brain these processes take place in order to later be able to understand how the circuits mediating these choice function. It is a testament to the idiocy of creationists that our research was featured on a creationist blog as supporting creationism. The opposite is the case: all brains possess free will precisely because there is no design in biology. Evolution is the only reason why we have free will and it is neither dualistic, nor spiritual, nor mystic: it is biological.

Posted on August 21, 2013 at 16:58 Comments Off

Aug20

Flashback: Noise in the brain?

In: blogarchives • Tags: free will, noise, spontaneity, variability

I was recently alerted to a group of theoretical publications which deal with the issue of apparent ‘noise’ in neuronal populations. The Nature Reviews Neuroscience article “Neural correlations, population coding and computation” by Bruno B. Averbeck, Peter E. Latham & Alexandre Pouget covers this area quite well.
Basically, the authors claim that the variability one can see when recording from the brain when the same stimulus is presented repeatedly is noise and must be detrimental for the tranmission of information and hence a problem the brain must solve:

Part of the difficulty in understanding population coding is that neurons are noisy: the same pattern of activity never occurs twice, even when the same stimulus is presented. Because of this noise, population coding is necessarily probabilistic. If one is given a single noisy population response, it is impossible to know exactly what stimulus occurred. Instead, the brain must compute some estimate of the stimulus (its best guess, for example), or perhaps a probability distribution over stimuli.

It needs to be noted that the authors do not refer to sensory neurons, which code sensory information with great precision. Instead, they look at neurons deep in the mammalian brain, many synapses away from the primary sensory afferents. What I don’t understand from their article is why this should be considered ‘noise’. Obviously, if high fidelity between the site of sensory input and the site of recording were required, there would be a single axon going there, and not via many syapses. Synapses are time consuming and energetically expensive. During development, unused synapses are being pruned throughout the brain. Thus, the variability must reflect some computation which takes place in the synapses from the site of sensory input to the site of recording. Let me illustrate this with a picture:

Of course, if one records from neuron N_R and stimulates sensory neuron N_S, as in A, there is a lot of processing going on in the synapses along N_1-4. This is happening even without any external input into the single conveyor belt of information. Of course, there never is such a conveyor belt, that idea is already misleading. After the very first synapse (from wherever you start), there are always inputs from other sites, feed-forward and feedback connections, etc. But even in this simplest model of information transmission, every synapse is a computational component and not just a link between neurons adding variability to the sensory signal for no reason. These synapses would not be there if this processing was not some important brain function. This is illustrated in B: if simple and reliable information transmission from N_S to N_R were important, there would only be one single axon from N_S to N_R, without any additional processing.

I would really like to hear good arguments as to why the recorded variability should be ‘noise’ and a problem for information coding, rather than a reflection of the brain doing what it’s supposed to do: finding out what the best action is under the current circumstances.

Averbeck, B., Latham, P., & Pouget, A. (2006). Neural correlations, population coding and computation Nature Reviews Neuroscience, 7 (5), 358-366 DOI: 10.1038/nrn1888

Posted on August 20, 2013 at 16:55 Comments Off

Aug19

Science, red in tooth and claw

In: blogarchives • Tags: open access, sabotage, stress, tenure

I’ve been contemplating the current competitive state of science here before. The gist of it was that science may be suffering from too much competition, leading to an increasing incidence of misconduct, such as falsifying or omitting inconvenient data. In this week’s Nature appeared a news-report which tells me that apparently the pressure cooker which is our scientific community apparently has been set to a notch hotter recently.

The article is about the sentencing of a postdoc who has been sabotaging the work of a graduate student in his own lab for several months. The postdoc has admitted – after being caught on secret camera – to have poured ethanol in the culture medium for the cell culture of the graduate student as well as contaminating Western blots of the student.

In my previous posts I speculated that fraud and other, related misconduct may be on the rise as more and more trained scientists are faced with less and less positions for which they compete. I did not expect this form of misconduct and neither did anybody else: sabotage is not officially part of the canon of research misconduct and thus no federal agency was able to prosecute the perpetrator.

As all of the cases which make it into the media, this is another anecdote and the plural of anecdote is not data. Nobody knows if the frequency of misconduct is rising or if the publicized cases simply come with the growth of the business. Nevertheless, this form of direct sabotage of researchers by researchers seems to be a novel quality of competition-induced research misconduct.

What will we see next?

Hot on the heels of the stunning sabotage case comes a seemingly unrelated report in The Scientist that US libraries are forced to cut scientific journal subscriptions by the thousands due to budget cuts:

New Mexico State University (NMSU) library announced the cancellation of over 700 journal and database subscriptions, the result of a perfect storm of rising journal prices and a slashed materials budget. […] A 2009 global survey of 835 libraries in 61 countries found that nearly one-third of academic libraries saw their budgets reduced by 10 percent or more that year. And journal subscriptions are taking the brunt of that loss: The University of California at San Francisco (UCSF) cancelled 118 print and 115 online subscriptions for 2010, as well as several databases (including Faculty of 1000 Medicine, publisher of The Scientist). Last spring, the University of Washington announced cuts of 1,600 print and electronic journals, databases, and microforms. The University of Virginia library sliced 1,169 journals, the University of Arizona downsized by 650 print and electronic titles, and Georgia State University cut 441 and is now considering the fate of another 1,092. The list goes on and on.

While on the surface these two reports seem unrelated, they in fact demonstrate the coming scientific system: too many highly trained scientists competing for a position in a system that is so cash-strapped that even access to the literature is threatened. Access to the literature is the most basic prerequisite for doing science. One of the quotes in the article demonstrates that: “I need the EBSCO databases like I need air or water!”

Just as now access to drinking water is a human right, access to the literature should be a scientific right.

German psychologist Bally in the 1940s and later ethologist Hasenstein in the 1970s coined the term “eased-up field” (entspanntes Feld) for a situation where all the basic needs are satisfied. They found that exploratory or playful behavior decreased in virtually all subjects tested, be it human or animal, whenever the animals were not in an eased-up field. Currently, science almost on a world-wide scale is heading towards a situation in which each scientist’s livelihood is threatened as well as one of the basic prerequisites for doing science, access to the literature. Neither of these trends alone bodes well for the quality of future science, but both trends together serve to basically block the emergence of the creative genius required for major scientific breakthroughs.

Posted on August 19, 2013 at 21:21 1 Comment

Aug18

Flashback: Nothing new in science?

In: blogarchives • Tags: behavior, decision-making, Drosophila, neurogenetics, phototaxis

In this week’s journal club, we talked about an old paper from 1918! “The reactions to light and to gravity in Drosophila and its mutants” by Robert McEwen, in the Journal of Experimental Zoology.

As the title says, the author studied how the fruit fly Drosophila responds to light and gravity. He tested this in walking flies and compared flies both with intact wings and clipped wings, wing mutations, clipped antennae, glued wings or clipped middle legs. He discovered that flies without wings or with mutated wing shape, show less movement towards light (i.e., less phototaxis). This finding was later confirmed by one of the founders of modern neurogenetics, Seymour Benzer (1967) and we also find this in our experiments. We have now set out to find out which neuronal mechanisms are involved in this drastic change in behavior.

In order to get the flies to show phototaxis, McEwen developed a machine to gently tap the tube in which the flies were placed, to get them to walk. He described the necessity for flies to be active in order to show a consistent orientation towards a light source: without walking behavior being either initiated spontaneously or by the tapping machine, flies would not walk towards the light themselves. If the flies were at rest, light was not an orienting stimulus for them. This key insight was formulated by McEwen at the very end of the paper:

Lastly, it may be well to emphasize the peculiar relation which exists in Drosophila between general activity and phototropism. This phenomenon has been clearly recognized by Carpenter and in general I agree with this author’s conclusions. The fact seems to be that this insect is not phototropic unless it is in a certain physiological state brought on by, or at least accompanied by, activity. When the fly reaches a certain degree of activity, induced by various means, it suddenly becomes phototropic. When it quiets down, however, it may still crawl about but ceases to be phototropic. Thus, when an insect has been exposed to constant illumination for some time, it no longer orients to light but wanders aimlessly up and down the tube. Eventually such an animal may even come to rest with its head away from the source of light.

The technique described mimics what other colleagues have later developed in other fly paradigms based on vision and walking, such as the “fly-stampede” paradigm. But the insight reaches much further than that. More recent research has shown that the state of the animal has minute control over how the environment is processed. For instance, leeches respond with various behaviors to local mechanosensory stimulation (i.e., touch). However, when they feed, the biogenic amine serotonin is released and prevents the mechanosensory neurons from transmitting the stimuli – the animal becomes unresponsive when it feeds (Gaudry & Kristan, 2009). Another study showed that motion-sensitive neurons in the optic lobes of the fly brain increase their gain when the fly is flying, as opposed to when it is not flying (Maimon et al., 2010). Analogous results were obtained when walking vs. sitting flies were compared (Chiappe et al. 2010). In another, also very sophisticated study, Haag et al. (2010) showed how an identified motor neuron responds more strongly to visual input when the animal is flying than when it is at rest. Finally, Tang and Juusola (2010) report evidence that the direction in which a fly attempts to turn changes the way in which the optic lobes process the visual information on the side towards the fly attempts to turn, compared to the contralateral side.

All these groups have, largely independently of each other, discovered the biological mechanisms for something that already McEwen (and Carpenter, cited there) had understood: animals don’t just respond to stimuli in always the same, stereotypical way: all animals have many different ways to treat and evaluate the incoming sensory stream, depending on what they are doing at the moment. The decisive factor for understanding animal behavior is not the environment, or the sensory organs, it is the animal itself. Apparently, this profound insight was known long ago and we’re just rediscovering it now, in various places, all over the world.

Something was new in all the recent studies, though: they all provide first mechanistic insight into how brains balance internal and external processing. All these studies show that there seems to be a smooth gradient between decision-making and attention-like processing, even in invertebrates: Gaudry and Kristan call it decision-making, when their leeches ‘decide’ to ignore stimuli while they feed, even though the incoming sensory stimuli are blocked already at the very first synapse. Chiappe et al., on the other hand, relate their phenomenon to attention and Haag et al. also mention attention in their paper, with their effects being observed many synapses downstream of the sensory neurons – the word ‘decision’ does not occur in either of the two papers. It appears as if future neurophysiological research is bound to show that the distinction between attention-like mechanisms and decision-making, which seems so intuitive and clear-cut, may dissolve when we start to unravel how brains actually do it. Now when will we come accross the ancient text that already pre-empts that insight?

References:

McEwen, R. (1918). The reactions to light and to gravity in Drosophila and its mutants Journal of Experimental Zoology, 25 (1), 49-106 DOI: 10.1002/jez.1400250103
Zhu, Y., & Frye, M. (2009). Neurogenetics and the “fly-stampede”: dissecting neural circuits involved in visual behaviors Fly, 3 (3), 209-211 DOI: 10.4161/fly.3.3.9139
Gaudry, Q., & Kristan, W. (2009). Behavioral choice by presynaptic inhibition of tactile sensory terminals Nature Neuroscience, 12 (11), 1450-1457 DOI: 10.1038/nn.2400
Maimon, G., Straw, A., & Dickinson, M. (2010). Active flight increases the gain of visual motion processing in Drosophila Nature Neuroscience, 13 (3), 393-399 DOI: 10.1038/nn.2492
Chiappe, M., Seelig, J., Reiser, M., & Jayaraman, V. (2010). Walking Modulates Speed Sensitivity in Drosophila Motion Vision Current Biology, 20 (16), 1470-1475 DOI: 10.1016/j.cub.2010.06.072
Haag, J., Wertz, A., & Borst, A. (2010). Central gating of fly optomotor response Proceedings of the National Academy of Sciences, 107 (46), 20104-20109 DOI: 10.1073/pnas.1009381107
Tang, S., & Juusola, M. (2010). Intrinsic Activity in the Fly Brain Gates Visual Information during Behavioral Choices PLoS ONE, 5 (12) DOI: 10.1371/journal.pone.0014455

Posted on August 18, 2013 at 10:28 1 Comment

Aug16

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

In: blogarchives • Tags: dunning-kruger, incompetence, publishing

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?

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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
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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