Science is a lot like sex.
Sometimes something useful comes of it, but that's not the reason we're doing it.
--Richard Feynman-

Welcome to the weblog of Björn Brembs, the owner of brembs.net. I'm a biologist with a wide variety of other scientific and non-scientific interests. Feel free to have a look around and let me know what you think.

Spot the difference news | email to someone | printer friendly
Now what could be the difference between these two photographs:
pz.jpg greg.jpg
Both depict the wafer pierced by PZ Myers' rusty nail. The left image is the one posted on Pharyngula, the right one is posted on Greg Laden's blog. Solution under the fold...



[ Continue reading ... ]

Friday 25 July 2008 - 08:04:01 ----- comments: 0

fun   religion   



Islamist and christian creationism alliance: DI terrorism? news | email to someone | printer friendly
I initially read this about 10 days ago on one of the conservative blogs I read along with the progressive ones: littlegreenfootballs. LGF being what it is, I noted it and waited to hear more about it from other sources. In his post, Charles had quoted from Reuters:
Edis doubted the rumors of funds from U.S. creationists, saying: “American creationists I talk to basically envy Harun Yahya’s financial resources. If there were any fund flowing, it would be from Adnan Oktar to the creationists.â€
The real name of Yahya is Adnan Oktar. Some of this piece of news later got picked up by Panda's Thumb.
Charles kept researching and in a later post provided an audio clip from the CBC, in which David Berlinski from the Discovery Institute explicitly states that the DI is working closely together with their islamic counterparts.
Two days ago, Charles reported on Imam Siraj Wahhaj, named as an unindicted co-conspirator in the 1993 World Trade Center bombing, is planning a barrage of subway train advertisements in Manhattan—during September—proselytizing for Islam: Muslim Subway Ads Linked to Terror Plots. Yesterday, Charles pointed out that the website of this radical islamist group prominently displays this large picture:

Now guess what it says on the website where you land when you click on that banner? "This site is based on the works of Harun Yahya". Could it be that the apparently insanely wealthy Oktar is funding both radical islamists and the Discovery Institute at the same time?

And I decided to write a post about this connection between islamic terrorism and the DI when I saw a similar post on Pharyngula this morning, but I must have been dreaming, because such a post does not exist there (anymore?). Anyway, now you have all the info I have.

P.S.: It is of course well-known that the so-called "intelligent design" moniker is just a DI-invented disguise for religious (christian) creationism:




Wednesday 23 July 2008 - 10:56:29 ----- comments: 0


Why Thomson's Bibliographic Impact Factor (BIF) is dead science politics | email to someone | printer friendly
Despite the recent downpour of evidence against the use of Thomson's BIF, I still get comments from people such as "However, IFs are still the most used way of evaluating a researcher's career and value. Even if we find this ridiculous, it's just the way it is." or "in our institution, every researcher has to publish in journals whose BIF is at least 5.". In the light of the current state of affairs concerning the BIF, this is just embarrassing. So here are the top three reasons why the BIF is dead:
  1. The BIF is negotiable and doesn't reflect actual citation counts (source)
  2. The BIF cannot be reproduced, even if it reflected actual citations (source)
  3. The BIF is not statistically sound, even if it were reproducible and reflected actual citations (source)
No go and spread the information so I don't have to suffer from these ridiculous statements any more. grin.png
And of course, there is some other, more transparent and accurate journal ranking tool available (ScImago) for those inclined to such siliness, but as journals will also become obsolete in the foreseeable future, scientific reputation building will happen rather differently than today.


Wednesday 23 July 2008 - 09:08:54 ----- comments: 0


Building a scientific online reputation science politics | email to someone | printer friendly
The other day, I was hypothesizing how one could provide incentives for scientists to comment on papers and blogs and to blog themselves. My solution was that there needed to exist a service which would allow researchers to somehow build a reputation by aggregating their papers, comments, blog posts, etc. As I learned from Michael Nielsen on FriendFeed today, there is already a lot of experience about how to set up Reputation Systems! Joshua Porter has two great articles on bokardo.com on "Social Design Patterns for Reputation Systems". When I read the introductory remarks, it occurred to me that of course this sort of system already exists in a lot of places and that a whole bunch of very clever people must've already spent long hours thinking about similar problems for their communities:
Of all the social software built on the web in the last two decades, none are as important yet as little talked about as reputation systems. Reputation systems have driven the entire business at eBay.com, much of the business at Amazon.com, drives activity at Digg.com, powers the moderation system at Slashdot, etc…and yet for all the millions of words written about web design very few of them have been dedicated to this type of software.
The articles link to Yahoo’s social design patterns for reputation systems, but the main content is an interview with Bryce Glass, an interaction designer at Yahoo! Glass explains the ideas and concepts behind Reputation Systems and the different way of implementing the right pattern for your community.
The content of the interview is especially pertinent with regard to a recent analysis by Euan at Nature's Nascent which showed that only 2% of BioMedCentral papers attract comments.

For me, this basically means that all the expertise and technical prerequisites are there to bring the scientific community into the 21st century. The advantages of the new system need to be succinctly summarized and widely publicized at the same time as the current system's disadvantages and idiosyncracies need to be pointed out and publicized along with the new proposal. And because criticizing is always easier than advertising, I'll start by summarizing why Thomson's Bibliographic Impact Factor (BIF) is dead.
devilmad.png
UPDATE: Actually, already last month, Maxine Clarke over at Nature Networks posted a question where these two articles provide all the answers: Better metrics for an individual's "value"

Wednesday 23 July 2008 - 07:46:09 ----- comments: 0


Post-publication paper assessment science politics | email to someone | printer friendly
There has been an interesting discussion going on at the message board for editors of PLoS One. I've posted a comment to this discussion I thought may be interesting to others as well. Here it is (slightly edited):

I may be thinking a little too far ahead here, but so is the entire PLoS One endeavor. I see at least two major reasons why any sort of journal impact is meaningless:
  1. It's absolutely irrational to assume that where something is published can say anything valid about the quality of a particular papers content.
  2. As most journals, in the long run, are most likely going to die out in their present form anyway, why bother comparing One to others (other than maybe during a transitional period)?
IMHO, individual paper assessment is the obvious way to steam ahead. No publication is providing a comprehensive paper assessment. Some are showing citations, others list their most accessed papers, but none of them exhaust the full technial potential. (un)Fortunately, there is no substitute for reading a paper, when you want to find out how good it is. "Quality" means something different for everybody. Hell, it means something different for me, depending on what kind of paper it is! The only thing quantitative measures can grasp is something along the ways of popularity, attention and fashion. This is not necessarily diminutive, as an attention grabbing paper mostly means something in science, not necessarily good, but very often. Therefore, I think every single one of the values Peter Binfield mentioned for inclusion in PLoS One papers are important:

  • Number of citations
    AFAIK, only the citations intrinsic to the PLoS system can be counted unambiguously. Ideally, PLoS could use this as an opportunity for developing an open citation standard, such that authors can collect a standard set of citations from multiple sources using a common protocol. This would be transparent and public pressure would force others (Google, Scopus, etc.) to adopt the standard, making it as transparent and complete as possible. One may then develop an interface to attach all of this to the paper itself, if one so wishes.
  • Number of downloads / views
    Access from the PLoS system can only give the lower bounds of access statistics, but cooperating sites could agree to add their request data to a common database (a solvable technical problem). Of course download doesn't mean read, but neither does citation. Nobody can get access to 'read' data anyway, so why bother? Gaming this system can be reduced by standard IP or cookie-based flood controls.
  • Amount of 'Relevant' Blog Coverage
    If people like/dislike the paper enough to leave a trackback, count the coverage. Just like 'quality', 'relevance' cannot be assessed unambiguously anyway.
  • Amount of News Coverage
    In each press release, encourage media to leave a (maybe separate from blogs) trackback, by visiting a link which is only acessible for accredited news media. This counter should include the press release itself, to how many outlets it went and how many agencies have picked it up (as far as technically feasible). That way, the press release is attached to the paper itself as well as at least some of the media coverage for at least some period of time (for those who want to check for the 'relevance' of the coverage).
  • Number of Times Bookmarked in Social Bookmarking Sites (analogous to citations)
    Great idea! Given the way these sites work, it shouldn't be to difficult to crawl them to get fairly accurate numbers. I don't think it will be very easy to game that system, unless you know a few hundred people who are willing to help you or have a few hundred email addresses to sign yourself up for.

The more variables there are to game, the more difficult it becomes. Now we have one variable (IF) and we all know who is gaming it ad nauseum. In this thread we have 5 measures, add ratings and comments and you have 7. This should be impossible to game for anyone but the hacker who can get thousands to machines on the net to just hype this one paper smile.png

All of these measures are relevant even long after publication. Some papers ignored by the media may later turn out to harbor the most important discovery of the century, while some of those tossed around everywhere turn out to be completely irreproducible. Having these measures in place, if nothing else, would allow us to quantify and study such events.

But again, no matter how many numbers you have, these measures cannot substitute for actually reading the papers! The numbers barely give you a rough idea of where a paper or a scientist can be placed with respect to others in the same field. Yet, these measures would be light-years ahead of any one-dimensional, irreproducible, obviously manipulated and corrupt measure such as the IF.

Monday 21 July 2008 - 11:55:28 ----- comments: 0


Journals - the dinosaurs of scientific communication science politics | email to someone | printer friendly
The recent kerfuffle caused by Butler's article in Nature seems to have gotten quite a number of stones rolling. What I thought would be a rather slow process seems to be speeding up considerably because of Nature's rather unclever attack on PLoS. Cameron Neylon's blog post "What I missed on my holiday or why I like refereeing for PLoS One" points out what the real danger of PLoS One is for basically all traditional journals:
From an author’s perspective PLoS ONE cuts out the crap in getting papers published. The traditional approach (send to Nature/Science/Cell, get rejected, send to Nature/Science/Cell baby journal, get rejected, send to top tier specific journal, get rejected, end up eventually going to a journal that no-one subscribes to) takes time and effort and by the time you win someone else has usually published it anyway. It also costs the authors money in staff time to re-format, rejig, appease referees, re-jig again to appease a different set of referees. I haven’t done the sums but worst case scenario this could probably cost as much as a PLoS ONE publication charge.  Save time, save money, still get indexed in PubMed. It starts to sound good, especially for all that material that you are not quite sure where to pitch.
[...]
To me the truly radical thing about PLoS ONE is that is has redefined the nature of peer review and that people have bought into this model. The idea of dropping any assessment of ‘importance’ as a criterion for publication had very serious and very real risks for PLoS. It was entirely possible that the costs wouldn’t be usefully reduced. It was more than possible that authors simply wouldn’t submit to such a journal. PLoS ONE has successfully used a difference in its peer review process as the core of its appeal to its customers. The top tier journals have effectively done this for years at one end of the market. The success of PLoS ONE shows that it can be done in other market segments. What is more it suggests it can be done across  existing market segments. That radical shift in the way scientific publishing works that we keep talking about? It’s starting to happen.
Today's system of scientific journals started as a way to effectively use a scarce resource, printed paper. Soon thereafter, the publishers realized there were big bucks to be made and increased the number of journals to today's approx. 24,000. Today, there is no technical reason any more why you couldn't have all the 2.5 million papers science puts out every year in a single database. It doesn't take an Einstein to realize that PLoS One is currently the only contender in the race for who will provide this database. For all the involved, it is equally clear what the many advantages of such a database would be. Consequently, traditional publishers are rightfully concerned that their customerbase is slowly dissappearing.
I'm now not alone anymore in believeing that we are seeing the beginning of the end of traditional journals. The acceptance of PLoS One is a quantitative marker of this development and the positive reactions I get from virtually everyone involved (even scientific editors at traditional journals) underscores the numbers.
Precurser to this publishing reform was access reform: scientific papers are the result of publicly funded research and should be publicly accessible. This reform appears now to be well underway and will probably conclude in 2-3 years. Both reform movements have their base in the more general open science movement. The goal of this reform movement is to have full public access not only to the published papers, but also to the raw data, ideas and reagents for sharing among scientists. There are still plenty of problems which have to be worked out before open science can become a reality, if it is even feasible. One of the more easy to solve problems (one that is shared with publishing reform) is that of how to attribute credit. If we all publish in the same database and share ideas online, how can two scientists competing for the same position or grant be assessed objectively? Cameron Neylon just returned from a conference on open science and writes in his summary:
I am sceptical about the value of ‘microcredit’ systems where a person’s diverse and perhaps diffuse contributions are aggregated together to come up with some sort of ‘contribution’ value, a number by which job candidates can be compared. Philosophically I think it’s a great idea, but in practice I can see this turning into multiple different calculations, each of which can be gamed. We already have citation counts, H-factors, publication number, integrated impact factor as ways of measuring and comparing one type of output. What will happen when there are ten or 50 different types of output being aggregated? Especially as no-one will agree on how to weight them. What I do believe is that those of us who mentor staff, or who make hiring decisions should encourage people to describe these contributions, to include them in their CVs. If we value them, then they will value them. We don’t need to compare the number of my blog posts to someone else’s – but we can ask which is the most influential – we can compare, if subjectively, the importance of a set of papers to a set of blog posts. But the bottom line is that we should actively value these contributions – let’s start asking the questions ‘Why don’t you write online? Why don’t you make your data available? Where are your protocols described? Where is your software, your workflows?’
I would disagree here and argue that a multivariate portfolio is exactly what is required. Different universities/employers will focus on different aspects of a researcher and value some of his/her contributions more than others. I don't think there can be too many measures to capture the complexity of scientific output. I'd like to see an aggregating service, maybe based on services like  OpenID, where a flexible portfolio can be organized such that employers can easily search for the traits they are looking for and find or compare the people who maximize their efforts on these traits.
The analogous problem to comparing researchers is that of comparing papers. I have already written about this problem and I think it is easy to solve. I think most researchers would gladly pay for a service which has a track record of picking the most interesting, groundbreaking and well-done papers from the 2.5 million every year. Today's professional editors would be a great pool from which such services could recruit employees.
blush.png Like dino-oil, there's still some use in long-dead structures. grin.png

Saturday 19 July 2008 - 13:13:40 ----- comments: 7


Incentivizing open scientific discussion science politics | email to someone | printer friendly
Coturnix' "obligatory reading of the day" brought me to this interesting essay on open science. I think it catches most of the most important idiosyncracies of the modern science business and offers some very promising avenues for change.
However, I think it treats one crucial, important point only in passing: there currently are too many incentives not to share ideas and critical comments with the rest of the scientific community. There is the very real risk of being scooped, of critical comments coming back to haunt you at your next peer-reviewed submission or of an important person in a search committee branding you as 'trouble maker' because you criticized his paper on your blog. On top of that, there's absolutely zero credit to be had for any such activities. On the contrary, writing a blog such as this one can be seen as time wasted better spent writing papers or doing experiments.
Apart from the question of whether the perfect scientist is the one who only spends his time writing papers and doing experiments, what incentives can one think of to provide for blogging, commenting, sharing? I think because all of science relies on creativity, information and debate, the overall value of blogging, commenting and sharing can hardly be overestimated, so what incentives can there be for the individual scientist?
To be honest, I don't have many ideas. I don't even have two. I have one: these sorts of activities need to be aggregated somewhere where it can be used to show to others as a sign of quality, creativity, ingenuity, whatever. A place that can be used to build a reputation, where people can compete for having the most creative thoughts and sharpest minds. How to technically implement this, I have some ideas, but I consider none of them to be in a state worth considering, yet.
That's pretty pathetic! What else is there?

Friday 18 July 2008 - 11:55:49 ----- comments: 3


Back in Berlin news | email to someone | printer friendly
Things have been (and still are) quite hectic after our symposium at the FENS meeting in Geneva, so I couldn't post any more news from the meeting as I had originally planned. The symposium went really well, the auditorium was packed and people seemed to mostly stay throughout the session. My talk also went well, without any major mistakes on my part, I think. So the whole thing was a big success, all in all, especially because the plenary speaker after our session, Barry Everitt was heaviy referring to our symposium during his talk, amplifiying the exposure we got.
Now I not only have to catch up with everything that has happened since last Saturday, but I also have a new student here for the next six weeks who needs to be supervised. It will probably take until next week before I have the time for another post.

Thursday 17 July 2008 - 11:59:34 ----- comments: 0

FENS   symposium   meeting   decision-making   choice   Geneva   talk   



Impending talk and chair news | email to someone | printer friendly
In about two hours our symposium on the neurobiology of choice and decision-making will start. I have uploaded my talk and taken a look at the room where the session will take place. The room has about 400 seats, let's see how many of them we can fill:
symp_room.jpg
I'm not really sure as to what I'll be saying to open the session. Maybe something along the lines that we have found seemingly similar principles of decision-making in vastly different model organisms and now are struggling to find a common nomenclature. We'll see...
I'll keep you posted on the event later today...

Monday 14 July 2008 - 06:10:55 ----- comments: 1


First full day at FENS science | email to someone | printer friendly
Today has been a good day. It got off to a late start as the first plenary lecture had to be cancelled (I heard Barry Dickson is in the hospital, I hope you are OK Barry!) and on top of that I had forgotten to switch my phone (my alarm clock) back from quiet so I overslept
I looked at some nice Aplysia buccal ganglion posters. One was from Romuald Nargeot from Bordeaux, France. He showed how a behavior-initiating neuron becomes stereotyped with operant learning. Before training, this neuron kicks off feeding behaviors in a highly irregular manner. Training then changes the biophysical properties of that neuron such that it starts to generate rythmic, stereotypical activity. This is really very neat because it dovetails nicely with our results that this kind of operant learning is akin to habit formation and compulsive behavior. Another Aplysia poster was from the lab of a really all around great guy, Mark Miller. One of the posters was about how neurons controlling the same component of feeding behavior appear to be electrically coupled. The hotly debated concept of the 'modular' organization of brains immediately comes to mind when one thinks of neurons who control the same thing coupling together. I honestly have no idea what the recruitment strategy of Mark is, but from my perspective he is at least doing one thing right. He always manages to have the most beautiful female graduate students at the posters (or are all girls in Puerto Rico so beautiful?)...
In the afternoon we attended a very stimulating symposium organized by David Glanzman promoting zebrafish as a model for behavioral neuroscience. I can only support that model as I have been working with these great little fishes for a short while as an undergraduate student. I could also imagine myself starting tot work on zebrafish if I had the opportunity to test out some ideas I have about operantly ocnditioning them.
Finally, I had a look at another great poster from Bordeaux in France. This one was in rats and compared drug-induced and food-induced memory processes. Unfortunately, there was nobody at the poster when I was there, but what I understood was that drugs of abuse somehow bypass hippocampal learning processes and instead directly kick off modifications in the striatum (a structure which has long been implied in habit formation). This fits very nicely with our hypothesis that fact-learning (or environmental or classical learning) inhibits operant habit learning, which leads to a shallower learning curve for habit formation. We can remove the environmental cues and get fast habit formation in flies. This poster seems to suggest that in rats, drugs of abuse get rid of a similar inhibition by bypassing the structures which inhibit habit formation when food rewards are used.
So this definitely was a good day so far. Let's see how the buffet dinner will be tonight and what tomorrow will bring. Tomorrow is already bound to be an exciting day because of our symposium

Sunday 13 July 2008 - 12:20:43 ----- comments: 0

FENS   meeting   Geneva   Aplysia   drugs   Glanzman   Miller   Nargeot   



Arrived in Geneva news | email to someone | printer friendly
I've arrived at the conference center "Palexpo" in Geneva. Everything seems to work fine, internet-wise, so I might be able to do some live blogging from the 2008 FENS Forum. The event started out really well with wine and tasty Swiss food at the reception. I've already met my (hopefully) future Post-Doc Julien and since he's Swiss I hope he will be my guide tonight, because now it's about time to go out and hit town...

Saturday 12 July 2008 - 13:55:25 ----- comments: 0

FENS   meeting   Geneva   



FENS talk slides uploaded science | email to someone | printer friendly
As promised, I have uploaded the slides for my upcoming talk at the 2008 FENS Forum in Geneva. You can get the PowerPoint file in the download section. I'll be leaving for Switzerland tomorrow and the talk will be on Monday, at 2.40pm (14:40). I used Moray/PovRay to create the opening slide:

fens2008.jpg


Here's the abstract of the talk:
Our past experience is one of the primary sources of information when faced with a choice. We ask ourselves: "what will happen if I do this?"
Accurately predicting the consequences of our actions is usually modeled by operant (instrumental) learning experiments. These types of experiments are often contrasted with classical (Pavlovian) conditioning experiments in a dichotomy. And indeed, different brain circuits mediate the acquisition of skills and habits (via operant/instrumental learning) and the acquisition of facts (via classical/Pavlovian learning). However, realistic learning situations always comprise interactions of skill- and fact-learning components (composite learning). Fixed flying Drosophila melanogaster at the torque meter provide one of the very few systems where the relationship of operant and classical predictors in composite learning can be studied with sufficient rigor. The latest experiments show that the textbook operant/classical dichotomy is misleading and that instead composite learning consists of multiple interacting memory systems. These interactions between predictive stimuli (classical component) and goal-directed actions (operant component) make composite conditioning more effective than the operant and classical components alone (learning-by-doing, generation effect). Rutabaga (rut) mutants are impaired in learning about the (classical) stimuli, but show improved (operant) behavior learning. This is the first evidence that operant and classical conditioning differ not only at the circuit, but also at the molecular level. The interaction between operant and classical components is reciprocal and hierarchical, such that the classical suppresses the operant component. Experiments with transgenic flies demonstrate that this suppression of operant learning is mediated by the mushroom-bodies and serves to ensure that the classical memories can be generalized for access by other behaviors. Extended training can overcome this suppression and transforms goal-directed actions into habitual responses. This interaction leads to efficient learning, enables generalization and prevents premature habit-formation.

I'll try to blog from the meeting, but it's never possible to predict what the circumstances will be like there and if the technical prerequisits for live blogging will be met.

Friday 11 July 2008 - 13:04:58 ----- comments: 0


And yet another two more gaps in the fossil record science | email to someone | printer friendly
Blogging on Peer-Reviewed ResearchAs I just got word from PhysOrg, Coturnix and Carl Zimmer (read Carl Zimmer's post, excellent background story!), creationists were just handed yet another victory: the number of gaps in the fossil record has just increased by one. A paper by Matt Friedman in the current issue of Nature details how he has found that some long catalogued and archived fossil fish actually represent a formidable transitional species halfway in-between a 'normal' fish and a flounder (a bottom-dwelling flatfish). The evidence is fantastic, see here for an example:
heteronectes
"So what?" you might say, "the fossil record is abound with transitional fossils!" Of course you are right, but creationists love every new discovery of transitional fossils, because then scientists have a real problem. In this case, the problem is not only one missing link but two: the missing link between 'normal' and the intermediate fossils as well as the one between the intermediate and the flatfish species of today - hooray!

As of this writing, Uncommon Descent doesn not have an entry on this research, yet, but I'll venture you'll have one, soon

Thursday 10 July 2008 - 04:56:56 ----- comments: 0


Schlafly hits rock bottom, digs news | email to someone | printer friendly
This time, for once, I'm not late for the party. I've deliberately waited a week after the initial hoopla to wait for a response from Lenski. You may have realized that there has been a hilarious homeschooling of Conservapædia's Andy Schlafly by Dr. Lenski last month. Unfortunately, there, so far, hasn't been any. What has happened? Schlafly actually is openly considering suing Lenski for sending him the E. coli samples for testing! While some people believe he is bluffing only to impress his famous mom, others think he is not even trying to sue Lenski, he is only trying to infuse a meme fostering doubt in the accuracy of science. Again others think that if Schlafly has such a plan, it is bound to fail and point out that even fellow creationsists are not jumping on the bandwagon.
My whole take on this is: if there is a legal way, send him the strains! Do it with a waiver that Schlafly is not going to scoop Lenski on any importat future results, but rather if there are any, include Lenski as an author. Moreover, Schlafly should of course pay any costs associated with getting the strains. The most likely scenario: it's illegal to send potentially harmful bacteria to individuals not equipped to handle them properly. If it is legal, I'd love to see a picture of a second-career lawyer (probably a few thousand bucks poorer, too) with a whole bunch of sealed petri dishes in his hands a puzzled (but oh so victorious!) look on his face.
Priceless! 

Thursday 10 July 2008 - 04:43:18 ----- comments: 1


Getting ready for the FENS meeting news | email to someone | printer friendly
On Saturday I'll be flying to Geneva for the 6th FENS Forum of European Neuroscience. This time around it will be a very special meeting for me as I will be chairing a symposium (together with Bernard Balleine). This is the first time I'm doing this, so I'm getting slightly nervous...
The symposium is number S28 and is entitled "The neurobiology of choice and decision-making". The symposium will cover evolutionary conserved mechanisms of behavioral choice in snails, flies, rodents and humans, so there's something in it for everyone. The symposium will be on Monday, July 14 at 2.15pm in the room Salève/Jura. I'm currently getting my slides ready and will of course post them for download before I leave.

Wednesday 09 July 2008 - 04:45:15 ----- comments: 0


The future of scientific publishing science politics | email to someone | printer friendly
I'm sure nobody ending up on this obscure blog could have missed the current frenzy about a Nature news article by Declan Butler attacking PLoS. In the meatime, there has been a follow-up by Nature publishing director Timo Hannay, also with comments and a reply by Timo. I think what we see here are the labor pains of a new scientific publishing model. People realize that things are not working effectively, some would maybe even claim that the entire system is broken and needs to be replaced. A good overview can be had from Coturnix in his post, but there are also comments worth noting individually such as Pedro Beltrao, Greg Laden, Lars Jensen, Mario Pineda-Krch, DrugMonkey or Bill Hooker.
Clearly, whatever the system will be that is coming out of this, at the very minimum, it needs to get rid of the following idiosyncracies (to put it mildly) of current scientific publishing:

  1. First and foremost, it is a waste of time and effort to submit and re-submit manuscripts with the same data but different formats until it finally is published. One single, exhaustive and critical instance (with X numbers of rounds) of peer review should be enough to find out if the manuscript under consideration has any scientific value at all. Once this minimum standard has passed, the manuscript should go into whatever form of database will then exist. Of course, all the papers in this database should be freely accessible to anyone. Personally, I care mostly for the access to scientists, but of course these are included in 'anyone' blush.png
  2. The quality of an aricle is not a one-dimensional value. Quality is not assessed by a certain elite group of gatekeepers who shunned professional science for whatever reasons. Quality is not assessed by a single number. Quality is definitely not assessed by where something is published. Some measure of quality is in the eye of the beholder, some measure of quality can be more easily quantified. Therefore, any new system will incorporate the capacity for a multi-dimensional quality assessment that works for scientists, administratotrs, the media and the general public, as each of these groups have different demands and different expectations of scientific quality.
  3. UPDATE: What definitely also needs to go is the requirement of searching in at least three different search engines with different syntax and strategies to be able to find really all the relevant papers on a given topic. What we need is one single search for all papers with an elaborate search mask and the possibility to search for citations in both directions.
Maybe there are more points (probably), but these are the most important ones. At the same time, any new system needs to retain the following two traits:

  1. Peer-review (Duh!)
  2. Trained, experienced professionals who provide their best estimate of what kind of relevance new research is likely to have for all of science or any field in particular. There is too much research going on to be able to follow everything. Human sorting is still required.
There probably are more good traits in the current system worthy of keeping, but right now I can't think of any smallgrin.png
You tell me!

Conflict of interest statement: I have published in Science and PLoS One; I volunteer as academic editor for PLoS One.

Monday 07 July 2008 - 08:41:05 ----- comments: 0


The definition of stupidity news | email to someone | printer friendly
I've always had my own ideas on who I felt (and I use the word 'feel' very deliberately here) was stupid and who intelligent. People, scientists and laymen alike, have always discussed what intellgence is and if IQ has any bearing on it. It always occurred to me that the definition of intelligence apparently was something nobody seemed to be able to agree upon and most definitions I have heard or read didn't really correspond to my own, admittedly intuitive definition. But maybe it's with intelligence as with many other seemingly 'unsolvable', endless debates. Maybe we are just picking the wrong fight? Maybe we should approach the dilemma from a different angle. In his book Just How Stupid Are We? Facing the Truth about the American Voter, Rick Shenkman gives us a definition of stupidity that I find rather satisfying:
Five defining characteristics of stupidity, it seems to me, are readily apparent. First, is sheer ignorance: Ignorance of critical facts about important events in the news, and ignorance of how our government functions and who's in charge. Second, is negligence: The disinclination to seek reliable sources of information about important news events. Third, is wooden-headedness, as the historian Barbara Tuchman defined it: The inclination to believe what we want to believe regardless of the facts. Fourth, is shortsightedness: The support of public policies that are mutually contradictory, or contrary to the country's long-term interests. Fifth, and finally, is a broad category I call bone-headedness, for want of a better name: The susceptibility to meaningless phrases, stereotypes, irrational biases, and simplistic diagnoses and solutions that play on our hopes and fears.
A short and pretty amusing 5-point characterization, IMHO. It appeared in a short excerpt of his new book on Tom's Dispatch (or AlterNet). Rick runs a blog of his own along the same veins of the book/article, you should go and cheggidout.
However, I'm not about to start blogging on politics, at least not that kind of politics (at least not before I have tenure, that is). I found the article rather interesting because it also helps understand why it is so easy for the flourishing business of religious nutcases (with members such as the Discovery Institute) to find suckers who buy into their -for the rest of the world- obviously stupid ideas. Most of the world has basically abandoned creationism about 150 years ago, yet in the US there still is a steadfast (and rich) few who seem to not have gotten the message yet. It's like these people have been stranded on an island for five generations and their descendants wonder whatever happened to the monarchies of the world and are now trying to bring some of it back. Stupidity, as characterzed above (whatever its reasons), certainly describes a great many of cdesign proponentsists or modern day creationists. I think it is undisputed that education lowers stupidity both in individuals and from an epidemiological perspective. Is it a coincidence that higher education is usually referred to with scorn in these circles? Rather than merely blaming stupidity, I find it more important to ask why being stupid can have such a high social value in certain fractions of the US population. Why do especially religious fanatics keep their children from schools in order to home-school them? It's more than just indoctrination with religious dogma - keeping kids stupid is a prerequisite for them to buy into the religious inanity of some magic man who waved his imaginary hand and just made things. In this extreme form at least, religion really is akin to child abuse.

Monday 07 July 2008 - 03:26:22 ----- comments: 0


Measuring editors' performance objectively science politics | email to someone | printer friendly
Editors of schorarly, peer-reviewed journals often claim that somehow their choosiness is the most important verdict on the quality of a scientific manuscript. Points in case are Nature Neuroscience's peer-review policy, a recent Nature News article or a follow-up on the Nature blog "Nascent". However, data on the 'impact' or quality of papers published in these very choosy journals varies greatly. Therefore, I have a suggestion on how to judge the performance of an editor. My suggestion requires that all peer-reviewed scientific primary literature is deposited in some database before any subjective editorial choice has been made. An example would be PLoS One, but any such database would do. Then, editors can thumb up or thumb down papers after they have been vetted by peers and promote or demote papers according to their judgement, very similar to acceptance and rejections in so-called high-end journals of today. Since all choices (also rejections!) are recorded, each editor (or goup of editors) will establish a track record. In a way, this is similar to the concept of the Faculty of 1000. Obviously, this will provide a great incentive to maximize their reliability as gatekeepers of scientific quality. How can their performance be measured? By counting downloads, citations, trackbacks, comments, ratings, media coverage, Fac1000 mention or any other measure deemed relevant of the papers they accepted/rejected.
That way, everybody would get their cake and eat it too: seemingly objective performance measures for both scientists and editors. Wouldn't that be fair?

Saturday 05 July 2008 - 06:42:51 ----- comments: 1


Nature: PLoS a threatening success science politics | email to someone | printer friendly
Coturnix alerts me to the fact that I'm late for a party yet again (as usual). Apparently, Nature is feeling the PLoS competition breathing down its neck. This can be seen in a Nature news article entitled "PLoS stays afloat with bulk publishing" by Declan Butler. In it, Butler describes with little attempt to conceal his arrogance and disdain that PLoS is very successful. According to the article, the means by which PLoS is generating income is mainly by philanthropic subsidies and authors' fees from PLoS One. Butler specifically refers to the ~2500 papers published in PLoS One when he says that
Public Library of Science (PLoS), the poster child of the open-access publishing movement, is following an haute couture model of science publishing — relying on bulk, cheap publishing of lower quality papers to subsidize its handful of high-quality flagship journals.

[...]

PLoS One uses a system of 'light' peer-review to publish any article considered methodologically sound.
Butler is dissing a probably century-old successful marketing strategy: first you convince some people with money that your product (PLoS) is the best since sliced bread (Nature). This step usually costs some money, but if you do it right you get a brand name with a reputation for quality. Once that has worked, you take the same product and sell it more cheaply to the masses and that is when the real money comes in. I'm not an economist and I have no idea if this really was the PLoS strategy, but it might have been. PLoS One could only become a success after the brand PLoS had a solid footing in the science community. And now the entire PLoS venture is working fine because of it and will probably be working fine for some time. So of course, for-profit publishers are getting nervous and so are its employees. Butler's arrogant and demeaning wholesale dissing of basically all the authors and 500 volunteer academic editors at PLoS One has, no surprise there, sent the scientific blogosphere up in flames and the comments on the article reflect this devastating criticism as well.
I only have a few sentences to add to the sizzeling hot discussion all over the place. The article in particular and the discussion in general again raises the old question:

Why, with today's technology, do we still have about 20,000 different 19th century journals around?

Butler's "non-light" peer-review is just a popularity contest anyway, Nature Neuroscience editor Noah Gray (among other colleagues there) admits freely that the toughest obstacle is getting past the editors:
Nature Neuroscience aims to send 30-35% of papers out to review, so getting past that stage is the biggest hurdle.
It needs to be pointed out here that publishing in these "non-light" journals decides over grants, tenure, promotions and thus peoples' careers and livelyhoods. So one could paraphrase the current system of publishing in science in the following way: If the scientific community were a large corporation, it would be out-sourcing it's hiring and firing to a group of ex-employees who either left the corporation because they didn't like it or were fired themselves. Now how many managers would implement such a system in their company?
Instead, we should have one single, decentralized, publicly accessible database where the current assessment by editors (i.e., the "non-light" component of peer review in e.g. Nature) comes after publication as one of many measures of post-publication review and assessment. The first review should be done by scientists on the science - whatever happens to the paper afterwards is open to debate. I, for one, value the input of professional editors and their expert judgement of scientific newsworthyiness and would not want to miss it.

Conflict of interest statement: I have published in Science and PLoS One; I volunteer as academic editor for PLoS One.


Friday 04 July 2008 - 08:12:32 ----- comments: 0


Editor@JoVE! news | email to someone | printer friendly
As of tomorrow, July 1, I am officially an Associate Editor at the Journal of Visualized Experiments, JoVE. I am already on their "Team" page and my new jove.com email account is also up and running. This will of course not be a fulltime job as I'm still a researcher first and foremost. However, I am committed to JoVE and to making the video approach to scientific protocols a success also here in Germany. I will select the most fascinating topics and the most useful protocols and bring them to JoVE fame.
Besides adding JoVE.com to your bookmarks you may also add the JoVE blog to your feeds, just to be sure you're not missing anything important elated.png

Monday 30 June 2008 - 02:27:57 ----- comments: 0

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