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For almost two years now I've been trying to find out if insects have a default-mode network. Last year, I applied to the European Research Council, asking for the money for a microscope and some research staff. The reviewers loved the science: Reviewer 1:
The project is conceptually interesting and original
Reviewer 2:
The project extrapolates from the popular concept of a default mode network derived from human work to propose a broad theory of interaction between operant and classical synaptic learning, basing the arguments on evolutionary principles and biochemical differences. The proposal consists in moving from man to drosophila and using sophisticated optical scanning methods and task free compared to stimulated flies (the description of behavioural manipulation techniques is fascinating). This is true frontiers research
Reviewer 3:
Ground breaking nature of research:
Yes, understanding background or resting activity is important.
Potential impact:
Recording from all different parts of the brain simultaneously with single cell resolution would be wonderful.
but were skeptical if we could pull it off technically. So we did some further experimentation, got some more experienced people in the boat, re-wrote the application and submitted the revised version to this year's competition. In the meantime, other people had become interested in our little idea and also thought it was a fantastic project: The Scientist asked me to write a short article for them detailing my plans "Do fruit flies dream of electric bananas?". Clearly, people thought this was research worth pursuing. Last week, I got the reviews from this year's ERC competition back: not funded, again. What was the reason this time? The reviewers thought the technique was just fine, but they were unconvinced by the science! Just the opposite as last year! The project is conceptually interesting and original
Reviewer 2:
The project extrapolates from the popular concept of a default mode network derived from human work to propose a broad theory of interaction between operant and classical synaptic learning, basing the arguments on evolutionary principles and biochemical differences. The proposal consists in moving from man to drosophila and using sophisticated optical scanning methods and task free compared to stimulated flies (the description of behavioural manipulation techniques is fascinating). This is true frontiers research
Reviewer 3:
Ground breaking nature of research:
Yes, understanding background or resting activity is important.
Potential impact:
Recording from all different parts of the brain simultaneously with single cell resolution would be wonderful.
Reviewer 1:
While the ambitious methodological aims of the project are spelt out quite clearly the actual neuroscience this would permit remains opaque.
Reviewer 2:
The proposal has an original and important conceptual framework, in that it aims to investigate the interactions between sensory driven task-related neural networks and spontaneous, default-mode networks that introduce randomness into behavioural patterns. It is not clear how the proposed experiments will actually address this question. The group will implement state-of-the-art imaging methods for rapid 4D 2-photon recordings of “spontaneous” GCaMP3 signals in the fly brain. Setting up the imaging system, already developed by another group, is envisioned to take 3 years, with 2 years then devoted to data acquisition and analysis. The group appears to have the expertise available to cope with the technical challenges. However, what will they learn from the spontaneous activity patterns they record? Where to look? How can you assume activity is not sensory-evoked, just because no explicit sensory input was applied? And most importantly, how can you address the functional significance of these activity patterns for ongoing behaviour? In short, the proposal does not even consider how they will determine the origin and impact of this spontaneous activity. The latter is of course particularly difficult, since the fly is not freely behaving, and the relationship between spontaneous neural activity and unpredictable behaviours can only be studies on a single-fly basis.
Reviewer 3:
Missing is a detailed description of what should be done after the microscope is up and running. The project plan itself contains too little scientific content, i.e. 60% of the time is planned to be spent to develop something that already exists, i.e. a 2P-microscope with AOD for fast scanning.
To summarize: the tools exist, we have the technological expertise to pull it off and the science is cutting-edge - we just didn't have all of that in the same application, even though both applications concerned the same project... Science funding doesn't have to make sense, apparently.While the ambitious methodological aims of the project are spelt out quite clearly the actual neuroscience this would permit remains opaque.
Reviewer 2:
The proposal has an original and important conceptual framework, in that it aims to investigate the interactions between sensory driven task-related neural networks and spontaneous, default-mode networks that introduce randomness into behavioural patterns. It is not clear how the proposed experiments will actually address this question. The group will implement state-of-the-art imaging methods for rapid 4D 2-photon recordings of “spontaneous” GCaMP3 signals in the fly brain. Setting up the imaging system, already developed by another group, is envisioned to take 3 years, with 2 years then devoted to data acquisition and analysis. The group appears to have the expertise available to cope with the technical challenges. However, what will they learn from the spontaneous activity patterns they record? Where to look? How can you assume activity is not sensory-evoked, just because no explicit sensory input was applied? And most importantly, how can you address the functional significance of these activity patterns for ongoing behaviour? In short, the proposal does not even consider how they will determine the origin and impact of this spontaneous activity. The latter is of course particularly difficult, since the fly is not freely behaving, and the relationship between spontaneous neural activity and unpredictable behaviours can only be studies on a single-fly basis.
Reviewer 3:
Missing is a detailed description of what should be done after the microscope is up and running. The project plan itself contains too little scientific content, i.e. 60% of the time is planned to be spent to develop something that already exists, i.e. a 2P-microscope with AOD for fast scanning.
Awesome webcam from the wilderness:Streaming live video by Ustream
Via PhysOrg.
Posted on Wednesday 06 April 2011 - 13:26:54 comment: 4294967293
| video eagle bald eagle nest live ustream |
Just over a year ago, Bruno van Swinderen and I published a paper in the Journal of Neuroscience (local copy) where we described numerous behavioral and electrophysiological defects in a fly mutant called radish. Many of these defects had to do with how the animals processed and responded to stimuli. These defects could be interpreted as a combination of a deficit in attention-like processes and a rather well-defined, oscillatory hyperactivity. Curiously, many of these defects could be successfully treated with Methyphenidate, the active ingredient in Ritalin which is the drug used to treat patients with, you guessed it, ADHD.What has not been tested for treatment with Ritalin, was the behavioral hyperactivity, an oscillation in the yaw torque behavior of the flies at around 2 Hz. Bruno was able to treat the 2 Hz hyperactivity in the 'brain waves' of the flies, but I needed to get a permission to buy Ritalin first, which I got almost a year later. Now we've treated both the wild type control strain 'Canton S' and the radish mutant flies with Ritalin as they were flying in the Drosophila flight simulator, controlling their flight direction with respect to four identical, vertical stripes. There were two major differences between the experiments I did back then and the experiments now: first, the genetic background was changed from Bruno's Canton S to the Canton S from the lab of Thomas Préat. Second, the patterns in the experiments differed, as the published experiments were carried out with two pairs of t-shaped patterns, to upright and two inverted T's. Now, the patterns were four identical, vertical stripes. In spite of these differences, we found essentially the same peak in the power spectrum of the yaw torque behavior (blue line):
We also found some other peaks, some also in the wildtype control (black line), but by and large, we were able to reproduce the result. Phew.
The most interesting aspect of this work is that the Ritalin treatment almost reduces this big peak to control levels. Not quite, but almost. We interpret that as Ritalin bringing the radish mutant flies closer to the 'normal' wild type flies. In fact, Ritalin even treated the flight defect - radish flies are reluctant to fly in my setup. There are other interesting aspects such as the strong reduction in power at the low frequency end of the spectrum even in wild type flies, but this discussion, together with a more thorough behavioral analysis of the data must be saved for a later time.
For now, I just wanted to share these results with everybody, as they were a big missing piece in our previous publication and if anybody wonders about the outcome of these experiments, I can now point them to this remarkable new platform for sharing figures and data: FigShare, which is where I posted not only the figure, but also the raw data which were used to generate the figure. This allows me to share the results even before they are published in a peer-reviewed journal. Maybe someone has a great idea on what else to do with these results, or has some clever way of further analyzing the data, then they can download the data and try around for themselves. We plan to study, in addition to further behavioral tests, the gene expression differences in essentially these four groups of flies, in a tissue-specific manner. These proteomics experiments will be done in collaboration with Daniela Dieterich in Magdeburg. We will use our behavioral tests as a read-out for the effectiveness of the Ritalin treatment and try to correlate gene-expression with the behavioral effects.
Maybe you also want to try FigShare to keep everyone posted as to what exciting discoveries your are making right now? It is very easy and not a lot of work at all. In fact, this blog post took me longer to write than to post the figure and the data.
Posted on Wednesday 30 March 2011 - 18:17:34 comment: 0
| ritalin radish ADHD methylphenidate proteomics FigShare |
After a busy day with posters and organizing a social yesterday, I now have finally found some time to blog from the 9th German Neuroscience Meeting in Göttingen.This plenary lecture was about insect acoustic communication, i.e. crickets, grasshoppers, cicadas and so on. Berthold first briefly recapitulated the anatomy and physiology about sound production and perception in the different insect groups. He then showed typical examples of how this communication is used by the animals, e.g., during courtship. There, he focused on crickets, showing how male calling song attracts females which approach the males which then, in turn, switches from calling song to courtship song.
The calling song in these crickets can be elicited by extracellularly stimulating the mushroom-body alpha-lobes. In this region sits a command neuron which controls singing behavior: it is sufficient and necessary for singing in crickets, which has been shown by intrecellular electrophysiology of this neuron.
After this command neuron was found, the researchers set out to find the central pattern generatr (CPG) controlling the singing movements. Initially, the CPG was localized to the last two thoracic and the first abdominal ganglion of the cricket ventral nerve chord. Intracellular electrophysiology revealed that only very few neurons in these ganglia are related to singing. For instance, there is the Metathoricic Opener interneuron, which fires in synch with the singing movements of the wings. The Abdominal Opener neuron can reset the singing pattern, meaning that it is critical for the singing rhythm.One of the next research areas planned to investigte is to use these neurons comparatively in different singing species to investigate their role in the evolution of song.
In the next section of the talk, Berthold Hedwig told us about impact of self-generated sound on the singing cricket itself. This was probably the work for which he is most well known, at least from my perspective. He showed that singing crickets protect their own hearing system from desensitisation during their own song by inhibiting sound-sensitive neurons during song using a corollary discharge (or eference copy). Some of this work involved the famous 'omega' neuron, which is named after the peculiar shape it has in the auditory neuropil. This neuron is inhibited precisely at the times when the cricket is producing the sound. This inhibition is mediated by the 'corollary discharge neuron' which connects the CPG with the auditory interneurons in the prothoracic ganglion by making direct inhibitory monosynaptic connections with the Omega neuron. The result of this corollary discharge is that the sensitivity of the auditory system is maintained even during very loud self-generated song.
Next was a section on female crickets, i.e., how they recognize the male song and then show positive phonotaxis towards the source of the song. He described how already the anatomy of the tympanal system is organized to make the animal highly direction-sensitive with regard to sound, i.e., a sound from one side of the animal results in large ipsilateral/contralateral volume differences within the tympanal canals. This leads to bilateral differences in tympanic membrane oscillations which are proportional to the direction from which the sound is coming. Manipulating different physical parameters of the male song and then recording the female response to these manipulated song, the researchers showed that females are tuned to the pulse period of the male song. How is the pulse period detected ? The scientists have found neurons in the female brain which fire only when the 'correct' pulse width is being played back to the femae. They sit in the 'ring-ike' neurpil, bilaterlly in the brain. The tuning curve of these local interneurons fits the tuning curve of the phonotactic behavior very well.
Posted on Thursday 10 March 2011 - 09:35:55 comment: 4294967289
| fun intelligent design religion evolution |
I'm starting to dig a little deeper into the recent 42 page tome of Richard Poynder on scholarly publishing today. Not sure how much more time I can spend on this, though. This post will be mainly about the first half up until about page 19-20 or so.On page 12 Richard writes:
the assumption [...] is that the more papers a journal accepts the lower will be the quality of those that it publishes.
Clearly, the assumption does seem intuitive: after all, the scarcer something is, the more value we attrribute to it. This intuitive notion works for new night clubs which create long lines in front of their doors and it already worked when the French introduced potatoes. The two examples also show how our intuition can fail us: scarcity does confer value but not necessarily quality. In scholarly publishing, the connection between scarcity in perceived 'quality' is very indirect. Specifically, for the journals with the highest rejection rates, it means the quality perceived by the editor, not the scientists. Nature editor Henry Gee explains this connection beautifully as always (and fittingly illustrates it with a picture of James Bond villain Dr. No): I reject at least four in every five manuscripts straight off the bat, before review; most of the rest perish in review. In the end, barely one in twenty new submissions makes it through to publication.
In less prosaic words: when you submit your manuscript, you have a 5% chance of publishing in Nature (it's actually ~8%, but let's stick with Henry's number for now), but once you got past the editor, it's a whopping 25% (other colleagues cite 60%, but let's stay with Henry here too). In other words, the peers are much more forgiving than professional editors.Henry Gee goes on to explain why rejection must remain high:
One reason for maintaining a very high rejection rate is to ensure that the quality of the material we publish is always high (which I maintain it is, even when one accounts for the fact that editors are only human and prone to err). This creates a feedback – if the quality is high, and is perceived to be high, people will tend to submit their best stuff to us. Were we to loosen our belts, lowering the bar (and increasing pagination) the quality would lessen, people would send us their just-about-okay stuff as well as their best stuff, and, well, it would be the end of civilization as we know it.
In other, less prosaic words: scarcity creates the impression of value, which leads to 'perceived quality' which leads to scientists submitting the work they think (or know) the editor will like to Nature. Once the editor likes it, peer-review is the lower hurdle.One may thus say that the 'letter to the editor' accompanying the submitted manuscript may be more decisive for the acceptance of a paper in a GlamMag than the paper itself.
Richard Poynder mentions the notorious 'wind setdown paper' in PLoS One as an example that a different way of selecting papers - sending virtually all manuscripts out for peer-review - is a less rigorous method as it leads to the acceptance of 70% of all submissions and not just 8%. In all fairness, the selection process differs in more ways than just this one. Specifically, reviewers for PLoS One are not asked how they feel about the paper or whether they find it interesting, but only whether or not "the science in this paper been done well enough to warrant it being entered into the scientific literature as a whole". From the interviews he conducted, Richard is not quite sure what this last statement means and indeed, while the instruction works in the large majority of submissions, it gets very tricky in a few borderline cases. In essence, what the instruction means is that the methods have to be understandable and transparent enough for a reviewer to believe the method can work. The statements in the manuscript have to be backed up by the data, which means that alternative explanations have to be ruled out. For virtually all 'regular' research papers from 'regular' institutions this means: do what you've been trained to do and you'll get your paper published, if you fix the few things that you didn't catch initially but the reviewers did. Which is exactly the way scientific publishing should be. However, with over 6000 published papers per year (meaning ~3k rejected papers a year!), of course there will be one or the other 'rogue' paper that did get published when maybe it shouldn't have been. Richard thinks the wind setdown paper is one of them and cites me as Academic Editor of PLoS One as corroborating evidence:
So was there a failure on the part of the reviewers? Brembs believes so. "I think two mistakes were made," he emailed me last year. "For one, there was no proper reference to the particular mythology the authors referred to. Second, there was no reference to alert the reader that the mythology in question lacks empirical support. Both mistakes should have been caught by the reviewers, or by the academic editor."
In other words: adding two references would have fixed this paper, in my eyes and nobody had any objections against the science in the paper. Apparently, Richard thinks that two missing references are a good example of 'inadequate' peer-review standards. To be fair, he cites other papers, but so can I: the now infamous arsenic paper in Science and, of course, my favorite 'worst paper in the field' published in Nature. No amount of reference adding could possibly fix these papers, so one could make the argument that the type of editorial selection taking place at the GlamMagz is actually much less adequate than the genuine peer-review at PLoS One.However, I don't want to make the same mistake I believe Richard is making: arguing from anecdotes. Are there any hard data which show that the selection process (which does include some peer-review also at the GlamMagz) in some journals is better than in others? This is not an easy task and fraught with its own difficulties, but any attempt at arriving at these data is surely to be preferred to enumerating personal favorites and other anecdotes? Unfortunately, even in 2011, there are very few options to quantitatively assess quality, mainly because what is a great paper for you may be horribly boring, dense, irrelevant or incomprehensible for me. But maybe we can find common ground on the other end of the spectrum? One lowest common denominator could be retractions: papers that have been retracted just simply cannot be of high quality, surely everyone would agree with that? So the journals which retract more papers than others have a worse selection process, letting more low-quality papers pass their supposed 'quality filter'? So which are the journals with the most retractions? PNAS, Science and Nature, by a wide margin. Thus, looking at data rather than anecdotes, GlamMagz fail at their 'perceived quality' control - all that remains is intuitive value by artificial scarcity together with deplorable social feedback loops.
To my knowledge, so far, no factual relationship between rejection rate in scholarly publishing and whatever one could construe as 'quality' has been offered that would stand any scrutiny.
Neither the GlamMag editor-selection system, nor genuine, traditional peer-review nor a journal ranking derived from such flawed approaches is able to provide us with the sort of filter we need to keep up with all the exciting new scientific discoveries. Therefore, all that is required at the stage of publication is a system that forces a few experts to read a submission, make sure that no or few and unlikely alternative explanations remain for the data presented and then release the work to the public (some would argue that not even that is required anymore, but I'm not -yet?- convinced). Most of the obvious crank papers will flunk in this process and the few remaining papers that do get through can be weeded out later (and invariably are, no matter where they have been published). What is indeed lacking and in dire need is a modern, information technology-based search, sort and discover (SSD) tool that assists researchers in navigating the scholarly landscape of today. Why are the people constantly trying to fix a modern problem with ancient, ineffective tools, instead of using adequate, modern technology? Sony did not see the iPod coming, Borders did not see Amazon coming, and so on. Today's corporate scholarly publishing industry does not see information technology coming. Trying to solve new problems with ancient technology will inevitably lead corporate publishers of today going the way of all the brick-and-mortar companies that failed to see the internet coming.
Like the iPod or the iPhone, PLoS has its flaws, but at least they attempt to use modern technology to offer an improved user experience.
Posted on Wednesday 09 March 2011 - 21:47:31 comment: 0
| peer-review publishing scholarly publishing PLoS quality |
Richard Grant at Naturally Selected recently posted his take on some recent discussions around scholarly publishing. In a comment, he mentioned that non-profit organizations may not be suited for scholarly publishing. I wouldn't know that so no contradiction there. But I thought it would be a nice thought exercise to make a rough, speculatory sketch of what the profit could buy that coprorate scholarly publishers make every year. The big three players are Thomson Reuters, Reed Elsevier and Wolters Kluwer. Together, they make about 5 billion US$ in adjusted operating profit (according to my slide #26 that I researched a few years back using available financial records). Clearly, not all of that will come from library budgets, but my guess is that the largest chunk will come from some public budget or another.So if these publishers would not make any profit at all, we'd have 5 billion every single year to spend on investments in scholarly communication. What would I do with that sum? I think I'd give it to libraries to be able to archive every single piece of literature and data their faculty produce. All that's needed for that on top of the infrastructure already present, is man-power and servers. So let's say we equip each and every university library on the whole planet (about 10,000 according to univ.cc) with a team of four experts (yearly salary of 100k) and a new $10,000 server each year. That means a total work force of specialists of 40,000 together with a distributed server park of 10,000 brand new servers. I'd think this should be overkill for any such task. Anyway, with just 4.1 billion per year you'd be able to equip every single university library on the planet with what should be more than sufficient resources to archive everything, make it accessible and provide efficient software to boot.
And then you'd still have 900M to burn on something interesting every year... wait, then the corporate scholarly publishing industry would be obsolete, so make that more than 10 billion every year.
Posted on Wednesday 09 March 2011 - 13:48:09 comment: 1
| scholarly publishing publishing corporations greed money profit libraries |
The future is bright - it's the present which sucks.I planned to post this as a comment, but it turned out to be too long. Moreover, Richard Poynder seems to moderate his comments, so I thought I'd just post the comment here, it'd be faster. Richard Poynder has posted a 42-page article on PLoS One, Open Access and the future of scholarly publishing. It's almost 2am here and I haven't had a chance to read this opus major in its entirety, but a few things just had to be commented on right away - in addition to the comments already made by Bill Hooker, which I agree with, of course.
The article seemed well-researched and nuanced and I sympathize with much of what I did read. I have a few remarks now, maybe more when I've read the whole article more thoroughly.
That something is an exponential growth in papers produced (since the end of WWII at least), accompanied by an apparent decline in the quality of peer review.
'Apparent' being the key point here. I'm not convinced a few quotes from researchers and publishers is sufficient to back that claim up. Rather, one would need some data of the type mentioned in this post, and even then, 'quality' is always in the eye of the beholder and sometimes even flawed studies turn out to be correct - more or less by accident.Either way, assuming the 'apparent' decline were real, one may still wonder by growing an enterprise like science without adjusting the infrastructure accordingly, maybe you'd expect a much steeper decline? Maybe we're doing much better than is to be expected given the circumstances? A point which is probably not necessarily a contradiction to the points Richard is trying to make.
Towards the end, Richard is hitting the nail on the head:
The fundamental issue that PLoS appears to have overlooked is that all publishers — not excluding PLoS, and not excluding learned societies — are so focused on maximising their income that they have become blind to the true nature of the crisis confronting scholarly communication.
...and with all publishers one should emphasize the corporate, for-profit publishers!Today, scholarship is a public good in private hands. This is one of the (several!) main factors underlying the crises Richard enumerates and explains in his article. We need to rescue scholarly publishing from corporate greed. I find it outrageous, cynical and unscrupulous to make profits off of a public good, even if it's not done in the blatantly prize-gouging way of Evilsevier et al.!
After all this praise, I must strongly disagree with the use of one single paper that had two major but fixable flaws (you cite me recounting them) as some kind of prime example for some sort of 'quality' decline. The history of scholarly publishing is not unlike some other human tomes, be it the Bible, the Quran or some other major text in that you can pick your examples to make your case for or against basically anything. For every PLoS One paper you find something 'bad' in, my scientist colleagues and I can provide you with at least two papers from so-called 'high-impact' journals that make the same mistake more often and worse. Multiple anecdotes do not data make.
I also must disagree with the impression I get from your description of PLoS financially: have you asked how much the CEO of Elsevier makes? I couldn't find the budget of PLoS (help?), but I'm sure it's less than the 700M Euros in adjusted operating profits that Elsevier is raking in every year.
However, I do agree that nothing is keeping publishers from going all author-pays and then hiking the prices like subscriptions now. Markets don't invariably decrease prices and many a community at least here in Germany are rolling back their privatization experiments, because often enough, markets don't seem to work very well for some public goods.
From what I have read, Richard's article makes it very clear that:
- The scientific community has long outgrown its infrastructure and only the discipline, dedication and passion of scientists has kept it from completely collapsing long ago. Scientific publishing is only the most visible symptom. Richard may be right that PLoS One in some respects made the shortcomings of current scientific publishing more visible. I, for one, welcome this trend, as I'm of the opinion that we should have started with serious publishing reform about a decade ago and not just now. If PLoS made everyone see all that's wrong with scholarly publishing today, it's a decade late.
- Journal hierarchies are deader than dead. Who cares where a 'bad' or 'good' paper has been published? The real scientific communication takes place elsewhere already! Sadly, nobody is really keeping track of it or trying to make a permanent record of it, because it caught the community by surprise even though it had it coming for about a decade.
- By refusing to give up historical baggage and embrace modern communication technology, scholarly publishing increasingly is starting to look like a horse pulling a Ferrari: a silly attempt at imitating a modern technology.
I agree: we must radically reform scholarly publishing and we should start by cutting out the middlemen: for-profit publishers have become obsolete. All the libraries need in order to archive scholarly communications today is a $500 PC - not a 5 billion publishing industry. (In this respect, I have been arguing for quite some time now that PLoS needs to be seriously considering phasing out their other journals, if they want to keep their credibility. But that's a minor point.) Peer-review is essential to science, whether it happens before or after publication and it is as alive and kicking today as it has ever been, as we can see whenever a 'bad' article is published: no matter where it appears, in Science, in Nature, in PLoS One or in the Journal of Cosmology: scientists spring to the fore and rip it to shreds. What is lacking is a system that's not decades or even centuries old to keep track of this process. Isn't it great that scientists just go out and seek their own communication channels since the community at large is not keeping up? Scholarly Publishing only looks doom and gloom for those rooted in the corporate publishing world and rightfully so!
The problems Richard describes in his article all have technological solutions, most of them are already available, just not for the scientific community - yet. PLoS One has put its finger in this gaping wound, poured salt over it and then stirred. I think that was about time - it could have come ten years sooner. Why don't we have these solutions, yet (or: why does Richard still, in 2011, have plenty of reasons to write a whopping 42 page article)? Historical baggage and 5 billions in profits every year make for some awesome inertia. Nevertheless, if there ever was a reason to believe that scientists can overcome this inertia, it's PLoS One, along with blogs, Twitter, Facebook, Friendfeed and all the other technologies developed by the general public and so far mostly shunned by the majority of scientists for, ironically, all but non-scientific use.
The future of scholarly publishing does look bright - just not for publishers.
The title of this essay is re-used (as is much of what scientists do and write about) from an article in Cell by Laura Bonetta where she describes the Twitter service and some of the scientists using it. She leaves it open if scientists should tweet, but I will be answering my question right away: yes, as a scientist you should be blogging.A few years back, David Glanzman, Professor at the Department of Integrative Biology and Physiology at UCLA, once asked me: "I see you write a blog. I read it every now and then, but I've never understood why you do it. I've never seen any reason why I or any other scientist should start a blog." Back then, I tried to answer it, but I don't think I did a very convincing job. At least, not convincing enough to make David start one of his own
I'll use this blog post to try and provide some more coherent and compelling reasons.There are a number of good reasons why scientists should be blogging. For one, a blog is a good way to bring early ideas into a coherent form and maybe get a discussion going in order to develop the idea into a potential research plan. As such, a blog can also help establish primacy, at least in terms of ideas. However, I usually have many more ideas than I could possibly try and experiment on. Maybe someday someone stumbles over these ideas and thinks they're worthwhile. This constitutes another benefit of a blog: get ideas and hypotheses out there for others to pick up. An increasing sector of the public is also developing an interest in how science works and what we, as fellow scientists think of the scientific discoveries of other colleagues. Blog posts about peer-reviewed research are aggregated at researchblogging.org.
I also think that the public deserves some insight into the work of scientists, as they pay most of what we do. I also blog about my own research and write about our discoveries before they appear in the scientific literature: I post PDFs of posters and presentations and provide summaries of the content. Not only does this help establish primacy (this time for the experiments and the data) if there ever was a dispute, I also think that this sort of openness is a good way to improve the way we do science. I agree with Rosie Redfield, Professor at the University of British Columbia in Vancouver Canada, who said in an interview (see also a more recent one here):
My other reason for writing a research blog is that openness fosters good science. That is, I believe that the more openly we do science the better the science is going to be. One example of the benefits of open science that we now take for granted comes from back in the 1970s. When the very first DNA sequences were being determined, the National Library of Medicine made a decision to set up what became Genbank, and journals made the decision to require that authors who published DNA sequences had to deposit this data in GenBank, where other people could have access to it free of charge. This was a pivotal decision, but they could just as easily have decided that sequences should be treated as confidential information so the researchers who generated them get all the benefits. This decision to be open was responsible for all of the research that used these sequences and all of the genetic resources we have today.
Science, in a lot of ways, is simply a market or ecosystem of ideas. The more transparent and open this market is, the faster ideas can find each other and produce news ideas and discoveries. Much of human history is characterized by an increasing information-flow between people accelerating the rate of discoveries and developments. Using the internet to connect billions of people is the afterburner on which the development of mankind will fly beyond the 21st century. Keeping your ideas from other scientists is akin to throttling the fuel supply to the afterburner.
But the ever increasing speed of innovation and research is only one aspect: another is the process by which we make sure each new scientific report is reliable. Again, Rosie Redfield's widely read blog post kick-started the criticism and scrutiny of a paper published in Science reporting the discovery of a arsenic-based life-form in Mono Lake. Blogging is starting to establish itself as an alternative mode of communicating science not just to the public, but also within the scientific community. Can you afford to be silent any longer?
In the last few years, realizing the shortcomings of the traditional way in which we communicate science, I've started to comment more and more on the various movements driving publishing reform: open access in particular, but also less visible movements such as those pushing to drive publishing away from journals run by corporate publishers and towards a single, de-centralized, peer-reviewed, open-access database of all scholarly literature and primary data. In these years, I've learned that the publishing industry rakes in just under five billion US$ each year in adjusted operating profits from scholarly publishing and related activities. I think these tax-funds could be more effectively invested in implementing the existing, modern communication technologies assisting scientists in the filtering, sorting and discovering of scientific publications, rather than to line the pockets of international shareholders. I use my blog to voice these opinions and to do my part in driving the spread of these ideas through the scientific community. It is exciting to see that these sorts of strategies and tactics work even on a much grander scale throughout the world today: spreading ideas brings change even to the most rigid regimes.
The communication technologies mentioned above already exist. I'd like to highlight a social service which incorporates a few crucial aspects of these technologies, FriendFeed. FriendFeed is a service which shares all of the features of Twitter but few of its limitations and provides many additional features valuable for scientists, in particular more effective filtering of scientifically relevant information. In her Cell article, Laura Bonetta quotes Jonathan Weissman, a Howard Hughes Medical Institute investigator at UCSF: "I could see something similar to Twitter might be useful as a way for a group of scientists to share information. To ask questions like 'Does anyone have a good antibody?' 'How much does everyone pay for oligos?' 'Does anyone have experience with this technique?'" It is precisely for such and many more purposes that scientists use FriendFeed, which allows the collection of many kinds of contributions, not just short text messages. In fact, I receive many more comments on my blog posts on FriendFeed than I do on my blog itself.
Comments to each contribution are archived in that context (and without a time limit), providing a solid base for fruitful, threaded discussions. In your user profile, you can choose to aggregate any number of individual RSS or Atom 'feeds', including scientific publications you bookmark in your online reference manager (e.g. CiteULike or Mendeley), your blog entries, social bookmarks (Google Reader, del.icio.us, etc.), and Tweets; and any other items you wish to post directly to your feed. You then look for other users whose profiles are relevant to your work and subscribe to them. Every individual item posted in your subscriptions will then appear on your personalized FriendFeed homepage, plus optionally a configurable subset of the feeds you subscribed to. You can choose to bookmark ('like') any of these items (Facebook copied this 'like' functionality just before it bought FriendFeed), comment on them, and share discussion threads in various ways.
At first, this aggregation of information and threaded discussions might seem daunting. However, the stream of information can be channeled by organizing it into separate sub-channels ('lists'; similar to but more versatile than 'folders' in email), according to your personal preferences (e.g. one for search alerts). In addition to individual users, you can also subscribe to 'rooms' that revolve around particular topics. For example, the "The Life Scientists" room currently has 1,477 members and imports one feed. Another very useful room is the “References Wanted” room, where colleagues are sharing hard to obtain scientific publications. Usually, a request for a paper is answered within 1-2 hours, sometimes even in only minutes. There are currently 282 subscribers to this room.
The feature that makes FriendFeed truly useful is its social filtering system. Active discussions move to the top of your FriendFeed homepage with each new addition, which automatically brings them to the attention of you and everyone else who reads those feeds. In a sense, the most current and the most popular entries compete for attention at the top, making notifications unnecessary. This means that your choice of both rooms and subscriptions affects and filters the content you see. In that way, for instance, you could set your preferences such that you would only see papers with a certain minimum number of 'likes' among your colleagues. Alternatively, you can opt to hide items with zero likes or comments, ensuring that only those that someone found interesting will reach you.
Thus, I find blogging already valuable for my research, especially when combined with social technology such as FriendFeed: I can get ideas and opinions out there and get feedback, comments and criticisms from other scientists. I've met new colleagues this way and developed new ideas, concepts and interests because of them. I have even been invited to write articles, present at conferences and to join editorial boards because of my blog. My work as a scientist would be poorer without blogging.
Acknowledgments: The FriendFeed portion of this article has been partially modified and re-used from a blog post which has received input from a number of FriendFeed users and was jointly blogged not only by me but also by Allyson Lister and Daniel Mietchen just over a year ago.
Posted on Monday 28 February 2011 - 16:50:31 comment: 0
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