I'm sure that promiscuous, non-functional phosphorylation occurs to a degree. Not sure that I buy the evolutionary argument. Phosphorylation may consume a tiny fraction of cellular ATP, but it's like the "what use is half an eye" question. Over time, would we expect selection for efficient use of ATP and against wastage, no matter how small the differences? - Neil Saunders
that depends on the selection pressure (effect on fitness plus population size). I don't think that there is enough selection pressure to purify most wasteful phosphorylation for the energy it costs. There is also a high turn-over of phospho sites so at any given moment (i.e. present time) there must also be a large number of sites that are under transition. - Pedro Beltrao
Think about that when deciding to apply for a PhD ;) - Pedro Beltrao
Given the circumstances, I'm probably going to "lab tech" a while before applying for a PhD... - Ricardo Vidal
Good move, Ricardo. For some reason I thought you were a postdoc, but since you're not -- think *hard* about what you'll be getting into if you go that route. (I'm not saying don't do it, just that not rushing in is a very good idea.) - Bill Hooker
Bill, if I had the opportunity I think I would probably dive into it (PhD). However, I think lab tech would be a good start - Ricardo Vidal
I suggest to all students that they consider working as a tech/research asst before they start a PhD. I did it myself, and it's the only reason I survived the PhD. You get an up-close-and-personal look at the job you'll be training for and hands-on experience that can't be beat when applying for grad school. If you are lucky (and perhaps prepared to move around a bit), you can often switch from tech to grad student on the same project, getting a flying head start in a lab where you already know you fit. - Bill Hooker
Bill, that's exactly why I'm considering tech/research assistant position (with whoever will take me) at a lab working on topics I'm really interested in. - Ricardo Vidal
Thats an interesting distribution of impact factors... - Duncan Hull
No "outrage" there, just some interesting facts. Anyone from Nature care to respond? - Bill Hooker
Thanks! No response from Nature so far - I guess they have given up responding to the flood of blog posts by now and just wait for the storm to pass ... - Lars Juhl Jensen
yes, this is a much better article even if I don't agree with him. - Pedro Beltrao
The article is mostly just a statement of facts about what PLoS has achieved on the business side, versus what they set out to achieve. It looks to me like an exceptionally useful document to OA advocates - OA journals need sustainable business models, and Timo is dead right that the best way to achieve this is open discussion. - Michael Nielsen
Much better than the original. Still I think Timo misses the larger point -- see esp. comments by Bjoern Brembs -- it's time to do away entirely with the *whole concept* of "high-end" journals. Journal-level metrics (impact factor, rejection rates, perceived prestige) simply do not work as a way to rank and evaluate projects, ideas or scientists. Let peer review do what it can do -- weed out the obvious crap -- and let search and database software and the research community do the rest. - Bill Hooker
It also amuses me to see Nature folks with their lace hankies pressed to their horrified mouths over the "kneejerk backlash" and "internet outrage". The original piece was outrageous -- I think most of the responses have been quite calm and reasonable. I guess it all depends whose ox is being gored, no? - Bill Hooker
I'd like to see a publication discussing the economics of scientific publishing in detail. It's clear that there are ways to sustain open publishing. I'd like to get a better understanding of the cost structure, esp in a purely internet publishing environment. - Deepak
@Bill - agree, some of the Nature people don't seem to get internet debate. Sure, it happens rapidly, is occasionally hasty and not fully thought through, brash or even a little rude at times, but we're hardly descending to, say, YouTube comment level here. In general I see commentary by interested parties, rather than a mob waving torches. - Neil Saunders
Hey - I missed this discussion but just posted to Timos blog saying basically what Bill H said --- the original piece was outrageous - Jonathan Eisen
I also commented on the post (of course with my usual plug on getting rid of journals). But I also had another idea: with editors choosing after peer-review, each editor would get the chance to establish a track record: how many of the chosen papers really were high-end? Measuring editor performance objectively... - Björn Brembs
I'm not seeing any comments showing up on the Nascent piece... - Bill Hooker
First he conflates (in his quoting of Helen) the goals of PLoS with goals of PLoS Biology. Then he writes "That's a great goal, ..... maybe even an achievable one. But it hasn't been achieved, and in some ways quite the opposite has happened." with no data to back that up! Has not been? Depends on who says so, and what the goal is. Opposite? How come? The rest is just insidious. If Declan's piece was laughable (like PRISM) due to its obviousness, Timo's piece is dangerous due to its insidiousness. - Bora Zivkovic
The fact I keep coming back to is that PLoS has been running for all of six years. Nature itself didn't turn a profit for 30 years, I read recently via one of Bora's links. So the people claiming that PLoS is failing or doing science some kind of damage are being either very impatient, or (let's try to be polite) disingenuous. - Bill Hooker
Also, would Nature make a profit on its own, or is it being subsidized by the NPG "second tier" the way PLoS ONE looks set to start propping up PLoS Biol? We'll never know, of course, because NPG won't put their finances in the spotlight. - Bill Hooker
Still no comments on the post itself - I wonder when they'll show up? They must be scathing.... - Bora Zivkovic
I think 20 mins at 1-2 slides/minute is about the perfect presentation time. Forces speakers to be concise; a talk is only a summary, not a detailed explanation of every single little point. 45 mins is about as long as most people can concentrate at a stretch. I never understand these 100+ slides presentations that I see at Slideshare. - Neil Saunders
I'd like to try all kinds of things at conferences and even routine labmeetings -- brainstorming, speedgeeking, pecha kucha -- but every time I suggest anything remotely new I get shut down. - Bill Hooker
I used to have the same idea (1-2 slides/minute), until I heard Larry Lessig talk. He uses a lot of slides, often with just one word on them, and can go through them quickly. But then not everyone is Larry Lessig :) - Deepak
I actually just spent a fair bit of this past weekend attempting to fix my death by powerpoint habit. I have done pretty well. Neil - Apparently it is about 10 minutes one can concentrate effectively during a powerpoint presentation. - Mitchell J Stanton-Cook
It feels like I always have about fifty slides. Doesn't matter how long the talk is. Ten minutes? Fifty slides. :) - Andrew Walkingshaw
I've seen presentations where they basically cut the figures out of their paper and made a slide out of each. It was way too busy and hard to follow. I don't know if that means that their figures were too busy to start with or what, but it was so boring. I felt like they didn't even need to be up there, and everyone was reading the figure legend instead of listening to the presenter. On the other hard, for a scientific presentation, you do have to show actual data, so you can't go too minimalistic. - Mr. Gunn
I also like a lot Lessig's style. I tried it once in a talk about open science. I think it works best for presenting one concept but I don't think it works so well for detailed scientific results (although some try to flash a lot of westerns at you but it is not the same ;) Dick Hardt's talk on Identity 2.0 is another good example of this style (http://identity20.com/media/OS...). - Pedro Beltrao
from an audience point of view, the best is to end it quick and see other angles during the discussion, it is just not 'polite' to talk too much without interaction - Attila Csordas
I learned in teaching class that people only have a 10 minute attention span, and if you need to give a talk that's longer than 10 minutes, you need to do something (anything!) after every ten minutes to recharge the audience. In our examples they were mostly little exercises, but that was for students. I guess a mid-talk question round would work too. - Eva
Something I like about Lessig's style is that it demands attention from the audience. There's a new chunk of information every few seconds, and as an audience member you always know exactly where your attention ought to be. It's almost flow-inducing, although it can be a bit draining (agree with Eva - a break every 10 minutes is good). Tough to pull off a talk in this style, though. - Michael Nielsen
Hey, I know that Lessig is cool and can handle the remote well but we need scientific presenter heroes, who and where are they? - Attila Csordas
Jaenisch is a very effective presenter. I saw him at the NIH and ISSCR a previous year. - Mr. Gunn
Nipam Patel is engaging, entertaining and scary smart. - Bill Hooker
Evan Snyder, stem cell guy: I am not sure about his science, but as a presenter he is good. His trick is being very enthusiastic about the topic. - Attila Csordas
Cool! Should add that to my other FOAF file... - Egon Willighagen
It's had that for a long time (get the Semantic Radar extension, detects all FOAF friendly sites). MyBlogLog has that too - Deepak
I wanted this from Nature Network: would be far more interesting to get such an automatic FOAF profile with publications, locations, tags (=interest), network... Many tools could be built from this informations: "I'm looking from someone who know somenone in germany who worked on HIV..." - Pierre
cool, who wants to write a spider for this? - Mr. Gunn
I decided to be polite but that article is lame - Jonathan Eisen
You know, I really do expect better than this from NPG. Very disappointing. - Bill Hooker
I was going to say that Nature article seemed a little tactless given how they've made it a point to bring down PLoS several times. - Kambiz Kamrani
Disappointing is the word. Especially since many of us know, respect and interact with NPG staff. It's hard not to interpret this as heavily-influenced by the NPG corporate overlords. - Neil Saunders
Not very surprising and good news for OA. Lower impact publishing would exist anyway even without PLoS ONE and BMC. It is great that by covering the whole impact spectrum PLoS is financially viable. I hope PLoS can now focus their attention on what they set out to do with PLoS ONE, to have additional ways of doing post-publication peer review and promote those articles that deserve the attention. - Pedro Beltrao
My sample isn't very representative but PLoS ONE seems to enjoy a solid reputation amongst my silent (as in non-blogging) peers despite the "light" peer review. - Roland Krause
Yeah Pedro, I would like to see the post-publication review on PLoS ONE, i.e. the comments on the papers, to be emphasized more. That's a killer feature that is under utilized. Similarly, I often link up PLoS ONE articles on my blog and never once have my trackbacks worked... strange, given that PLoS ONE is one of the only journals I know that allows commenting and trackbacks on articles, but the trackbacks don't work. - Kambiz Kamrani
There was also the little interesting remark (from an unidentifiable source) stating that BMC is already profitable and for sale. It will be interesting to see if this is really true, who ends up buying BMC and what will happen to BMC in the future regarding their publishing policies. - Pedro Beltrao
PLoS ONE serves a valuable function; it publishes "sound science". Not amazing or ground-breaking, but solid and worthy of attention. The kind of work that the majority of us do, I imagine. Disclaimer: my boss is an academic editor and I'm a reviewer. I don't think "not ground-breaking" equates to "lower review standards". Didn't Bora mention on his blog that 50% of submissions are rejected? - Neil Saunders
I really don't get the negative spin on the good financial results. NPG is also diversifying a lot with a growing list of Nature branded journals that include for example Nature Protocols (an experimental lower tier version of Nature Methods?) along with many other journals that do not carry the Nature name (http://www.nature.com/siteinde...). - Pedro Beltrao
I've just read the comment thread to the Nature news story. There is outrage about the "slurs" the commenters feel are cast upon PLOS but no factual responses to the facts presented in the article. I'd be more impressed if one of the commenters pointed to a factual problem with the article, rather than the usual "internet outrage" reaction because something is published that the commenter happens to disagree with but can't be bothered to support rationally. - Maxine
By the way, my disclaimer (comment above): I am an editor at Nature, the journal. - Maxine
A journalist writes: grass is green, sun is yellow, sky is blue. Declan writes: grass is green and that is BAD, sun is yellow and that is REALLY BAD, sky is blue and that is REALLY, REALLY BAD. He may have gotten all the facts right but he painted them in puking green in a way that suggests that good is bad, up is down and we are now in war with Eastasia. - Bora Zivkovic
Maxine, Paul Peters commented on the original, making a point that many have made (NPG has its own stable of "second-tier" journals). That's a fact, but you chose to obscure it in your response to Paul by focusing on the "Nature Whatever" group, which makes up about 1/3 of the ~60 journals published by NPG. It's not even (see Bora, above) a criticism of either publisher -- where did this idea come from that publishing solid science was bad? - Bill Hooker
Further, Butler seriously misrepresents the PLoS ONE review process, skirting the edge of disinformation in an attempt to paint it as somehow less rigorous than other journals. PO reviewers do not "only check for serious methodological flaws" as Butler claims. This is a petty smear, carefully worded to keep lawyers at bay but clear in its intent. - Bill Hooker
Sorriest (and most blatantly wrong) attempt I've seen by a for-profit publisher to debase the open-access movement. Incidentally, I do think there are reasons to have a different pricing structure for open-access than PLoS, but the attack on the review process at other PLoS journals while touting the lesser Nature journals rings hollow. Incidentally, it was a slanderous and misguided enough attempt to get me to join the commenting section of Nature and this website to talk about how bad it was. - Evans B
I've confused by your point about my reply to Paul Peters, Bill. I thought it was clear enough and it contained the URL (not a live link) to the numbers in question. I didn't "choose to obscure" anything, I am not that kind of person, I was correcting an error of fact that this commentator made. - Maxine
Bora, the news story didn't say green is green, etc, it had numbers in it. I haven't looked at the comments on the Nature site since this afternoon, but when I did, they were mostly of the "shock horror, Nature has run a news story about another publisher" variety. We often run news stories about scientific publishing/publishers. Do we need to write that we are one do you think? - Maxine
Sounds like it's all tits-up for toll access - Graham Steel
Yeah, no conflict of interest here. are Nature commentaries peer-reviewed research? - Timothy Driscoll via Alert Thingy
Maxine, thanks for the responses. Do the editors at Nature really miss the subtext of the following lines? "PLoS stays afloat with bulk publishing", "bulk, cheap publishing of lower quality papers", "PLoS One uses a system of 'light' peer-review to publish any article considered methodologically sound." The subtext is clear, that things are different in a bad way from how things are at Nature ... so where's that graph of Nature's financials? - Evans B
As a followup, are we really to believe that Nature recently added all the new NPG titles for any other reason than to capitalize on the very thing you condemn PLoS for doing? - Evans B
Yeah, sorry Maxine, didn't mean to say it quite like that. Mea culpa, I apologize. - Bill Hooker
My point, more carefully phrased, is that Paul's comment (though he made an error which I think effectively obscured the larger point) is just an example of a point that many have made: NPG has, indeed most publishers have, their Glamour Mags and their workhorses. Declan makes it sound somehow heinous to do this, but it's a standard business model. - Bill Hooker
What I'd like to see is a PLOS ONE with 0$ cost to the authors, where the light review puts it at a different level (counts for tenure points) from Nature Proceedings, but it still is free - community based - open access. The PLOS ONE reviewers don't get paid anyway right? So the only cost would be only for computing infrastructure, and a few people for organizing/moderating peer-review (infrastructure can be covered from donations, people can donate time). Imagine if this thing picked up like Wikipedia... - Ntino
factual points for maxine: a) the live link you (maxine) gave us only shows the impact factors of the "nature xxx" journals, not those of the >40 other lower impact factor journals that npg publishes. the PLOS accounts are public, and nature is entitled to publish the results of its sleuthing, but for the analysis to be convincing or useful, a comparison with the publishing models of other groups (or at least that of NPG) is essential. b) how exactly is evaluating a paper for methodological soundness "light" review ? and how does adding on a subjective assessment of potential impact somehow makes the review "heavy" (or "rigorous") ? more on all this in the original nature thread ... - mad -
Since not everyone has access to nature, I'll re-post my comment here: Why do we, with today's technology, still have about 20,000 different 19th century journals around? Nature Neuroscience editor Noah Gray points it out: "Nature Neuroscience aims to send 30-35% of papers out to review, so getting past that stage is the biggest hurdle." http://network.nature.com/foru... Why does this step come *before* peer-review? Shouldn't this come afterwards? Why is this considered "non-light"? : - Björn Brembs
Let scientists decide what is good science in their field and then have ex-scientists which usually are smart, knowledgeable, experienced and eloquent decide what is "hip" right now? Let's exaggerate our current system slightly: "non-light" peer-review is mainly a review by ex-professional scientists (either voluntary or involuntary ex-) for popularity. Publication in such journals usually decided who gets grants, tenure, a life. So basically, we have a system going in which ex-members (either members who left or didn't cut it) decide which members get promoted and which get fired. How many corpporate managers do you think would want to implement that in their company? Conflict of interest statement: I have published in Science and PLoS One; I volunteer as academic editor for PLoS One. - Björn Brembs
@Bjorn - Right now the different tiers of journals work reasonably well at sorting out the potential interest of an article. It is far from perfect but I don't feel I a missing important articles by not reading lower tier journals outside my field of research. Still I am interested in knowing the latest news on the very important discoveries in science. I agree that in principle this "sorting" could be done after peer-review and publishing but we don't have the tools to do this .. yet. - Pedro Beltrao
maxine wrote earlier: I'd be more impressed if one of the commenters pointed to a factual problem with the article, rather than the usual "internet outrage" reaction. ok.. now there are numerous pointed criticisms of the article, on the internet, much of which can be recapitulated by paraphrasing this thread. so now.. i'd be more impresssed if maxine/declan/one of the people at NPG actually responded to the most substantial of these comments in a factual manner, rather than merely cherry-picking the weakest links/arguments in rapidly posted comments and choosing to counter them. - mad -
In summary: should Nature journals write about the publishing business? I think the problem is that Nature see themselves as representing science; science publishing is a hot topic, articles about it in Nature journals are fair enough. Other people, however, see Nature as an arm of NPG with the business interests and conflicts of interest which that implies. It's always going to be controversial for them to discuss other publishers. - Neil Saunders
Timo Hannay at NPG has written a post at Nascent, one of the NPG blogs, about this news story on PLOS. It is being discussed by this FF group. - Maxine
Timo's article is even nastier than Butler's, if that is humanely possible. Where and when will Declan defend himself? All the damage control so far has been done by Maxine, Timo, Euan, Bob, etc. When will Nature give Declan a green light to defend his own words, his motivations, and his "information"? - Bora Zivkovic
Thanks. I just saw it and added it to the ever-growing linkfest. I had to go offline as we had another bad storm here so I wanted to unplug my computer. - Bora Zivkovic
The Wellcome Trust Sanger Institute has sequenced the equivalent of 300 human genomes in just over six months. The Institute has just reached the staggering total of 1,000,000,000,000 letters of genetic code that will be read by researchers worldwide - Duncan Hull
Yeah, I had the same reaction. Hadn't seen the Discovery Channel commercial - it's pretty cool. - Michael Nielsen
Found a translation of the Bengali lyrics here (see "Stream of Life) - http://www.schoolofwisdom.com/... - "The same stream of life that runs through my veins night and day runs through the world and dances in rhythmic measures. It is the same life that shoots in joy through the dust of the earth in numberless blades of grass [...]" - Michael Nielsen
What I like about it is that it is so simple. I was wondering today about social/cultural context. Would this video evoke similar responses around the world ? - Pedro Beltrao
@Pedro His dancing made lots of others dance around the world, so I think it would have similar responses around the world (with exceptions). - Ricardo Vidal
He talks a bit about how he got people to join in in one of his blog posts. Says that in countries where email is popular he just recruited people to dance who had seen one of his earlier videos and emailed him. In poor countries with little email he said that people were happy to just join him. In rich countries with little email (he talks specifically about Kuwait) he says that people weren't so willing to join in. - Michael Nielsen
LIKE LIKE LIKE! I also wish I had 10% of the background necessary to attend and understand his course. - Mr. Gunn
Mr Gunn - Cosma has a lot of fantastic materials from past courses also on his website. And his notebooks are also wonderful - very, very highly recommended for a browse, if you haven't already done so. - Michael Nielsen
I've seen those. It's such a fascination of mine that I'm always thinking of ways to incorporate this type of thing in my current projects. - Mr. Gunn
Thanks for all your help with this so far guys. I tired to make it very explicit that the answers to this will be released into the public domain for analysis. I wasn't sure but the laws here in the UK are some what strict about releasing information people have given so I thought I should try to be as safe a possible about this. - Michael Barton
Any feedback on the legal implications would be welcome. - Michael Barton
I also deleted any previous answers that had been entered so far, because I wasn't clear about how the data would be used. So if you've filled out the survey once, and are happy about your data being released, you'll need to do it again. - Michael Barton
http://en.wikipedia.org/wiki/D... should be enough to figure if you're covered. Data is anonymous and if everyone who takes place understands the data is to be released, not sure what the problem would be - Daniel Swan via twhirl
Michael, for Nationality, should I put "American" or "United States"? "American" is geographically (though not practically) ambiguous. Too bad those fields aren't drop-down boxes so the input is standardized and idiot proof. :-( - Chris Lasher
I've only studied bioinformatics briefly but should be eligible to fill out the survey and I may be able to forward this to some researchers I know - Julian Baldwin
Big thank you to everyone who has reposted the survey. - Michael Barton
@Chris Yes, I agree. I had planned to standaradise nationality with a set regular expressions but a drop down list would have been better. Also if I had used stardard ISO country codes I could have displayed the data on a map using the Google chart API. - Michael Barton
it is interesting though to have a little check of the journals in which Prof Struhl publishes his own research... ;-) - Thomas Lemberger
Wasn't there a discussion about this article in Nature Network a while back? the article's from January, so I imagine so, and I think some people from the publishing side of things joined the discussion, as well. - Mr. Gunn
Got it. The comparison to MP3 sharing is apt, with all the implications that entails. A hot feature for them would be online backup integration, so you're not limited to running it from one PC and so people could share references without having to actually mail the PDF. - Mr. Gunn
I want in too. If possible ... obrigado. - PauloNuin
Ah, reading the license terms: "You may (at your option) use our Software to make a regular back-up copy of your Academic Papers to our servers so that you can access your Academic Papers using the World Wide Web and you hereby grant to us a limited licence to upload, copy, store, use, modify, display and reproduce your Academic Papers for the sole purpose of providing our back-up service to you." I like this very much. - Mr. Gunn
We may from time to time provide interactive services on our Site, including, without limitation: "facilities for the uploading and sharing of users and members Academic Papers with other users or private user groups you have created" This is perfect! The social networking angle of the online service, linking people via authorship, looks really nice and pretty much kills SciLink. - Mr. Gunn
Don't mean to live-blog my reading of the license here, but I should include: "You may use our Site and our Software only for lawful purposes. You may not use our Site or our Software: to send, knowingly receive, upload, download, use or re-use any academic papers or articles without the permission of the copyright owner." - Mr. Gunn
Finally, "You may link to any of our publicly available pages, provided you do so in a way that is fair and legal and does not damage our reputation." I'm going to blog my review, just as I have with 2collab and Connotea. I hope they don't close my account because I say something too critical. - Mr. Gunn
Mr. Gunn, how about a blog post about the license terms? Sounds like you have some opinions about them. - Ricardo Vidal
That's coming, once I get some hands-on time with it. The import from Connotea is putting the doi in the notes field instead of the doi field, which is apparently Connotea's fault. Two killer features I hope they add soon: automatic download of PDF once metadata is added and adding to library via bookmarklet. If they don't have the second feature, I'll probably still use Connotea or something and periodically update Mendeley, provided. It needs to be easier to select a range of papers in Connotea by date - Mr. Gunn
Mr. Gunn - "I hope they don't close my account because I say something too critical." We sure as hell wouldn't! We know that we still have a lot of work to do, so our technology as well as our license terms are far from perfect - both will be modified based on our users' feedback. Any ideas are appreciated! Just one remark regarding the current license terms: As you can tell from the language, they were largely written by our lawyers with the main intention to protect us from lawsuits... - Victor
The license terms quite strangely resemble readable prose, so props for that! I'm still trying to find an import format that works 100% for Connotea/2collab -> Mendeley. I takes about 20 sec on my machine to import 550 records. It's becoming apparent to me, and probably has been for a while to Ian et al, that RIS kinda sucks. Every app seems to expect things like DOI and URL and notes to be in a different field. - Mr. Gunn
Thanks - we tried to intervene and rephrase where possible, but our lawyers were adamant on some points! To be honest, we hadn't planned with a Connotea/2collab import specifically; we just tried with BibTex and RIS files generated by Google Scholar and EndNote XML... If you feel so inclined, it would be enormously helpful if you entered any import/field mapping problems into our bug tracking system: http://mendeley.com/trac?compo... - Victor
I tried it yesterday. I think I imported around 400 articles. There were several errors in import but these are understandable. However I wanted to go through the errors and add tags etc but it was a bit to slow so working on it was a bit frustrating. Is it just me or is it slow for other people as well ? - Pedro Beltrao
Hey Victor, any way to get an invite? Thanks ... - PauloNuin
I second Paulo's question for an additional invite.. - Daniel Jurczak
Paulo, Daniel - I feel rotten for having to turn down your request, but unfortunately, we can't currently invite new testers. Sincerest apologies! The reason is that we've got our hands full fixing the bugs and implementing the feedback brought up by the current testers. I know it seems arbitrary, but there's also a waiting list of people who signed up on our website (www.mendeley.com). May I ask you to register there? You'll be notified first thing we go public beta... - Victor
Pedro - Maybe we can help? If you enter your problems (along with your operating system/machine specs) into our bug tracking system, we'll try to sort out the errors and the slowness as soon as we can: http://mendeley.com/trac?compo... - Victor
That's fine, but I guess you should change the text on the website. People might think they will get an invitation/registration soon. - PauloNuin
Thanks anyway Victor, I will just register on the website - Daniel Jurczak
That's what I was saying regarding new citation metrics and evaluating the importance of online contributions. Let the feed-forward loop work a little while and the solution will become clearer, but don't stop doing something because there's no obvious benefit in the present. Do what moves you(within time constraints), and the application will come. - Mr. Gunn
Different tools have different advantages. Blogs are great for "real-time" discussions but are horrible at solidification of content (Wikis are best here). Still, a lot of the hits I get for things that are not on the front page of the blog are for people searching for something in particular so blogs + links + search engine work ok at ranking scientific content on blogs. - Pedro Beltrao
Scientific blogging is great networking also, good tool to make connections if you have not enough data/money to go to conference. - Alexey
Deepak, I think you're right... there are so many alternatives, more and more every day, that one has to make choices... NatureNetwork has a negative score (for me; that's personal, not general, and up to now): more investment than return. Chemical blogspace/Postgenomic.com: little investment, much in return. Not just data, also ideas. But I agree, it needs to have a positive balance. - Egon Willighagen
Like I keep saying, the data should be social, not the people (or at least, the people later). Absolutely agree with Egon: it's site design that determines the cost/benefit of participation and NN falls down on that point. - Neil Saunders
I, too, have very little time for all these networks, but it is horses for courses. For me personally, Facebook and MySpace do nothing, nor does Twitter. Friendfeed and Nature Network on the other hand are both great for what I do. I'm not a life scientist on the cutting edge of data sharing technology like you guys. Nature Network is an experimental site, and like all these community building enterprises, it is good for some things, not so good for others. It is not, and was never intended to be, a data-sharing site, for example. But, to take an example of its usefulness, many scientists are not very familar with the "social web" (the vast majority of Nature authors for example). Two ways in which they have used NN is (1) online discussion of Commentary material -- they feel a bit safer, I think (guess), commenting in our "News and Opinion" forum there, rather than on the open Internet -- and we've had some interesting views expressed, some of which have been published in the journal as a result; and (2) pre - Maxine
It's also depends on what you get out of a service. Facebook, for me at least, has little to do with science. I am miles away from home, my friends are spread out around the world (people I went to school and college with, as well as family and colleagues). That's the role Facebook fills. But in the scientific sense, the key is how can I get the most with the least effort. In the end, the internal marketplace in the head sorts it all out. - Deepak
It's true, services serve different roles. Facebook serves the role that Deepak described and does it well. I think too that we can learn from the design and code of social websites and apply that elsewhere, even if we're not interested in what the site offers. Facebook's usability is due in large part to Ajax, for example. We're all waiting for the science networking site with the right combination of features, usability and discovery via data. Imagine a FriendFeed-type interface to NCBI, or PDB. - Neil Saunders
Hmm... PubMedFriend? Has anyone invented that yet? - Richard Akerman
Great resources both of these. There is really a growing number of binding domains (both protein-dna or protein-protein) for which we now have enough data to make domain binding models. The interesting direction now will be to find a way to combine these domain models in network models. MacBeath gave a talk here a while ago showing some nice results on this (http://sysbio.harvard.edu/csb/...) - Pedro Beltrao
"In addition, much of the dynamic network behavior may not yet have been surveyed, given that the bulk of the data reported in Isalan et al. were collected in rich media" ... A lot of it is buried in supplementary materials but we tried several experimental conditions. - Pedro Beltrao
That's a cracking paper, went down well as a paper talk in our lab meetings! And yes we noticed a certain name on the author list ;) - Daniel Swan
I've also looked for such functionality and ended doing the drawing in Inkscape. I was thinking about hacking TeXtopo for that purpose, but never actually started. - Pawel Szczesny
