Sign in or Join FriendFeed
FriendFeed is the easiest way to share online. Learn more »

Abhishek Tiwari › Likes

Why people do not comment online articles? What is wrong with the online commenting system? I think this is one of the central issues in Science 2.0. Here is the test case, which is very demonstrative:
Definitely a blog post in this but I would say the answer is simple - the commentary feeds off itself, you need a community in place for that to happen and there isn't any such community at the PLoS ONE site. The existing community provides people (obviously) but also context and a space which isn't empty. Comes back to the issue of modularity of contributions as well. But bottom line, the people are here (and probably elsewhere in coffee rooms etc) so the conversation happens here. - Cameron Neylon
Exactly. The conversation will happen where the people are. It's up to the publishers to figure out how to harness those conversations. Given the API, and the activity here on FF, would be cool to pull those discussions into the article itself. - Deepak Singh
If you study carefully the test case above, you will see that there are two characteristic features 1) It is easier to start a discussion where the people are (but for that it is enough just to send a link here, and discuss there), and 2) people obviously do not want to disclose their real names under critical comments. This suggests to me that the current PLoS commenting system is wrong in forcing people to register before the post, and not allowing anonymous comments. - genereg
I think its been established pretty strongly now through things like OpenWetWare and other sites that completely anonymous commenting is probably not helpful or desirable in science. Those sites that strongly encourage or require the use of "real names" see little or no vandalism, and it could be argued, a more constructive approach to discussion. I admit to being conflicted about the... more... - Cameron Neylon
But the people here at FF, they _are_ very online persons. They know all details on how to comment and so on. Still, they choose not to comment under their real names, and are very upset when their critical comments appear to be linked to a wider online audience. Afterall, scientific reviews have _always_ been anonymous, and there is no reason why online reviews should not be anonymous... more... - genereg
How do you reach that assumption? I know the real names of pretty much all of them, and most of us have "handles" that are associated with names. Online anonymity is becoming a strict no-no pretty fast. - Deepak Singh
That is why FF is NOT anonymous. But people who feel safe here (perhaps because it is not that easy to search, an so on) do not feel safe to expose their names on the _publicly_ available web site, where their comments will be associated with the article forewer - genereg
"people obviously do not want to disclose their real names under critical comments" What's your evidence for this? Me? I am fine with making critical comments under my own name -- it's not as though I thought the FF thread was magically invisible to everyone but my BFFs. I'd prefer to word things a bit differently in direct comment to an author (specifically, I'd explain why the lack of... more... - Bill Hooker
I am still a little confused by how you can reach that conclusion on anonymous commenting. There seems to be no real evidence or suggestion for that. Yes there are people afraid of online commenting in general, but that's a general problem. Those people don't show up on Friendfeed either - Deepak Singh
The test case above was at the FF. The people there are both _online_ people, and experts, and interested in commenting on that particular article. But they are still afraid to comment on public. - genereg
@Bill, read the last comments in that thead by Ian York - genereg
Ah, missed Ian's last couple of comments -- genereg, I think you're reaching if you are putting Ian's part in that thread forward as evidence for your claims about anonymity, too. I'm all for anonymity being available to those who want/need it, but I don't think it's any kind of answer to why article commenting hasn't taken off. - Bill Hooker
Genereg, I think you are misintepreting Ian's comment (although I'm not sure and I have asked him on that thread). I think he is making a point about asking permission before re-publishing but he makes it very clear that there is nothing "wrong" with re-publishing just that doing it to (perhaps) make a point is a bit impolite. - Cameron Neylon
In addition, I personally, would not comment that article at PLoS One under my real name. One of the reasons would be that I don't want my name to be associated with THAT article. - genereg
In addition, I do know a number of articles which I would like to comment (and I am quite an _online_ person to figure out how to do this) but I don't comment just for the reason that it requires a registration - genereg
I'd guess the difference is to a large extent due to the way PLoS One and FF are set up. PLoS One allows comments, FF is set up for commenting. FF has more comments, but they're also more ephemeral. Comments that are going to sit on my paper should be well thought of and not pesky one-liners. As such, maybe linking from the biophotonics paper to FF was a mistake. OTOH, I'd want all 'activity' somehow linked to my paper, but in a different way. - Björn Brembs
"The test case above was at the FF. The people there are both _online_ people, and experts, and interested in commenting on that particular article. But they are still afraid to comment on public." ... I am not sure how that last conclusion was made. Pretty much all of us (there will always be exceptions) are more than happy to be public with disagreements regardless of forum. It's just that much more convenient to discuss here - Deepak Singh
@Deepak, Pretty much all of us would be happy to be on public with positive or neutral comments, but honest comments on the artticles are in most cases critical... That is why the standard way the peer-review goes is through anonymous systems. - genereg
Key is --- little comments on PLOS, but many here on FF ... because the (trusted) people (in your network) are here, so the conversation happens here. --- How to move this? Backlinking FF on PLOS should be technically possible? Which FF tracks are discussing this article? A little bit like natures, which blogs are discussing this article. - joergkurtwegner
genereg, that's a very narrow point of view and does not reflect my experience. We are providing public peer review, if you want to call it that. As scientists we are quite happy providing "critical" reviews at conferences and posters, it's not like that people are necessarily averse - Deepak Singh
I think jkw has pin-pointed the most interesting question (also mentioned by Bjoern and several others): how can PLoS pull in value from conversations happening elsewhere? I think it would be a great idea if every PLoS article had a "conversations" tab as well as a "comments" tab, and under "conversations" provided links to, or inline versions of, all the commentary online in blogs, FriendFeed, etc etc. A one-stop shop for "who is talking about this article?". - Bill Hooker
There is a point in this that echoes what Eric Weinstein says about "going short" or long on an idea. The concept that peer review fails precisely because there is no personal consequences for rejecting a paper and getting that wrong. Eric uses the language of hedge funds to suggest that people should be required to "unwind their positions" - which absolutely requires identity and... more... - Cameron Neylon
I think PLoS is interested in pulling this commentary in to the article space. It would be a great way of connecting up commentary. I think it is technically non-trivial but it also raises the issue of how you might summarise or aggregate the commentary in a machine readable and parseable form. Sure it is helpful seeing a lot of people saying something is great or rubbish, but how do you present that in a way that makes it possibel to triage 50 papers to find the one you're after? - Cameron Neylon
If you want (noisy) links, just use Google with link:to_article, e.g. . This does not give quality backlinks, and also not any real-time information like FF. So, some additional comment semantics (microblog, blog?), grouping (Wordle?), or central service is required (FF,Twitter). - joergkurtwegner
All our talks about some kind of federated comment system in the past year or so have ended up with "we need a researcherID to incentivize people". That's the opposite of anonymity. Would G Bilder care to comment on how things are going on that front? - Mr. Gunn
You guys don't believe me, but here it is -- a simple solution to the question why people do not comment online articles. Allow anonymous comments (no IP tracking, no registration requirements) and you will get at least 1 comment per 100 views of each article. That is a lot, and enough to get the system working. I am telling this both as an active scientist and as a person with ~10 year experience of online administration and moderation. It is very easy to check this idea. - genereg
I think there's different kinds of comments - some throwaway comments, some are metacommentary, some are spam, and some are thoughtful and considered reviews. The PLoS appspot comment categorization experiment that was done a while back showed this. - Mr. Gunn
PLoS has a hard enough time staying afloat. Aggregating comments like is suggested here would be a full time job for someone over at PLoS. Yes, there are software solutions, but most of them require human editting or verification. FWIW, guest commenting is a must for starting any on-line community. Having to register is a gigantic barrier to building a critical mass of users. Get the guest comments and conversations going first and once the community gels, people will WANT to register. - Brian Krueger - LabSpaces
Nature Network is probably the example they have in mind here, Brian. Am I correct that it takes more time to moderate the craziness in open discussion than it does to assemble aggregated content? - Mr. Gunn
It is clear that in the majority of cases conversations dont natually happen at the journal site itself. Therefore, PLoS would ideally like to aggregate all the externally located conversations that happen *about* a paper, *onto* the paper. In this way, a reader would use the paper as the launching off point - they read it, and then follow links from it to read the relevant conversations. If the 3rd parties allow it, then the text of those conversations could also be imported to the journal site. - Peter Binfield
The only problem is how to reliably link the paper to an external conversation that could have happened anywhere, without any consistent linking protocol, and at any time from the day of publication onwards. They dont all happen on FF I am afraid (some of the Darwinius discussions appeared on Wargaming bulletin boards!). This is a problem that we have some ideas about, and that we are working on... - Peter Binfield
You still don't believe that just removing the mandatory registration is enough to get the comments system working at the journal web site.... Well here is one more argument: look at the web site of BMJ, and compare how much more frequent is commenting there in comparison with PLoS. The ONLY difference is that BMJ does not require mandatory registration for posting comments:... more... - genereg
@genereg: how many man-hours and dollars does BMJ spend on moderation of their comment system? See: Revitalising rapid responses Davies and Delamothe BMJ.2005; 330: 1284 - Bill Hooker
compare: to that is, compare 2% to 18% (of papers commented on in BMC vs. PLoS ONE). - Bora Zivkovic
BMJ is the British Medical Journal, not to be confused with BMC. BMC is the same as PLoS from the point of view that you need to register in order to comment. - genereg
sorry, not meant to imply they are the same, just to point out that commenting on ONE is not shabby and the only available comparison is that to BMC. - Bora Zivkovic
Note also that you don't have to register for BMJ but you do have to send your comment by email, providing an email address and name, current occupation and place of work (including postcode). Perhaps you could try making up fake info and see if it gets published, but I'd say simply registering once under a carefully guarded netonym would be easier and safer. - Bill Hooker
@Bill, I was just able to sumit a post to BMJ with the word test in all fields, and it takes ~30 sec. It's not by email. Their submission form is the simplest form that one can imagine, you can fill whatever, and finally there is a simple antispam filter, that's it. No registration, no email validation. - genereg
Where'd you comment? I bet it won't be published. - Bill Hooker
I did not press the "submit" button, so it would not publish. It takes 30 sec to do everything before pressing the final submit button. As I said, then it depends on the moderation policy, whether the journal has a premoderation or postmoderation, I don't know what they have, both options are OK. - genereg
As far as I can tell it's pre-mod, and I don't think Dr Ano Nymus, email, is going to appear in the BMJ rapid responses any time soon. I'd love to know if they require email validation. To be clear though: I'm in no way against anonymous commenting, even if it does have its problems. BMJ had to tighten its moderation policy considerably, but only after about the 50, 000th... more... - Bill Hooker
"and get the community growing" -- the obvious thing is that the "community" which might be willing to comment on the online articles is the Whole Scientific Community. Most people today get articles from the web, not from the local libraries, so it is not a problem for them to comment online if there are no artificial barriers such as a mandatory registration. Something like 1 comment... more... - genereg
Genereg - I think I agree with you on one point, which is that signon for all these things could be a lot easier. Setting up yet another account is a pain and we need better systems for that. But my belief is, and I think this is backed up by a growing amount of experience, that anonymity in particular destroys trust in conversations and leads to a very poor quality of discussion. In... more... - Cameron Neylon
Cameron, suppose, the comment under the article says "you guys have to reshuffle the axes on Figure 2. He-he :)". You look at the article and realize that indeed the axis X refers to Y and axis Y refers to X, so they should be reshuffled. And you might not notice that without the anonymous comment under the article. Does it make any difference for you, who has made that comment? - genereg
It might make a difference to how much attention I paid in the first place - but my argument is that those helpful comments would be totally outweighed by comments like "man, your colour choices are so bad, which idiot did you get to make that graph?" - or the cost of moderating those out would rise to unsustainable levels. First law of comment forums - you can have anonymous commenting... more... - Cameron Neylon
I think that comments like "man, your colour choices are so bad, which idiot did you get to make that graph?" would be absolutely OK if rephrased "I think the color choice is wrong". The moderation policy may depend on the journal, but in general, both the Netiquette and Scientific Ethics are well-developed things, they can be written down explicitly as the rules for the moderators, and... more... - genereg
I'm guessing we're going to have to agree to disagree on this one. The nice thing being of course that as we are scientists we can hopefully agree once there is some evidence in! :-) I definitely would agree with the argument that we need more experimentation in this space - Cameron Neylon
"First law of comment forums - you can have anonymous commenting or unmoderated commenting, you can't have both" -- In fact, I have seen many online communities, where both anonymous commenting, registered commenting and different types of moderation perfectly coexist. - genereg
definitely some scientists really afraid give a critical comments online, just because of academia and grants system (in US at least) is fucked up (in case if author of paper that you critically commented on will be you peer-reviewer in future...)! For me also could be a problem, because i'm a postdoc and my blog reading some professors(on whose papers i can comment) who going to review my papers and grants in the future. - Alexey
I express some of my thoughts here - - Alexey
I disagree that commenting for scientific analytical blogs should be anonymous, because blog content should be updatable and readers should trust information that they see. In this case it's important to link to the comment associated with particular name in the field to estimate how much we can trust this information. - Alexey
Alexey, I agree on blogs, but blogs is a different story, blogs are mostly for self-promotion and self-expression, while comments on scientific articles are mainly to fix scientific problems. The motivation to fix a scientific mistake is usually strong enough to do this even anonymously. - genereg
If there were an easy solution to this, it would have been solved already. Many, many very smart people have tried to fix this already. I think, like Cameron says, we're more or less waiting for the transition to where online comments matter. To where they're taken seriously, to where they have an effect on the overall profile of your research. To where the argument can be made that... more... - Mr. Gunn
Mr. Gunn, I understand your point about the importance of self-promotion and career track, but I think that commenting online articles has nothing to do with this. - genereg
So you think your blog and your online presence have nothing to do with your career? Why post your CV on your blog, then? Nobody that matters will see it, right? - Mr. Gunn
I don't understand completely why scientists afraid to comment papers online under their real names. I do comment on PLoS and Nature under my real name even i have a some risks as a postdoc. It's everything about your scientific authority. I want professionals in the field to know me. - Alexey
Mr. Gunn, Blog as I said is a self-expression, and self-promotion, but comments at online journals are not. PS. Please read my message concerning your blog post! - genereg
I'll do that, but you probably want to go back through your comments here and remove all the ones where you linked to your own blog. - Mr. Gunn
Alexey, are you sure you can say everything you want there under your name? As you said, you consider some risks for you as a postdoc. Now, assume that your risks as a postdoc are minor in comparison with the risks of a senior scientist, where there are million-dollar grants on stock. - genereg
@genereg , @Cameron - I am not interested in anonymous comments. I am an industry person working in drug development, which is probably one of the most intellectual property sensitive industries. So, anonymous comments? Not for me, even not in my private time ! If you want comments from people in industry, then we seriously need a review mechanism, not only by the blog owner, but a... more... - joergkurtwegner
We have just witnessed a next round of the test case, with my own name not associated with my FF account being found in the internet and posted in a blog article discussing this thread . Not a big deal. However, this opens up a new large series of questions... more... - genereg
genereg, perhaps the misunderstanding lies in the fact that you thought you were anonymous but you really never were. I didn't go searching the internet for your name - you linked directly to your blog from here. There are ways of being anonymous on the internet if that's what you really want. What your doing seems to me the equivalent to leaving your house open and unlocked, telling... more... - Mr. Gunn
Mr. Gunn, I am never hiding my identity, but it is also not directly associated with my profile. This means that I am safe in terms of the search engines, and my real name is associated only with things with which I want it to be associated. That is also true, if you are commenting a strange (wrong) journal article: even if you are right and they are wrong, your name will be forefer associated with that wrong article. - genereg
Unless you got out of your way to make it so, anonymity does not exist, so we should probably just get over it and worry more about being presentable. I'll offer myself up as an example - Search for either William Gunn or Mr. Gunn and try to find something embarrassing about me. Go ahead, I'll wait. - Mr. Gunn
LOL I am too old for these games. And I know Internet. And Science. The real anonymity is impossible even with anonymous peer-review. But there are a lot of reasons to have _some degree_ of anonymity in science and in the internet. It just works like this. It can't work without this. - genereg
genereg, on that last issue I have to disagree. If we want to use the web in general to discuss science, it's very difficult to separate the two. Google is not going to index you separately as a scientist and as a web participant. Well, it might, but managing that level of identity is hard, and one could argue that the two shouldn't be completely separated, just the communities might... more... - Deepak Singh
Deepak, I understand the point. However, here are additnial 5 cents, why anonymous commenting might help. At some point, there was an evaluation of BMC comments, and it revealed, if I am not wrong, only 17% critical comments. while in an anonymous peer-review most of the comments are critical. Thus, even if we forget about the decreased number of online comments due to the registration... more... - genereg
genereg, if this statistics is correct, that show to me how immature the scientists and science online. They afraid to disclose their name and status because of money-grants-career and poke each other by critical anonymous commenting like a kids in the sand box. Be open, be confident in your data and expertise scientists, be able to accept critical comments and reply nicely and be able... more... - Alexey
You are assuming that comments must be critical to be useful. Useful comments can include questions, concerns, and criticisms, and even the latter can be framed properly. I have said this before, and I will reiterate that there is one primary reason for anonymity; that you're afraid of making a fool of yourself in public. I admit that this fear might be related to concerns about your... more... - Deepak Singh
genereg, yea I can tell not everything from my blog, but a lot. I criticize a lot, but if i'm wrong, come and tell me about it. I'll accept and we will find the truth in discussion. I can't tell many things that I don't feel like i have enough expertise and knowledge but I can ask my readers about their opinion based on their expertise. - Alexey
Alexey, this means that you criticize the things which are safe to criticize :) - genereg
Deepak, assume that you are at a journal club in some friendly lab. Now, how many of the questions from there would you dare to ask at the comment section of the online journal? :) - genereg
How many journal club questions would I "dare" ask in a journal comments section? All of them. genereg, are you familiar with - Mr. Gunn
All of them?! good! If this is the case we will soon get the system working :) I did not get your point about - genereg
genereg, all of them. If there is something to say, it will be said, regardless of forum. The language might change, but the questions and comments won't - Deepak Singh
good. unfortunately other people do not behave like this. we have seen it in the example with Biophotonics paper. Many people wanted to say that it is wrong, but none said this at the journal web site.. - genereg
Let me ask this question. If this was presented at a conference, do you think people in the audience would be quiet? - Deepak Singh
not, sure. the question still, is why they don't comment. - genereg
Could it be as simple as they are not that comfortable on the web? They don't comment on Friendfeed either (the ones who do are active everywhere). - Deepak Singh
nope, i discussed this with a couple of active bloggers. they are not at FF, they are active bloggers, and they have seen the article at the journal we site. we discussed it online, that's it - genereg
Do they blog anonymously? and if not, would they blog about this? Sorry if that's been discussed before - Deepak Singh
nope. what's the reason to blog anonymously. it was discussed before. blog is to express and advertise yourself, peer-review is something absolutely different - genereg
I just don't get it. An opinion is an opinion, regardless of medium. To think that the medium somehow makes that opinion different and you are not willing to stand behind your opinion just does not compute in my head, but that's me - Deepak Singh
Just try to think why the anonymous peer-review was invented. - genereg
The primary reason for anonymous peer-review is the elimination of bias. If the reason for anonymous peer-review was to be able to criticize anonymously, then the system would be even more flawed than it is today (and it is flawed). - Deepak Singh
"Several of the other journals published by the BMJ group[10] allow optional open peer review,[11][12][13] as do PLoS Medicine, published by the Public Library of Science[14][15]. The BMJ's Rapid Responses[16] allow ongoing debate and criticism following publication.[17" - genereg
These journal comments that we discuss should have been that "open peer-review" - genereg
Open = No anonymity, otherwise it's not open, and like Neil said, comments and an "open peer review" process are different beasts - Deepak Singh
right. but if it does not work this way, we can try to figure out another way - genereg
That I won't disagree with, but anonymous commenting is not the right way - Deepak Singh
it depends, what is more important for you, the ideas or the people who say them. for me, the ideas - genereg
Both, anonymity, IMO is ripe for abuse. - Deepak Singh
well, as I said, just removing the mandatory registration does not mean a complete anonymity. plus the moderation.... - genereg
Agree that scientific identity is an area with a lot of potential for innovation. The way I see it, we aren't that far apart in intent. - Deepak Singh
Haha, this is what I get for waiting a day to come back to the feed!! @Mr.Gunn for sure moderation is a time consuming job, although I think that aside from blocking spam (and this is relatively easy) that the vast majority of posts will be on topic. Things might get ugly, but implementing a community self moderation system usually works really well ex: add a "Flag this comment" button,... more... - Brian Krueger - LabSpaces
Here is what I think. Never underestimate the number of possible compliance regulations people can violate. There are many of them, and the number is just growing. - - joergkurtwegner
Interesting how the discussion around the original article quickly drifted away from the scientific content and toward a meta-discussion, which was continued here. Could there be something more fundamental at work here? Also, anyone got any hard data on just how unused the PLoS commenting system is? For example, "the average number of comments on a PLoS article is 0.55 - here's how we calculated it." An analysis of that sort could offer new insights. - Rich Apodaca
Rich - There are plenty of examples of deep online discussion of scientific papers that stays on-topic, and doesn't drift off-topic. But so far as I can see, it's mostly happening on blogs. See, e.g., the n-category cafe ( ). - Michael Nielsen
Rich: there's this ( and a couple other workups of the same data. - Bill Hooker
wow, direct critique only 7%. Again as with BMC there is a shift towards positive and neutral comments, probably due to non-anonymity, as opposed to the typical comments obtained during anonymous peer review - genereg
I would be curious to see the age groups for any comment percentage numbers - joergkurtwegner
Another reason may simply be technical: PLoS ONE uses a kind of pop-up window (duuno the tech term for these) that blocks the whole browser. If I am to write thoughtful comments, I usually check some sources relevant to the statements I make, so I do not find this implementation particularly user-friendly. Just now, my browser (Firefox 3) froze after I had pressed "submit" in this window, and I had to redo the rating (fortunately, I had drafted the text in a separate text editor). - Daniel Mietchen
I think there should be a shift towards neutral and positive comment between the peer review process and after a paper has been accepted. If there's no shift, the peer review process isn't doing its job. - Scott Joseph Kennedy
That is true. But in general it seems that in Internet most serious comments to serious articles tend to be critical, because neutral comments do not add anything (so they are close to spam unless they provide some additional usefull information), and writing positive comments is not self-motivating (you spend your valuable time just to say that you agree with something). - genereg
I'm thinking Jorge Cham from PhD comics must have seen this thread. - Mr. Gunn
LOL, that's exactly what the "neutral" comments are. This spam can only happen in the absence of moderation. - genereg
Related thread at StackOverFlow: Why aren’t people rating questions? - Daniel Mietchen
January 11, 2013. Today I have read with great interest a recent article in the Guardian, which also proposed anonymous post-publication peer-review (, and have one essential comment to it. The idea of the anonymous post-publication peer-review was firstly introduced here, at FriendFeed in 2009 (see the... more... - genereg
January 26, 2013. Today I noticed a great new web site which has implemented the ideas that I have proposed above. Ok, three years later it is still not too late :) It would be nice if the authors contact me, because their web site still lacks a couple of essential components that would be needed - genereg
Shirley Wu
A co-worker mentioned to me yesterday that a colleague of his is thinking about starting an online journal club type website for scientists. The idea seems to be discussions about papers, data sets, and other web-publishable materials, from any source, in a central location. It would also have discussions about scientific culture, which made me...
It would be a place where people (students, junior faculty, etc) could learn the ropes of academia and science without the pain and misery that traditionally is required. The differences I can see from existing services is the focus on journal club-style discussions and maybe a low barrier to entry - Shirley Wu from twhirl
But obviously, whatever he ends up pursuing should learn from the trials and tribulations of the many related services out there (including services like FF, which is also discussion-oriented) - Shirley Wu from twhirl
It's easy to immediately discount any proposal that sounds like yet another facebook for scientists, but there are still some interesting and potentially good ideas out there. Unfortunately, people who aren't as familiar with the existence of these tools always think of facebook as the ideal and as a brand new idea if applied to the scientist community. Hopefully I convinced my co-worker otherwise, while still encouraging the more innovative aspects of the concept. <end rant> - Shirley Wu from twhirl
Thanks for doing that. - Mr. Gunn
AcaWiki is built around a very similar concept, and John Wilbanks makes an argument for bringing journal clubs online (cf. ). - Daniel Mietchen
Shirley, Besides AcaWiki (great place to have these discussions, but I'm biased! ) your colleague also might be interested in GradTurkey, a journal-club discussion wiki originally aimed at grad students: - Jodi Schneider
can discussion on AcaWiki be linkable and embeddable for public like you can do on FF? If not, so why don't do journal club on FF? Can't get it - Alexey
my comments on the topic in 08/07 - Attila Csordas
Knol has many journal features built-in. Here is an example of a successful research journal on H1N1: - no name
John Wilbanks mentioned doing journal clubs online in his talk here recently: - Walter Jessen
this topic came up during a discussion today with Mike Eisen of PLoS, re: why commenting hasn't really taken off - his thought is that people are more likely to comment if there's a central place to do it rather than individually at each journal website for each paper (how many of us access papers directly through journal websites except through PubMed anyway?). The whole time I was... more... - Shirley Wu from twhirl
can somebody point to the platform for journal club online better then blog post? It's combine everything - presentation (ppt embedded from SlideShare or Gdocs, video embedded from YouTube/Vimeo...) presenter's opinion, discussion section under the post, embedded comments from FF, ranking of the presentation and number of views. Importantly you don't need to register or get account for commenting, it's public and linkable, moderatable . Whole world can participate. What can be better? - Alexey
@Neil Saunders Were you thinking of JournalFire? We recently updated the site and are looking for feedback. I posted about it yesterday: - John Delacruz
Matthew Todd
Just started a Mendeley group on Open Source Drug Discovery:
Ramy Karam Aziz
Microfluidic co-culture model... surprised that JOVE has no "Share" button @brembs
Jonathan Eisen
Not sure, but something doesn't smell right about this : Twins not genetically identical #Ineverthoughttheywere #Didyou?
Bill Hooker
Open and Shut?: PLoS ONE, Open Access, and the Future of Scholarly Publishing -
This will generate some heat. - Bill Hooker from Bookmarklet
"Although we would be the first to agree that PLoS ONE isn‘t perfect, neither is any journal, as Richard points out – although not until around 30 pages into the article." - Heather Piwowar
I've skimmed most of this now. I think I agree overall with the general thrust at the end but the 30-odd pages of criticism based on a few papers seems a strange way to get there. Or maybe I'm just reading in the conclusion I want to see? - Cameron Neylon
A lot of it feels a bit disconnected and out of date to be honest. I usually find myself nodding along with Richard's pieces even when I disagree and that wasn't the case here... - Cameron Neylon
Sounds like skimming it is the best way to read it :-) the general thrust I think everyone get agree with, some of the arguments seem somewhat odd, indeed. - Björn Brembs
Credit to Richard for elevating the PLoS response to a separate post, rather than leaving it languishing at the end of his long-ass essay. Also, this may be the least of his mighty works, but it does raise very important questions about peer review and pricing. - Bill Hooker
Oh I definitely think he has some important points in there - just unconvinced about the frame he puts them in. And I do believe that costs at PLoS should come down in time - just not convinced that the attack via standards of peer review is the right one. - Cameron Neylon
Yes, that line of reasoning bugs me too. Here are two ways to get actual data on the question: 1, what proportion of papers are published eventually? Iirc, it's around 70% -- in theory, since P.ONE will publish anything worth publishing, it should be around the same as the P.ONE acceptance rate, except to the extent that people are selectively sending their better or worse stuff there.... more... - Bill Hooker
I really wish I had time and access and expertise to do the second study... - Bill Hooker
Interesting idea, pace issues with impact factor but any other metric would also do. The figure of ~70% keeps coming up but I don't know of any good recent studies that bring that figure up to date and check across different disciplines. Second study you propose is an interesting one, if for no other reason than how would you control it properly... - Cameron Neylon
I'm no quite sure what to make of the 42 page doc. I think I made it about halfway through, and then started really skimming. Seems like he wants it both ways. Authors should pay less money to PLoS ONE because is is just peer review lite, and it is a cash cow, but the journal should have higher quality standards and a higher rejection rate. Which way do you want it? Do you want the... more... - Doge Joe
Joe: Sounds like you're talking median, not mean. The average (mean) could be 4+ cites per year with only one out of ten papers getting 4 or more cites. Is the median for PLoS.One paper cites available? If so, that's a much more meaningful number. (Won't comment on the Poynder thing 'cuz I haven't read it all yet.) - Walt Crawford
You can't really use IF for any of these calculations... - Björn Brembs
@Bjoern, that's true, I was being lazy. Eigenfactor might be better, or a simple mean/median/variance of citation numbers. @Cameron, not quite sure what you mean by "control" in this instance. - Bill Hooker
This article is also discussed at - Doge Joe
Marking os I remember to look at this later today when back in my office (wish there was a bookmark this for later feature) - Hedgehog
Heather Piwowar
ok R. It's you and me. Enough of this undocumented spaghetti code silliness. Have inlinedocs, no excuses. ready, set, GO!
Got any recommendations for a starting place (site or book) for a newbie with R? - Brian Westra
Alas I don't, offhand. I've been doing R (badly) for years and I think there are better docs out now, somewhere. Does anyone have a recc? - Heather Piwowar
All I know is that all our R books are always checked out. And I imagine the ebooks get pretty high use too. (Fortunately most of our licences will pay for unlimited use.) - John Dupuis
Brian, there are a few good readings on the website, and the whatever you do, STOP READING, and start using it. Really, pick any R tutorial, and start actually typing what they show, change it, and just use R. That's the best way to learn it. Using R is a skill, not a theory you can learn. Skills just need practice, not reading. - Egon Willighagen
Egon, I agree. I don't retain skills I don't use on a regular basis. - Brian Westra
Björn Brembs
The future of scholarly publishing is bright - if you think long term -
pq -- "The future of scholarly publishing does look bright - just not for publishers." It even looks pretty good for publishers who aren't insanely greedy. :-) - Bill Hooker
I wonder if they've overdone it so much, that the backlash will wipe for-profit publishing from scholarly communication entirely. IMHO they have... - Björn Brembs
@Björn: you quote "...accompanied by an apparent decline in the quality of peer review." The lack of journal / editorial standards should not be underestimated... refereeing would have been very much better, if the editors properly trained and/or corrected them. They don't. Anyone: feel free to post a poll on who ever had his referee report rejected. One layer here is editorial... more... - Egon Willighagen
BTW, coulnd't leave this comment in your blog: STOPPED: KEY_FILES FOLDER NOT WRITABLE - Egon Willighagen
Sorry, Egon, moved servers and haven't ironed out all the permissions yet! Thanks for the info!! Should be working now... - Björn Brembs
Confirmed: it works now. - Egon Willighagen
Thanks, Egon. I replied there (basically agreeing with your point about peer-review standards). - Björn Brembs
Work in a Swedish company? Self-employed American in Sweden needs your helps -
immigration laws are a pain. Hope things work out for Andrew - Rajarshi Guha
yep, I have many stories of immigration laws - pn
Bill Hooker
Goodbye academia, I get a life. – blog.devicerandom -
"Until not so long, I thought that it was worth it. It was something that I had never questioned so far. I wanted to be a scientist since when I was five. I had done everything to become a scientist. I was a scientist in one of the top universities of the world, in one of the top five research groups on the subject. I had won a personal fellowship to fund myself. Most of my self-esteem, of my very concept of self-realization, relied on myself being a scientist. The very idea of quitting academia was a synonim of personal failure." That right there is the engine of the pyramid scheme. - Bill Hooker from Bookmarklet
I've heard more senior scientists dismiss this attitude as a 'typical cynical postdoc, not skilled/smart/hard working enough to make it to tenure'. These same senior scientists were junior scientists in a very different time, usually before the huge expansion of the number of available PhD candidates, where the ratio of supply to demand of graduates wasn't nearly as imbalanced. This... more... - Andrew Perry
Re: the pyramid scheme that BH and AP bring up -- I completely agree and want to add one additional point: its not just that an untenable economic situation has emerged which grad schools sweep under the rung -- its that the community itself seems to look down on those who leave academia to join industry/business or publishing or something else entirely. High rates of failure at achieving tenure at impressive school X would be ok if young students/scientists felt they had viable alternatives - Benjamin Tseng
I agree Benjamin - I've noticed that in many academic institutions career options outside that system are rarely discussed openly, and leaving academia is considered failure (even if someone leaves to do something arguable more useful). Granting bodies usually want to encourage collaboration between industry and academia through special funding opportunities (eg, the ARC Linkage grants... more... - Andrew Perry
some more comments here: and I agree with Andrew .. thats why we should fight against even the language that is used (i.e. "quiting science") - Pedro Beltrao
Mateusz Koryciński
John Dupuis
If you don't have a blog you don't have a resume... -
OTOH, if you neglect your blog as I do mine, does that mean you have a resume but it's crap? - Bill Hooker
I hope not! - Mr. Gunn
I'm not sure what my blog says about me... - Elizabeth Brown
The thing that I like about the post title in this case is that at least it grabs your attention! - John Dupuis
The actual post on Science of Blogging is here: - John Dupuis
Jan Aerts
YouTube - Next-Generation Sequencing Technologies -
YouTube - Next-Generation Sequencing Technologies
Is the presentation available online? - Benjamin Tseng
Pierre Lindenbaum
Champagne ! Our paper is accepted in "Nature Genetics" :-)
Congrats! What's it about? Or doesn't that matter? :) - Egon Willighagen
@Egon, I'm going to wait for the publication of this article before talking about it :-P - Pierre Lindenbaum
Congrats!! - Björn Brembs
I'm glad you got a paper out, but I'm sorry you couldn't get it published in a real journal. - Bill Hooker
@Pierre... ah, embargoed... obviously increases dissemination of scientific results :) - Egon Willighagen
Congrats !!! - Mitsuteru N
science3point0 - The launch of – Please test it out - “A lot of time and money is being wasted by groups around the world duplicating research that has already been carried out. We are a data sharing platform where you can add figures that would otherwise go unpublished. In doing this, other researchers will not...
Victor / Mendeley Team
Deepak Singh
"data science is more than just an opportunity to have fun and make the world a better place — it might even be how you make an honest living!" - Deepak Singh
Andrew Su
GSEA analysis is designed to find pathways in which differentially expressed genes are enriched. I'm looking for publications where the differential expression of a _single_ pathway gene results in altered pathway activity and phenotype. Seems mechanistically reasonable, and presumably these would escape detection by GSEA... Examples or ideas?
Given pathway connectivities, genes with high centralities might be expected to show such an effect - Rajarshi Guha
Very good suggestion, especially as a way to find genes to test. But short term, I'm hoping to find a published example that I can just cite. (Edited the post to clarify that.) - Andrew Su
Heterozygous lethal mouse strains in JAX, about 50 genes, vascularization and imprinting. - John Hogenesch
E.g. +/- Vegf mice are poorly vascularized and embryonic lethal. PMID 8602242 - John Hogenesch
Jan Aerts
Bio and Geo Informatics: ngs / high-throughput sequencing pipeline -
Mickey Kosloff
Productivity shortfalls in drug discovery: Contributions from qualititative, consensus- dependent, technology-driven preclinical science? — JPET -
Jan Aerts
Just submitted manuscript. Fingers crossed...
WikiLeaks cable: No quick fix for pharmaceutical market - WikiLeaks - NZ Herald News -
'The elite journals have a rejection rate, typically, of more than 90 per cent. For no good reason, this rate is used to justify the quality of a journal and becomes a target for others to emulate. Editors have become judge, jury and, mostly, executioner.[...] Where will this end? Perhaps a journal will announce that it has achieved a rejection rate of 100 per cent - nothing by anybody is considered good enough to grace its pages.' - Kubke
'On this issue, business schools are at the cutting edge of bad ideas. It is time for a rethink. Above all, I urge a moratorium on journal-ranking lists. Meekly accepting constraints on where we publish limits academic freedom. It means that what we research, how we do it and what methods we employ are driven by criteria at odds with what is important or interesting. Our careers are dehumanised, our scholarship damaged. This is a spectre whose haunting days should most definitely be terminated.' - Kubke
"I can imagine few better methods of reducing intrinsic motivation, extending managerial oversight and demoralising people. It is part of the commercialisation of the academy, often justified in terms of "accountability". Such is the trajectory on which journal rankings, whatever their original intent, have placed us." - Björn Brembs
"The most lauded journals are based in the US, and reflect the positivist and functionalist orthodoxy that dominates the discipline there. They pay relatively little attention to such problems in management theory and practice as exploitative working conditions, race or ethics. " - Christina Pikas
‘Tis the season… - http://buildingblogsofscience....
…to file my Annual Performance Review. Nothing makes me shiver as much as the Dean’s email reminding us that it is time to file our Annual Performance Reviews (APRs). This year shivering does not begin to express the feeling I got upon receiving that email. What have I achieved this year? ‘Nothing’ was the first [...] - Kubke
Matlab Sucks sometimes !
David Bradley
Paypal pays up, releases Wikileaks' funds -
In the midst of various DDOS attacks, Paypal has moved to release Wikileaks' funds from it's account, after it was suspended late last week for a breach of the sites Terms of Service. - David Bradley
Now, I would be more impressed if they acknowledged their mistake in closing an account in absence of any conviction (anywhere), and reopen the account again. It's not a bank's role to play jury and judge. - Egon Willighagen
Exactly right Paypal. Same applies to the US agency that is shutting domains that the RIAA tells it are pirates without due legal process and before the law has actually come into force. Something similar will happen in UK soon and probably rest of EU. But, that said, P2P DNS will get around that particular problem, at least. - David Bradley
Rajarshi Guha
NASA - NASA to Hold News Conference on Astrobiology Discovery <br /> <i>Science Journal Has Embargoed Details Until 11 a.m. PST On Dec. 2</i> -
NASA - NASA to Hold News Conference on Astrobiology Discovery <br /> <i>Science Journal Has Embargoed Details Until 11 a.m. PST On Dec. 2</i>
Wikileaks, we need you now! - Noel O'Boyle
intriguing... - Jean-Claude Bradley
Mr. Gunn
Underclothes That Display The 4th Amendment When X-Rayed by TSA -
Underclothes That Display The 4th Amendment When X-Rayed by TSA
Mr. Gunn
How did the Lancet publish this utter crap? Every heard of normalization? And why did NPR report on it credulously? -
I came to an entirely different conclusion from the same data - Mr. Gunn from Bookmarklet
NPR has kinda been failing lately. - Mr. Gunn
If you normalize the data, you assess the risk for the individual. That's not what they appear to have been studying. For me, it looks like they wanted to see which drug, as a whole, as the strongest effect on society, as a whole. And there, not surprisingly, it turns out that alcohol does the most damage, because it is the most widespread drug. I think that makes perfect sense and is... more... - Björn Brembs
Good point Bjørn ! However, it's the news-coverage that really sucks here, - the NPR-piece says ".....evaluated substances including alcohol, cocaine, heroin, ecstasy and marijuana, ranking them based on how destructive they are to the individual who takes them.........", which underscores the point Dr. Gunn is making on normalization. - Nils Reinton
Paper is at (subscription required) and (registration required). - Daniel Mietchen
Interesting how they arrived at the relative weights. Anyone willing to try to assess coffee, chocolate, Döner Kebap, salted peanuts or some such on this scale? - Daniel Mietchen
Well, they do admit their data is not 'objective' and that it also ignores positive effects the drugs may have. - Kubke
@Daniel, I would agree, given the criteria they use, it might be interesting to see where something like 'fish 'n chips' would score in this analysis compared to some of the 'illegal drugs'. - Kubke
Other ways to read this feed:Feed readerFacebook