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Jordan M › Likes
Science Commons Symposium – Redmond 20th February - http://cameronneylon.net/blog...
Jordan M, Björn Brembs, Jean-Claude Bradley and 2 other people liked this
Image by dullhunk via Flickr One of the great things about being invited to speak that people don’t often emphasise is that it gives you space and time to hear other people speak. And sometimes someone puts together a programme that means you just have to shift the rest of the world around to make sure you can get there. Lisa Green and Hope Leman have put together the biggest concentration of speakers in the Open Science space that I think I have ever seen for the Science Commons Symposium – Pacific Northwest ...
- Cameron Neylon
Great new blog post by Hope Leman (http://friendfeed.com/hleman) "Book Review : Internet Cool Tools for Physicians" http://blog.nextbio.com/2009...
marlene, Bora Zivkovic, Steve Koch and 6 other people liked this
parents comments are too funny -- may be why I never blog.
- Mickey Schafer
Love the parents' comments :)
- Steve Koch
Re: Scientific citations in Wikipedia - http://iphylo.blogspot.com/2009...
Tom.Pasley and Jordan M liked this
"Based on my experience parsing Wikipedia taxonomy articles, the format used for citing articles varies a lot. Some articles use the {{cite}} templates, some use {{citation}}, some just use <ref> tags without {{cite}}, and some just have lists of references (often recognisable by starting with the {{aut}} template for authors). The {{cite}} template makes parsing the reference relatively straightforward, but without {{cite}} it becomes a world of hurt with regular expressions. I'm trying to catch all these forms. I suspect there is an element of user's knowledge at play. If the user knows about {{cite}} (or sees {{cite}} used on the page and is curious about it), they may use it. Perhaps it's analogous to whether people use reference management software such as Endnote when writing manuscripts -- not everybody uses such a tool."
- Roderic Page
A couple of weeks ago I put together an event called Making the Web Work for Science. There was an excellent panel discussion with Stephen Friend, Jimmy Wales and John Wilbanks moderated by Tim O'Reilly. We were lucky enough to have a film crew and as of today the footage is online! http://www.vimeo.com/6077540
Mickey Schafer, Andy Maloney, Mary Canady and 22 other people liked this
excellent discussion - hopefully some people who are new to these ideas will come across it
- Jean-Claude Bradley
The opening statement by Tim was great. I wish I could have been there, but it's nice seeing Jason representin'! ;-)
- Mr. Gunn
Someday we will all program in Python - http://davidbau.com/archive...
Jordan M liked this
Here is the presentation that William Gunn & I did for the San Diego Biotechnology Network May 28 http://sdbn.org/sdsms Most attendees were fairly new to social media; will post results of survey of them soon. We set up a friendfeed room for them, but not seeing traction so far. Experimenting with Facebook page as well-bring mountain to Mohammed?
Jean-Claude Bradley, novoseek, Jordan M and 7 other people liked this
Cool, when are the survey results being posted?
- Sally Church
Was this the event where I predicted you'd get no bench chemists? Well?
- Matthew Todd
William Gunn & I finally got all the numbers crunched, here is the poll data from the event. N=75. Surprises included number of C-levels we got, Biology discipline most represented, interest in science blogs (future, not current). Most not involved in primary research. Slow uptake on FF/Twitter since event, moving to FB & watching... http://tinyurl.com/sdsmspoll p.s. yes bench chemists in audience (via Arena layoffs ;)
- Mary Canady
Great blog post by Hope Leman http://friendfeed.com/hleman "The Four Musketeers" http://blog.nextbio.com/2009...
novoseek, Pawel Szczesny, Steve Koch and 2 other people liked this
RIN: "retractions at Wiley-Blackwell are now running at more than one a week" - http://www.rin.ac.uk/node/653
Björn Brembs, Jordan M, Lisa Green and Jean-Claude Bradley liked this
Science, the last bastion of disinterested search for reliable knowledge... oh wait. Wish I had more data on this. COPE might have some but all their stuff is members-only.
- Bill Hooker
from Bookmarklet
I wonder sometimes if this sort of thing is bad or good news: bad that there are so many retractions, or good that we're doing a better job of finding them and sorting them out.
- Bob O'Hara
I tend to see it as a positive sign, since it helps to clean up and provides yet another reason to get rid of impact factors. Would be interested to see web-based impact measures coupled to something like http://bit.ly/Hrg4t for retractions and other kinds of post-publication changes to an article.
- Daniel Mietchen
Great blog post by @hleman "Hope, Twitter Search, and the Pursuit of Appiness" http://www.vimeo.com/groups...
Jordan M liked this
"Swine Flu Science: First Wiki, Then Publish" by Carl Zimmer:- http://blogs.discovermagazine.com/loom... This is the most recent example of ONS that I'm aware of. Addendum - Open Science.
Mike Chelen, Pierre Lindenbaum, Jordan M and 5 other people liked this
Also of interest:- "Now, a little over a month later, they’re publishing their results in the journal Nature. Normally we press folks would get a press release about the paper a week before publication, and it would be under strict embargo till it appeared in the journal. This morning, however, I got a press release pointing me to the published paper. And while Nature normally requires you to subscribe to read a paper, the flu paper is published under a Creative Commons license, which means anyone can get it and use it under the license’s terms". NPG, my cap is tipped.
- Graham Steel
Most interesting. From a quick look at the site, it's not ONS (not enough raw data, unless I'm missing something), but this is clearly an open (input restricted to authors, however?), collaborative research project that has paid large dividends on a timely research problem. Would be interesting to hear about the timescale of the work, and how the collaboration went, vs. more traditional closed collaborations.
- Matthew Todd
Mat - it would be interesting to hear from those in the field if they consider this to be ONS. It certainly seems to be very detailed and a wonderful example of Open Science.
- Jean-Claude Bradley
I hadn't actually clicked on the wiki until just there. By my reckoning for those directly involved and *actually doing* ONS, it sure would be worth connecting with this team http://tree.bio.ed.ac.uk/groups... to discuss ONS and Open Science, generally.
- Graham Steel
Excellent idea Graham - I'll contact them
- Jean-Claude Bradley
Top man. I owe you a pint.
- Graham Steel
Graham - just sent Andrew Rambaut an email about the discussion here
- Jean-Claude Bradley
You is now racking the pints up - please stop it ;-) That's great. OT but relevant, following in the footsteps of others http://is.gd/11Qou , I too have now embedded a FF thread into a blog post http://is.gd/11QtO and look forward to seeing further experimentation(s) in this area.
- Graham Steel
Graham - I received a notice that Andrew is out of town for a week so I contacted Samantha Lycett - we'll see what happens....
- Jean-Claude Bradley
Graham et al: Nature (and Nature journals) publish all genome sequences via creative commons licences, have done for a couple of years now. Glad you like the policy. Details are here: http://www.nature.com/authors...
- Maxine
I heard back from Sam Lycett - she responded to my question: Were you providing sufficient raw data for anyone conversant in your field to be able to follow everything that you were doing in real time? Yes I think so. I would expect a talented post-graduate student (e.g. from one of our courses) to be able to follow what was happening. - Since they completed the project I added the link under Archived ONS: http://en.wikipedia.org/wiki...
- Jean-Claude Bradley
Next month there is going to be a great talk by Stephen Friend (Sage), Joi Ito (Creative Commons) and John Wilbanks (Science Commons) in San Francisco. https://tickets.commonwealthclub.org/open...
Mike Chelen, Mr. Gunn, Deepak Singh and Jordan M liked this
I started a group for the discussion of Science Commons and open science in general. There wasn't a group dedicated to open science before and I think it will be useful. Hope you subscribe! Lisa http://friendfeed.com/science... (via http://friendfeed.com/the-lif...)
Roseanne Wincek, diego morelli and Jordan M liked this
Landmark study: DRM truly does make pirates out of us all - Ars Technica - http://arstechnica.com/tech-po...
Jordan M and Nathaniel Thurston liked this
"A UK researcher has spent years interviewing people about whether DRM has affected their ability to use content in ways ordinarily protected by the law. Surprise! It has, even leading one sight-impaired woman to piracy."
- Michael R. Bernstein
from Bookmarklet
Drew Endy's first blog post: State of the OWW | OpenWetWare Community - http://blog.openwetware.org/communi...
Jordan M, Heather, Jean-Claude Bradley and 7 other people liked this
An excellent "state of the OWW" and call to action for all OWW users and potential users.
- Steve Koch
from Bookmarklet
An important discussion - where does it all go? And at the end of the day are we prepared to pay for it?
- Cameron Neylon
See also: http://friendfeed.com/openwet...
- Steve Koch
Thinking...
- Heather
The 2009 Kyle Bryant Translational Research Award sponsored by Ride Ataxia, the Friedreich’s Ataxia Research Alliance and the National Ataxia Foundation http://www.scangrants.com/grant...
Jordan M liked this
Open Knowledge Foundation Blog » Blog Archive » Two new board members: James Casbon and Paula Le Dieu! - http://blog.okfn.org/2009...
Jordan M and Jean-Claude Bradley liked this
Anyone know who James Casbon is?
- Deepak Singh
from Bookmarklet
Great talk next month at The Commonwealth Club of California "Making The Web Work For Science". Stephen Friend, Joi Ito and John Wilbanks. https://tickets.commonwealthclub.org/open... Who is going to be in San Francisco on July 28th?
Richard Akerman, Steve Koch, Jordan M and Ruchira S. Datta liked this
I'll be there! Really looking forward to that talk.
- Jordan M
Social Engagement in Science: Traditional Science, Tradigital Science and Science 2.0 - http://www.abhishek-tiwari.com/2009...
Hope Leman, Maureen, Nicolas Bertrand and 14 other people liked this
Just to point out you wrote "tradigtial science" instead of tradigital. What about including "virtual places" such as SL in Science 2.0 category?
- novoseek
@novo I guess virtual meetings includes everything conference, second life based instances. "tradigtial meeting" instead of tradigital ?
- Abhishek Tiwari
ok, I thought it included it but wasn't sure. Yes, in the picture you wrote "tradigtial" instead of "tradigital" ;)
- novoseek
Ups thanks, its kind of very funny
- Abhishek Tiwari
Maybe the concept was "tragidital"?
- François Dongier
haha good one @François! But seriously, do you find this tragical or digital?
- novoseek
tragical+digital=tragically digital
- Abhishek Tiwari
I used to be number 3 on Google when searching for Salvagno. Now I am last on the first page. At least I'm still there, but yet I'm not happy. Quick, everyone do a search on my last name, click my OWW link, and boost me back to the top! (via http://friendfeed.com/anthony...)
Fossil Huntress and Jordan M liked this
My blog bumps to the top when I'm working and uploading active content. Always wondered what drives you to number one...
- Fossil Huntress
SEO is mystical, but clicking from searches doesn't ring a bell as something that increases your number. It seems to be based more on content updating, links in, and keywords in your title and description tags.
- Brian Krueger - LabSpaces
I also thought there was some aspect of association. IE clicking a link from a search would bring you higher to the top of that search. As for updating and all the other that too makes sense, although on my personal blog I guess I need to use my own name more because it has almost no association with me (search wise). I also can't seem to get it to come up in a search of its own name. It's really weird.
- Anthony Salvagno
Make sure your title and description tags include your relevant keywords. The keywords tag is pointless. I'm not sure if you can edit that info at OWW though. Search my name. My profile at my site is the 6th link down, only beaten by linkedIn, zoominfo, briankrueger.com and wikipedia, which make sense.
- Brian Krueger - LabSpaces
The important thing is your open notebook is the #1 hit for: anthony salvagno science !
- Steve Koch
Having people click on your link won't bump your position; doesn't work that way...
- Eric Miltsch
This is a little spammy - can you restrict this stuff to your feed in the future (instead of using the life scientists/science 2.0 pages?) And yeah, don't sweat search positions - write good stuff, and the links and pagerank will take care of themselves.
- Chris Miller
+++1 for for Steve
- Abhishek Tiwari
Thanks, Abhishek...Chris, I think that's a bit hair-trigger on the spam ID. I know you don't know Anthony, but he's a dedicated practitioner of open notebook science and has some friends in this room who may appreciate the light-hearted change of pace. Plus it did generate some useful discussion.
- Steve Koch
@Steve Ah - okay. I didn't recognize the name, and anytime I see SEO-type stuff mentioned, it raises a warning flag.
- Chris Miller
PLoS ONE: How Many Scientists Fabricate and Falsify Research? A Systematic Review and Meta-Analysis of Survey Data - http://www.plosone.org/article...
Khader Shameer, Jean-Claude Bradley, Bill Anderson and 9 other people liked this
fabrication, falsification, “cooking” of data,
- Abhishek Tiwari
from Bookmarklet
As if the Merck / Elsevier fake journals didn't shake my belief in our system of science enough...
- Jordan M
Doh... Right after I blog about how we need to trust science more :P... Well, I did end by saying "science is a human endeavor" - it has its share of bad apples
- Shirley Wu
"A pooled weighted average of 1.97% of scientists admitted to have fabricated, falsified or modified data or results at least once -- a serious form of misconduct by any standard -- and up to 33.7% admitted other questionable research practices. In surveys asking about the behaviour of colleagues, admission rates were 14.12% for falsification, and up to 72% for other questionable...
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- Bill Hooker
amazingly like the first hundred years of anything resembling the hallowed halls of a church, too much power/ego at stake. too bad they think the reputation won't be at risk
- Lane Rapp
"A pooled weighted average of 1.97% of scientists admitted to have fabricated, falsified or modified data or results at least once –a serious form of misconduct by any standard– and up to 33.7% admitted other questionable research practices. In surveys asking about the *behaviour of colleagues*, admission rates were 14.12% for falsification, and up to 72% for other questionable research...
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- Iddo Friedberg
The Daily Mail headline from tomorrow: "Scientists admit to making up results and wasting your tax money on prostitutes."
- Mr. Gunn
Bill, I've never heard the argument articulated about the field only rewarding "First" -- do you think there's a way to productively reward second, third, etc?
- Benjamin Tseng
That's one of the topics that keeps coming up in this and the Science2.0 room. Recognition for peer reviewing, publication of negative, confirmatory and incremental results, credit for software and database development... there are a number of ways that the emphasis on First Place could be reduced. There's always going to be a certain kudos that comes with being first, but it's...
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- Bill Hooker
It was slashdotted: http://slashdot.org/submiss...
- Bora Zivkovic
It's out of the queue and into /. proper: http://science.slashdot.org/story...
- Bill Hooker
Main Page - GMOD - http://gmod.org/wiki/Main_Page
Khader Shameer, Michael R. Bernstein and Jordan M liked this
"GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. GMOD tools are in use at many large and small community databases."
- Mike Chelen
from Bookmarklet
Will Francis Collins be the next NIH director? I'm taking a poll on the NextBio blog. Please come vote and see how others are voting. http://blog.nextbio.com/2009...
Michael R. Bernstein and Jordan M liked this
There are some interesting comments on the blog about Francis Collins -I am surprised that they are mostly negative.
- NextBio
You're surprised??
- Jordan M
These questions were asked on the blog and I don't know the answers: "Just what control does the director of the NIH have? Does the director have the power to dictate whether or not other researchers can work on stem cells?" Can someone explain what powers the NIH director has?
- NextBio
Great story re Steve Blank's Customer Development Process and Nassim Taleb's "Fooled By Randomness" : http://bit.ly/13jDFI (see reason #3). - http://twitter.com/telanon...
Jordan M liked this
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: http://friendfeed.com/the-lif...
Noah Gray, Jordan M, NextBio and 29 other people liked this
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...
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- 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...
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- 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...
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- 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...
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- 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. http://www.google.be/search... . 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.http://scintilla.nature.com/node...
- 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:...
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- 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: http://blogs.nature.com/wp... to http://blogs.nature.com/wp... 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 no@thanks.com, 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...
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- 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...
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- 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...
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- 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...
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- 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...
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- 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 - http://hematopoiesis.info/2008...
- 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...
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- 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 http://friendfeed.com/genereg... 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...
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- 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 http://synthesis.williamgunn.org/2009... . Not a big deal. However, this opens up a new large series of questions...
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- 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...
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- 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...
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- 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...
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- 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...
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- 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...
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- 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 http://researchblogging.org
- 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 http://researchblogging.org
- 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" http://en.wikipedia.org/wiki...
- 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,...
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- 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. - http://ff.im/3haYq
- 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 ( http://golem.ph.utexas.edu/categor... ).
- Michael Nielsen
Rich: there's this (http://blogs.nature.com/wp...) 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. http://bit.ly/9oBAM
- 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? http://stackoverflow.com/questio...
- Daniel Mietchen
Interesting blog post by my friend Brandon : "New Computing Pioneers? Not Really!"
http://www.brandonallgood.net/blog...
Ruchira S. Datta, Khader Shameer, Steve Koch and Jordan M liked this
Today, I read the cover article of Chemical & Engineering News entitled New Computing Pioneers and was overwhelmed at how much the article touched on the many of the things I have been working on and how much credit it pays to (in my honest opinion) undeserving Big Pharma. The author tries to paint a picture of how slow-to-innovate Big Pharma is defying its stereotype by embracing cloud computing. From my perspective, they are just the next big industry to realize some of the potential of cloud computing and are now dipping their proverbial toe in the cloud. What they claim to have done in the article isn't all that innovative.
- Lisa Green
PHD Comics on science comment sites: http://www.phdcomics.com/comics... (via http://friendfeed.com/the-lif...)
Jordan M, Ricardo Almeida, Thomas Lemberger and 10 other people liked this
Pep Rally - http://xkcd.com/588/
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"You know, pep rallies weirded me out in high school, and they've only gotten creepier in retrospect."
Check out this great post about science blogging by Jean-Claude Bradley "Is it becoming dangerous NOT to blog?" http://blog.nextbio.com/2009...
Patricia F. Anderson, Allyson Lister, Jordan M and 8 other people liked this
one more related post- Scientific Blogging: Ignore It and Be Ignored? http://depth-first.com/article...
- Abhishek Tiwari
@2ndlife: Not directly chemistry but closely related is the Embryo Physics course : http://slurl.com/secondl... by Richard Gordon (every Thursday at 2-3pm Pacific Time). I will talk on MR imaging and spectroscopy (so yes, a bit of chemistry, too!) of frog embryos on July 16.
- Daniel Mietchen
@Abhishek Tiwari I really liked that Scientific Blogging: Ignore It and Be Ignored? post. Anyone who enjoyed Jean-Claude's post will most likely be interested in it. Thanks for putting the link in these comments!
- NextBio
Nice post. I agree in general. However, the argument “The only thing that matters is that at least one of your competitors is willing to blog their research and that the traditional journals in your field are willing to accept blog posts”, this argument requires more thinking. In fact, a blog post can not be used to prove the priority of your idea, because as a web site owner, you are...
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- genereg
Would be useful to have a service that can vouch that a blog post (or part of it) existed at a given moment in time. Should be simple to implement (e.g. using a SHA hash); the hard part would be getting people to trust the integrity of the service...
- Eric Jain
"a blog post (or part of it)" - here is a tricky thing, would you then prohibit editing by the author? I am editing my posts several times normally...
- genereg
If you edited a post, you'd loose the ability to prove that your post existed prior to the edit. Unless your blogging system supported versioning, in which case you could submit versioned URLs to the service (could write a plug-in for the blogging system to do that automatically). This way you could "prove" the entire history of your post.
- Eric Jain
That's one reason the UsefulChem project switched to wikispaces from a blog setup -- wikispaces supports versioning, so it doesn't matter how often you edit, you always have a timestamp for each version. Plus, the timestamp is not under author control.
- Bill Hooker
Ok, but personal blogs _are_ under author control
- genereg
Even if the author isn't in direct control: How can we know that the organization that happens to host the versioned resource has a policy to not let anyone manipulate the version history? And do we want to trust them? A dedicated verification service might also have trust issues (especially while it isn't well established), but it can offer a single set of policies that apply to any web page regardless of where it is hosted.
- Eric Jain
Links are also timestamps: if you don't trust Google (wikispaces) not to let me manipulate their versioning system ( !), or if I'm using a blog, how about the date established by various links to my pages? Or the datestamp in the Wayback Machine? By the way, what's your trust rating for traditional notebooks, which are pretty evidently available for manipulation but which, as I understand it, are the basis of many a patent claim?
- Bill Hooker
Links just prove that a page existed, not that it contained specific statements. I don't know who is behind Wikispaces - for all I know it could be your aunt :-) The Wayback Machine might be fine (wonder if it has been used in court?) but you can't rely on them picking up your pages fast enough (or at all). Lab notebooks can be faked so I wonder if companies follow certain procedures to make them more credible in court?
- Eric Jain
You're right about links, although they can contain context ("check this out" says nothing, but "hey, Eric just discovered the kinase responsible for blah blah blah" is evidence). It's not as easy as I thought to find out who is behind a service like wikispaces -- I should have done it sooner, turns out I was wrong all this time, Google has Google Sites and wikispaces seems to be a...
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- Bill Hooker
There are standards for paper notebooks: each page dated, signed and counter-signed; carbon copies; no erasures or removals; and so on. This conversation is making clear that development of similar (eventually court-tested?) standards for electronic lab notebooks is going to be necessary... I wonder what developers of existing ELN software are doing about this issue?
- Bill Hooker
What about third-party hosted backups? They could offer a verification service at the same time. Might be a business model in there.
- Bill Hooker
I suppose backup companies could offer such a service: If you told them which files you want to make publicly verifiable, they could e.g. show the hashes and timestamps of these files on some web page or (for an extra fee) in notarized documents. But this doesn't seem convenient for blog posts, wiki pages or even more fine-grained things such as these comments. Neither is it suitable for material that you don't want to give to *any* third party.
- Eric Jain
"material that you don't want to give to *any* third party" -- Thinking further, don't some biotech and pharma companies use electronic notebooks? They must have developed provenance protocols and standards to go with 'em.
- Bill Hooker
this discussion is exactly why I have been pushing for a few libraries to archive our Open Notebooks and all associated files http://usefulchem.blogspot.com/2009...
- Jean-Claude Bradley
We have received some spidering code from Will at ChemSpider and Andy is in the process of integrating it into the ONSbackup tool we are currently using: the result will be that anyone can set the code to run as a Scheduled Task on Windows and automatically archive everything - all we need is a few librarians to agree to host
- Jean-Claude Bradley
But even without the distributed archive, someone who uses blogs and wikis routinely to record their work has a deeply interconnected web of documents that chronicles their work - you might be able to fake a single blog post timestamp (with third parties like Blogger I still doubt it would be that easy given their internal record keeping) but you can't fake an entire web of records on third party platforms, especially if there are a bunch of people who follow what you're up to
- Jean-Claude Bradley
Creative ways to semantically enrich an Open Access PLoS research article - http://everyone.plos.org/2009...
Steve Koch and Jordan M liked this
That's very cool. I hadn't appreciated until now that that kind of thing was possible due to whatever PLoS licensing is. I guess it's a CC attribution license?
- Steve Koch
Steve, CC-BY: http://www.plos.org/journal...
- Bill Hooker
BBC NEWS | Science & Environment | Simulated brain closer to thought - http://news.bbc.co.uk/2...
Marcus5s, ozgur koca, michael sean wright and 11 other people liked this
"A detailed simulation of a small region of a brain built molecule by molecule has been constructed and has recreated experimental results from real brains."
- Abhishek Tiwari
from Bookmarklet
This is incredible, does anyone have a link to a paper explaining how they did this? BlueGene is immensely powerful, but given the difficulties we have simulating single-celled bacteria, I wonder how they were able to get a molecular simulation of an entire brain region!?
- Benjamin Tseng
@Benjamin try this talk from the 2008 Neuroinformatics conference. Henry Markram explains bluebrain. http://neuroinformatics2008.org/congres...
- Christopher Harris
Without really knowing the details, I think it would be a safe bet to say that it is not really "molecule by molecule". More likely, they have tacked on some known biochemical pathways for e.g. long-term potentiation onto the electrophysiologically based neuron models.
- Mikael Huss
@Mikael it's not molecule by molecule but Blue Brain is by far the most comprehensive cortical modelling project out there. it's a lot more than just a few known pathways, they actually try to get dendrites and synapses to exactly where they 'should' be, far as I understand.
- Christopher Harris
@Christopher you are very correct that at just now its not at molecular level but next phase is molecularisation where they will add all the molecules and biochemical pathways to move toward gene level.
- Abhishek Tiwari
I for one welcome our new silicon overlord..
- Christopher Harris
Thanks @Christopher, and I'd call you a traitor, but who am I kidding, I already have an overlord -- he's called "Blackberry"
- Benjamin Tseng
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