The UK still uses lots of imperial units - miles, pints, stones.
- Matt Hodgkinson
we are special, Bill. The US government tried to make us use the metric system back in the 70s and the only change that resulted was the 2l bottle of soda. I've noticed metric measurements are steathily creeping into product sizes here if they can make the container slightly smaller than the US measurement size so no one will notice.
- Elizabeth Brown
The UK has been in process of conversion to metrics for decades now. I'm guessing it has officially stalled, although the EU is doing its best to force us (so jam comes in 450 gm jars now... yes, that makes sense!).
- Chris Rusbridge
While I was living in Australia, we converted to the metric system in a VERY short time period, maybe 2-3 years. Sometimes in phases: first "Tomorrow will be 100 degrees (that's 38 Celsius)", later "Tomorrow will be a Very Hot 38 Celsius". Road signs were changed from miles to kilometres in about a month. It was surprisingly painless. I remember the retort from a 80-year-old friend when someone helpfully translated 600 Ks to 400 miles. "Young man" she said "don't confuse me"!
- Chris Rusbridge
In graduate school, I noticed international students getting overly worked up over the issue. I think a big part of it was mixing up need for metric system with the ease of decimal system and scientific notation. There no reason you can't say a kilopound. Or 1 milliinch. And it's not like you ever have the right allen wrench handy, no matter whether it's 4 mm or 3/16 inch.
- Steve Koch
A few years ago, one of my Swedish friends quipped (words along these lines) "Is it true that the you in the UK are going metric, inch by inch"?
- Graham Steel
@Steve milliinch is a bad example. machinists have long used mils as a unit of measure.
- Christina Pikas
It's not the kilopounds that are the issue, it's the decipounds. They just don't relate to the next smaller size measurement (ounces) cleanly. I wish we could just do it and be done with it, but the way some people here think anything proposed by the government is an evil plot of some sort (vaccines, CFL bulbs, environmental measures of any sort, I could go on forever) I'm not optimistic this will happen anytime soon.
- Mr. Gunn
@Christina: yes, but that one kills me -- because it's not metric, I'm not expecting the SI prefix, so my poor brain goes on sound and expects one mil to be one-one-MILlionth of an inch. This confounds me on a regular basis since I moved to industry.
- Bill Hooker
And why hasn't the mere name of the system -- "imperial" -- caused it to be tarred, feathered and run out of the US on a rail? Is it because the alternative is the Système international d'unités and we don't want no truck with no furriners?
- Bill Hooker
Yeah, if it were called New American Units I think it would get much better traction. SI? That's not even in English! (note: I've heard those exact words spoken before by otherwise smart people)
- Mr. Gunn
@ Christina, that's exactly what I was thinking of. I did a lot of machining in grad school and really didn't care whether it was metric or imperial. I did, though, for a while get thrown off by "mils," since I was thinking millionths not thousandths. Oh, Now I see Bill had the same trouble. :) I really do think people confound the issue of decimals with SI versus imperial though. The stock market changing from fractions to decimal helped a lot. :)
- Steve Koch
@ Mr. Gunn, my scale weighs me in decipounds and it works fine. I only care about ounces when I'm at the bar or when a friend emails me baby stats and I have to convert to decipounds in my head. I run 10K races just fine. What's the big deal?
- Steve Koch
Conversation with police station in Connecticut (pre Internet): 'there is a suspicious person in the parking lot'; 'please describe him' ; White, about 1 m 70, 80 kg'; sorry, I don't know what that is- if you can't provide details in feet and pounds we cannot help you' - never bothered to call again
- Kubke
from iPhone
I also rethreadthread all my American rigs since they wouldn't fit new Zealand screws :)
- Kubke
from iPhone
Technically, the US does use the metric system, but also uses foot-pounds. Elizabeth: 2L sodas are hardly the only example. 3/4 liter wine? 1.75 liter booze? Lately, sigh, 1.75 liter orange juice... Still, guessing foot-pound won't go away in the US within my lifetime.
- Walt Crawford
Why do we use gallons, feet, and dollars and cents? How were these measurements created? Why do we not use the metric system, and why do so many cities and states have grids visible from the ground and the air? To answer those questions and more, British historian Linklater brings to life the creator of the system we use today, a rector named Edmund Gunter, along with a host of major...
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- Thomas Page
No mention of friendfeed, so what about writing a correspondence piece on this? It could be based on http://ff4s-paper.wikidot.com/start and perhaps also put the recent NIH grant for a "Facebook for Scientists" ( http://ff.im/beKk7 ) in perspective by providing an overview over existing tools along these lines and why they are not widely used.
- Daniel Mietchen
http://www.cell.com/authors... / Correspondence: "The Correspondence format provides our readers with the opportunity to respond to an article in Cell—either a research article or Leading Edge article—that has been published within the last 2 months. Correspondence should be no more than 900 words in length with up to five references and should be of interest to the broad...
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- Daniel Mietchen
Now that sounds like a good idea! I'm all for it - especially mention the gazillion "facbook for scientists" already out there.
- Björn Brembs
333 words so far, and once the generic FF description and some highlights from the spreadsheet are in, we will be near the limit. So probably no time to dwell on fb4sci, though I would still like to mention the NIH grant in the hope that those people will build on the ideas we lay out.
- Daniel Mietchen
Maybe steer away from a "but we want to talk about friendfeed" towards more "there is a much richer set of tools out there...and here is a good example..."? Might mean the Fb4Sci stuff can get squeezed in?
- Cameron Neylon
I would actually prefer the Fb4Sci stuff in there, and the article would be more balanced if we were to name a few more services that offer microblogging (I listed some in the Organization part of the document). FF can then be described in two sentences as a particularly useful example because it provides hierarchies of threaded conversations in which the most current and the most popular entries compete for the top of attention.
- Daniel Mietchen
Correspondence has to be submitted within two months, so we got four weeks to go if we are to submit something on the matter. Perhaps we can indeed expand this into a general overview on the potential of web 2.0 stuff for science. To this end, I just started a vote on the "open science breakthrough of the year" at http://ff.im/cidKG .
- Daniel Mietchen
thanks guys - a very interesting read (the paper, these responses, the etherpad document). I've added a couple of possibly-relevant points to the etherpad doc. :)
- Allyson Lister
...bumping to remind me to try and do something about this before deadline...
- Cameron Neylon
To those coordinating this: let me know if you need any extra help with anything...
- Allyson Lister
Allyson, help with shortening the FF part and with adding in something on the non-FF alternatives would certainly do something good to push things forward at this stage. Thanks!
- Daniel Mietchen
Edited a bit and tried to merge the new contributions into the draft. The word count for the FF part now stands at ~570 excluding FF real science examples. I still don't see how we can give an overview of more than one of these services and accomplish anything better than a boring enumeration without spirit. On the contrary, people will just get the impression that scientists can't make...
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- Björn Brembs
Thanks, Pierre, was already mentioned. Just added some examples from this spreadsheet. Word count is now at 760. Tasks remaining (if you agree on the general structure): polishing and final, concluding paragraph. Tasks remaining if you don't agree: re-write :-)
- Björn Brembs
have removed a few words, tightened things up. will do more as time permits
- Allyson Lister
953, so some trimming needed. Mentioned the NIH grant in the roundup section. Which references to take?
- Daniel Mietchen
Good job, Daniel! I think the references are fairly clear, most of them are in the text already (i.e., papers from FF). We have until December 30 to get it all finalized, so we have some time, but I'd rather get it there sooner than later. I think a few more runs of polishing and honing and we should get the final author list together and submit. I suggest everybody who wants to be an author leave the URL to their FFfeed at the end, that way readers get an idea of what FF looks like.
- Björn Brembs
What about signing with a group pseudonym (something like D H J Polymath; http://arxiv.org/find... ) and a link to this thread or the etherpad?
- Daniel Mietchen
I have inquired with them whether links count as references.
- Daniel Mietchen
What about the title? "Should you be sharing science online?" would be my favourite but it is not reflective of the current emphasis. Any suggestions?
- Daniel Mietchen
Pierre - good one. Perhaps add FF as initials?
- Daniel Mietchen
BTW, the doi does not resolve - anybody has the correct one?
- Björn Brembs
I like Clay's idea for a title: "It's not information overflow, it's filter failure " :)
- Allyson Lister
884 words, and a few more slight tweaks. This means we could probably fit an entire sentence about other approaches' existence, if we wanted :)
- Allyson Lister
Right now this sentence is a mixture of DOIs & links: which to use? : "Such conference coverage has even received direct (e.g. ISMB09 http://www.iscb.org/ismbecc..., BioSysBio09 http://dx.doi.org/10...) or indirect (e.g. ISMB08) support from the conference organizers, see e.g. http://friendfeed.com/ismbecc... ." We can convert them all to links, & save some of the 5 publications, but all three examples here have papers associated with them (well, ISMB09 paper is accepted)
- Allyson Lister
Ah - actually it looks like the ref we would use for ISMB08 is actually ref 1 - am I correct? There isn't much detail in ref 1 yet. That could solve part of the problem
- Allyson Lister
I'd also like to find that out, but the DOI does not resolve (for me?). Haven't looked at ref1 yet, to determine if it's redundant.
- Björn Brembs
Sorry - yes, @Daniel, the DOI seems broken, but the genomebiology link is the correct one. If we're limited for references, we could just link to the FF room, which is http://friendfeed.com/biosysb...
- Allyson Lister
We have 5 references and thus I added Allyson's to make it 5 :-)
- Björn Brembs
Question as to whether its advisable to include reference to the RW room. I think someone raised this somewhere but I can't see the discussion now.
- Cameron Neylon
Otherwise made a few very minor changes
- Cameron Neylon
@Cameron - yep, a few of us have brought up that point (me and michael and some others I think in the etherpad doc). I'm happy to go with whatever the owners of the room, or the general consensus, wants :)
- Allyson Lister
RW room discussion is in the header of the document. IMHO there are several crucial reasons for finally going public: it's a grey area probably still fair use; more subscribers mean more access; readers will see the usefulness of this room, even if they don't get any of the other features; the kinds of hoops we have to jump through to get access need to be made public and the room has a significant record now.
- Björn Brembs
I think we need to drop ref 6 since we only have 5 and it's not a journal article, correct?
- Björn Brembs
With Etherpad deleting everything by March 31, we should think of ways to archive existing pads - particularly relevant for this one, as it was meant to be citable. As far as I can tell, none of the currently available options preserves the version history, so if we want to have that, we should do a screencast.
- Daniel Mietchen
Indeed, we need to think of something!
- Björn Brembs
Incidentally, the threat of such services disappearing certainly contributes to the hesitation of people to adopt social networks, and the best ways I see to cope with that problem is to have either open standards on data portability, or - better still - social networks (or at least one of the most suitable ones) that are built entirely open source platforms, with open configuration (and of course data portability too). Any suggestions on whether and how this could fit into the concluding paragraph?
- Daniel Mietchen
Isn't it already in there, sort of? Where we write that these tools are in development and NIH funded?
- Björn Brembs
from iPhone
Haven't seen mention of open source and open standards in the news on these NIH grants, so it may be worth making more clear that this is needed.
- Daniel Mietchen
Upon feedback from Graham, I took the RW reference out. Still think some mention of Open Source would be good. http://www.nih.gov/news... does not mention it. 816 words.
- Daniel Mietchen
Can we be part of that feedback, please? I find the RW functionality so convincing for non-social web users that I fear the whole article might be wasted, i.e, preaching to the converted, without this component.
- Björn Brembs
It was in a DM that I just forwarded to you (dunno whether that works), and I asked him to comment here too.
- Daniel Mietchen
Did anyone manage to do a screencast? I could try and do that today if its useful? But maybe better to wait until you feel is finished?
- Cameron Neylon
I think we should wait until it's basically submitted.
- Björn Brembs
Nothing wrong in testing, otherwise I'd also wait till it's submitted. @Björn - sent you screenshot.
- Daniel Mietchen
I'll comment once I get back form work (only have internet access here during lunch hour).
- Graham Steel
Right. 1) Having consulted with Bill, we have (the same) mixed views vis a vis raising the visibility of the RW room. 2) We don't feel that we "own" the room though, it belongs to everyone who uses it. 3) We agree that a poll should be set up for subscribers of the RW room to vote on the issue of whether or not they feel it appropriate to raise visilbility of the room outwith FF. 4) The poll is http://www.micropoll.com/akira... and I'll post a link to it in the RW room shortly.
- Graham Steel
Apart from inclusion of the RW room, the title has not been decided yet. Two suggestions are in there now (I threw away my older one).
- Daniel Mietchen
Also, what about the "like=bookmark" discussion? I would like to see that paragraph go back in.
- Daniel Mietchen
I thought that like=bookmark was clear from the context? If not, then it should be easy to add a sentence to make it explicit.
- Björn Brembs
Björn - see chat bar - Michael was not comfortable with the notion. Any other opinions? Also turned Shirky quote from title to quote and set the title to "Social filtering of scientific information - a view beyond Twitter".
- Daniel Mietchen
Besides, FF search has now been unusably slow for weeks, so I wonder whether we should take this formerly excellent feature off the draft. See also http://ff.im/cO3Jw .
- Daniel Mietchen
Two weeks left to submit. I plan to do it on Sat (Dec 19) around noon UTC. Still to address: RW room and perhaps ephemerality of non-Open Source services like FF. I think I saw somewhere that FF have released (part of) their source code, or plan to do so. Anyone know details?
- Daniel Mietchen
Added "the permanence of services whose source code is not public" as an unresolved issue. brushing welcome. What about the RW room?
- Daniel Mietchen
Also, authors need to identify themselves in the document, or they will be missed. Academic affiliations and FF feeds, please!
- Björn Brembs
Like the current version a lot! Also the source code permanence point was important! We should get it ready, clear authorship and author order. My suggestion is Daniel in front, me in the back and whoever feels should have a place in the middle, but I'm flexible (or does author order matter here at all?). From Bill's argument, we should leave the reference to the RW room in, but I'm also flexible there. If there are no storms of protest now, let's keep it the way it is.
- Björn Brembs
I did some more brushing - 899 words now without the title (spot landing). As for authoring, I would really like to go for a group pseudonym (as explained above), but the submission process will probably ask for the usual contact information (incl. email) anyway. Order does not matter to me. Will check back in about 36h, with the intention to submit.
- Daniel Mietchen
I was only pointing out that if you mention the RW room at all, you might as well name it. The poll stands at 41 votes (~25% representation, but it seems to me that there aren't many more than 41 really active contributors/users). The tally is No - 56%; Yes - 32%; Unsure - 12%. I don't think the piece loses much by deleting the mention of the RW room, and it seems to me that the users prefer to continue to keep quiet for now.
- Bill Hooker
I tend to agree with Bill. It seems to me that mentioning (and in doing so effectively naming) the RW room is not what users (that cared to vote) want FULL STOP
- Jan Wessnitzer
from iPod
(1) The point of the letter is to attract scientists who are not using social media for their work to FF. As far as I can tell, the one single thing that everybody can profit from that doesn't already exist in mailinglists etc. is the sharing of papers. Moreover, this is also the one single aspect that touches every single reader, as nobody has access to all the literature. So while it...
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- Björn Brembs
(2) This has been mentioned before, but I see no reason why one would have any interest other than supporting closed access, in keeping quiet. The purpose of the room clearly is to 'document', so nobody in his/her right mind would think that their actions remain anonymous. This means that everybody participating must have been well aware that one day this documentation will be...
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- Björn Brembs
(3) I have now voted often enough to skew the results to more than 50% 'yes'. Who can verify that this has not occurred before, on the 'no' side?
- Björn Brembs
Bjoern, I do agree with your arguments. W.r.t. (3), I was merely trying to argue that the vote should be respected (if it were representative). Allowing multiple votes clearly screwed that up beyond repair! ;)
- Jan Wessnitzer
BTW, I voted 'yes' and maybe the only way to do this now is to vote openly here in the Forum!
- Jan Wessnitzer
@Bjoern: "I see no reason why one would have any interest other than supporting closed access, in keeping quiet" -- are you going to pay my legal bills for me, if I get sued? That's a completely serious question. I'm one of the heaviest suppliers of papers in the room -- if anyone is targeted, I certainly will be. I have said many times that I don't think I am doing anything wrong OR...
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- Bill Hooker
@Bjoern, cont'd: I see no reason to think that (before you fucked it up :-) ) the vote was not representative, which means that most of the RW room users were less willing than you to take up arms against their closed-access oppressors. Judge that as you will, my friend, but some of us have limited resources. If even one publisher sends even one cease-and-desist letter to FriendFeed we...
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- Bill Hooker
@Bjoern, cont'd: I fucking HATE that I have to make this calculation. I would rather publish and be damned -- if the publishers do send lawyers, mount an international campaign in defense of the room and its users and bring their shitty empire crashing down around their beancounting ears. But I have my newly acquired all-American cowardice to consider: I have no health insurance and my...
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- Bill Hooker
P.S. I do not really think I can be accused of "supporting closed access"... merely of refusing to fight it to -- not my, but my family's -- last drop of cash...
- Bill Hooker
I cannot sit here and say nothing in light of recent input. I'll be brief simply by saying, 'as Bill and D0r0th34 say(s)'. I too am not willing to put my livelyhood on the line over this (single) issue. All my (OA) eggs in one basket re. this one? I think not.
- Graham Steel
IMHO, the 'no' voters here are blowing the matter way out of proportion. I'll try and put it back into proportion, which may or may not work :-)
- Björn Brembs
@Neil: Good point. I think it may not be all that much of FF for us, but for people not using social media for their work, it may well be *the only* useful thing they can see in this article. That's one of the reasons I'm fighting for it to remain in the letter. I agree, for anybody who is already using this technology, the RW room may only be a minor benefit, compared to the rest of the features.
- Björn Brembs
To all those who "are not willing to put their livelihoods on the line": what part of "document" did you not understand when you signed up? Bill used the right description for this kind of behavior: cowardice. But if you really think our little room of 40 scientists with inadequate access to scientific literature will wake a sleeping giant, I have several additional accurate descriptions.
- Björn Brembs
(1) Delusion. If you really think someone like Elsevier is risking their 800 millions annual profit in tax payer money by going after people who can barely support themselves, you must be deluded. The music industry doesn't have any profits left to lose, but publishers do. They wouldn't be making record profits during the worst financial crisis in 80 years if they really were so stupid to go after us.
- Björn Brembs
(2) Stockholm syndrome. How many salaries and healthcare plans could you pay from 800 million each year from Elsevier alone? Basically, these guys take your salary and your healthcare and then hold you ransom to shut up and keep your head down - and in response you have nothing better to do than to defend that behavior and cozy up with your captors? You must be the only ones who can see any shred of sanity in such behavior.
- Björn Brembs
(3) Hypocrisy. Isn't it hypocritical to oppose a regime on the surface but then support it when real action needs to be taken? Isn't it ironic that a German is arguing for and volunteering to putting your actions where your mouth is and Americans are arguing in favor of personal safety long before any hint of a serious threat is even perceivable?
- Björn Brembs
(4) Paranoia. There is no precedence of any publisher going after individuals. Publishers have much more to lose than we. Thus, the only potential threat is purely in your minds. There isn't even the slightest hint of any hazard for any one of us on the horizon, yet you defend yourselves against imaginary future actions of your oppressors. More than any of the above, this paranoia...
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- Björn Brembs
(5) Documentation. This thread, more than any number of exchanged papers documents how bad corporate publishers are for the scientific community. Their stranglehold on the community stifles freedom and liberty, intimidates all community members to the point that they delude themselves, develop paranoia and act hypocritically. I think this thread documents more than anything else in this...
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- Björn Brembs
(6) Anticipatory obedience. It is a well-known consequence of dictatorships around the world that individuals in these dictatorships support the dictator even if there is no explicit force, merely because they imagine some bad consequence for themselves or their family if they wouldn't support the dictator. In Germany, every child is raised with what the term 'anticipatory obedience' means. We are being taught how it works to stop all potential threats to democracy at the roots.
- Björn Brembs
1) Elsevier has lawyers on retainer, sending a take down letter costs them very little and makes a point - compare to RIAA - how many college students did they take to court? they are actually legally in their right so you would lose without even a trial 4) it's not paranoia if they really are after you. There is a precedence - in the OSTP letters someone complained about ACM going after a Taiwanese grad student
- Christina Pikas
Björn, don't take this for more than the friendly advice that it is: I don't think it will win over many people in a debate (or win you many friends) to accuse those who are not willing to publicly encourage illegal activities of suffering from delusions, Stockholm syndrome, hypocrisy, and paranoia.
- Lars Juhl Jensen
Re-reading my posts from this morning, it seems indeed I may have over-exaggerated my points a bit too far. It was and still is my purpose to rouse people and ruffle some feathers on a topic which to me is the worst side of my job. In my frustration that even people who I thought were on my side don't dare to leave their comfort zone for something I find so important, I may have gone a...
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- Björn Brembs
Hadn't voted earlier, but vote now for the references to RW to be included in the article. (nice commentary/response BTW) . RW room is one great thing that you guys are doing and should be proud of. People like me who have no access to any scientific literature (that OA or PNAS or some other because of my country of origination (india) ) are able to do science because of that support;...
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- Sandeep Gautam
I am basically offline now and thus postpone submission until Dec 22. Hope to be able to comment in more detail tomorrow night.
- Daniel Mietchen
@Bjoern: I do understand your position, and I cannot disagree with a lot of what you say. But this is my point of view when I step back a little. 1) the number of subscribers to the room cannot claim to represent the sceintific community (they may or may not be representative, but the claim cannot be made based on the numbers). Nor do I think it can claim to represent the scientific...
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- Kubke
@Kubke: Indeed, very measured words. Last night I've also come to the conclusion that apparently, the situation is not bad enough, yet, for people to seriously push for change. It first has to become a lot worse, before it will get better, I totally agree.
- Björn Brembs
I just rephrased the critical section (lines 45-47). further brushing welcome.
- Daniel Mietchen
That letter looks great! Kudos to all of you!
- Kubke
Sorry, won't make it today. Next online time scheduled for 27, just in time.
- Daniel Mietchen
@Daniel - thanks for submitting, and for including me :)
- Allyson Lister
Just caught up on the thread as I was on vacation for the past week or so. I'll just say that although I am not a member of the room in question, I am in agreement with those who did not wish its inclusion.
- Allyson Lister
Got mail from Cell: "Dear Dr. Mietchen, Thank you for your proposal to write a Correspondence for Cell in response to the article on tweeting by Laura Bonetta published in the October 30th 2009 issue of Cell. Your proposal has now been discussed by the Cell editorial team. We think that your proposal would work well as a 500-word online comment. Our new online comments feature enables...
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- Daniel Mietchen
I hadn't even noticed the comment feature before but here are three previous comments on the Bonetta article: http://www.cell.com/comment... . The first one by Jo Badge ( http://friendfeed.com/jobadge ) already tells much of our story, and we could simply build on it. An easy way to comply with the 500-word limit (which is stated as 8000 characters in the guidelines for posting comments) would be to just split it in two.
- Daniel Mietchen
Found out why I hadn't seen the comment feature before: The comments are only visible if you access the article directly via cell.com (I usually go there via sciencedirect.com).
- Daniel Mietchen
It seems the comments are not indexed by Google - taking the first sentence of Jo's comment as a search string does not yield any results: http://www.google.de/search... . In other...
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- Daniel Mietchen
I just tried to add our comment. It was below 8k text chars but contained links, which blew it up to well over 10k, so it was rejected automatically. I thus think it is best to post the stuff jointly on our blogs (using the title "Social filtering of scientific information - a view beyond Twitter") tonight, and I have put the HTML source for that into http://bit.ly/7ejHlJ .
- Daniel Mietchen
I'm surprised that the comments aren't indexed, and that does make it much less inviting as a method of replying to the article.
- Allyson Lister
Thanks! I'm reading through some of the guidelines for editors and learning a lot. One good thing is that I learned that post-publication comments by the academic editor of the paper is encouraged. I wasn't sure of this, because for the papers I've read on PLoS, I don't think I've ever seen this.
- Steve Koch
The tragedy and comedy of peer review. I'm glad you've kept your sense of humor about it -- the baboon sleepwalking comment is hilarious!
- The Neurocritic
Reality is stranger than fiction. I didn't make that up. A colleague who published a rat behavior paper was asked by a reviewer to do just that! Not surprisingly that reviewer was trying to stall the paper because he had a similar story in the pipeline.
- Hysell Oviedo
You forgot to mention the part where he actually had to awkwardly address that concern in the rebuttal letter. Without laughing. Or cussing. Didn't want the editor to think he was slacking off and ignoring bits of the review...
- Noah Gray
Thanks everyone :) Here's the abstract: "The neuronal network controlling feeding behavior in the CNS of the mollusc Lymnaea stagnalis has been extensively investigated using intracellular microelectrodes. Using microelectrodes however it has not been possible to record from large numbers of neurons simultaneously and therefore little is known about the population coding properties of...
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- Christopher Harris
J. Neurosci., Vol. 25, No. 19. (11 May 2005), pp. 4766-4778. Genetically encoded fluorescent probes of neural activity represent new promising tools for systems neuroscience. Here, we present a comparative in vivo analysis of 10 different genetically encoded calcium indicators, as well as the pH-sensitive synapto-pHluorin. We analyzed their fluorescence changes in presynaptic boutons of the Drosophila larval neuromuscular junction. Robust neural activity did not result in any or noteworthy fluorescence changes when Flash-Pericam, Camgaroo-1, and Camgaroo-2 were expressed. However, calculated on the raw data, fractional fluorescence changes up to 18% were reported by synapto-pHluorin, Yellow Cameleon 2.0, 2.3, and 3.3, Inverse-Pericam, GCaMP1.3, GCaMP1.6, and the troponin C-based calcium sensor TN-L15. The response characteristics of all of these indicators differed considerably from each other, with GCaMP1.6 reporting high rates of neural activity with the largest and fastest...
- Björn Brembs
gCaMp3, newly reported in N Methods is pretty amazing, performance-wise...
- Noah Gray
I'm just about done submitting an ERC starting grant. If we get funded, we'll screen all of the available ones for the best performance in characterizing resting-state activity in fly brains (aka fMRI for flies).
- Björn Brembs
Jeff Lichtman once claimed that learning after birth consists only of synaptic pruning :-)
- Björn Brembs
So we "lose" 9.0*10^15 (~9000000000000000) synapses somehow? What's the number of synapses that are being killed by binge drinking for example? I doubt such activities could account for it though?
- Alexander Kruel
Chris, that number seems off by a factor of ten. I thought that I have typically seen 10^14 as the estimate for adults...?
- Noah Gray
@Björn A lot of work conducting longitudinal microscopy of dendritic spines (putative synapses) in rodents suggests exactly that: major pruning. In fact, although learning or experience can induce more spines in the short term, over long periods, most are subsequently loss; i.e., there is no net gain.
- Noah Gray
For the non-experts like me it sounds like a child has at least 9 times more synapses than an adult. This may help: http://en.wikipedia.org/wiki... (Heard about it for the first time.)
- Alexander Kruel
@Noah I got those numbers from some lecture notes, very recent notes but probably just lifted out of a textbook, and I guess everyone's counting method is different. I was just struck by the 10-fold difference. No surprise kids can learn 3 languages simultaneously to the point of fluency. Wonder what else they learn..
- Christopher Harris
I suppose as long as you're not entering a different universe for everything else you'll have to learn, the residual synapses and the knowledge they represent are enough to build on for prevailing similarities of artifacts, actions and frameworks of the intermediate world in which we reside? Maybe that's why it is so hard to learn about quantum phenomena, grasp relativistic circumstances and make sense of probabilistic behavior within artificial frameworks and of quantum/cosmologic scales?
- Alexander Kruel
Thx 2 Le Monde I now know about xtreme ironing! Ths hibrow pub must find it baffling 2, its bn on the front pg 4 months http://www.youtube.com/watch...
"Why does a scientific society have to go to Facebook for social web technology? Why doesn't it have that technology built-in? After all, social and society don't share the same etymological ancestry for nothing (i.e., the Latin word socius meaning "companion"). I'm sure over 40,000 members are a large enough base where most current tools would work fine. For instance, imagine you could have a buddy-list of other SfN members. Then, when the program of the next meeting is available, you can choose to pre-populate your itinerary automatically with all the presentations by your buddies."
- Björn Brembs
I think the problem might be hassle of getting permission to automatically add members - and when asked probably the vast majority will ignore the request. Then even if there is a network I suspect it will be accessible only to members of that society.
- Jean-Claude Bradley
The idea is to be only accessible to members - after all they're already using the site for plenty of other things anyway. The idea is that societies should use social web technology to deliver the kind of improvements societies were founded for initially: improved communication between members with a common interest.
- Björn Brembs
maybe I'm in the minority here but for me one of the biggest advantages of social software is meeting people you didn't know existed - so I don't see the incentive in participating in a closed network
- Jean-Claude Bradley
Good points! Indeed, because in principal every member of these societies could meet in meatspace, meeting new people is *not* one of the goals I had in mind. Rather, keeping track of who of the 40,000 members of SfN is doing what. I regularly miss people or their presentations at meetings, simply because I don't have the full record of people in my head at all times. If there were a way of tracking their activities automatically, this would be easier.
- Björn Brembs
Basically, my idea was to leverage social web technology to have people spend *less* time on the society's website, but getting *more* done. This may only work for large societies, where the number of people in your field attending has become too large to track by hand, but science in growing...
- Björn Brembs
Scientific societies are anti-social in general
- Alexey
from iPhone
how about having a SFN society / group on NING. Only sfn members may be added to the social network and it may be what you desire...though being a non-member (and having no hope of becoming a member) I'll always support open forums:-)
- Sandeep Gautam
I don't think I've made myself clear at all. Maybe an example will help: Every year, I try to remember every name of every person I know who may possibly attend the SfN meeting. I spend several hours populating my online itinerary (with their presentations as well as by keyword), only to always forget some individuals. Now, if I had a buddy list on the SfN website (where I go regularly...
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- Björn Brembs
That's a great idea Bjorn. Especially at a meeting like that which is so enormous! It'd be nice (and really easy to program) an automatic itinerary generator.
- Brian Krueger - LabSpaces
IMHO, what defines a "social network" is not who's in the network, but what you want to do with the network. I think what you're describing are still social activities (tracking other people's movements and activities) and I think they're not unique to scientists. Therefore, I think SfN is right to go after a generic network like FB. This is the part that I think the "FB for scientists"...
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- Andrew Su
As part of the selected few to try out the RSC's new 'social networking' site (which doesn't have the same good ideas to be fair that Bjorn has suggested (at least not yet)), my (and my peers) view is that it is just _another_ site that needs to be logged into, checked, etc. The reason we all suggested FB was that 1. all of us were already using it and 2. we had already initiated...
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- Anna Croft
Anna and Andrew, those are great points and make a lot of sense! I know too well how little I want to have to track yet another site. In this case, one would have to find a way to get the functionality implemented on FB, I wouldn't mind that at all - as long as I have the functionality. It would also still have the added benefit of scientists using FB for science.
- Björn Brembs
On the other hand, every single attendee of SfN (30,000 every year) *has* to use the SfN website just to see the program (or get accommodation!) and without your own itinerary, you're basically totally screwed. In other words, disregarding the website is not an option, tens of thousands of people are using it already anyway, most of them also more than just once a year. The society's...
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- Björn Brembs
Bjorn, I think you're right, if SfN (or ISMB) made a FB app to track the program, speakers, and attendees, I think that would be pretty fricken cool. And, I think, more productive than trying to reimplement a social networking site from scratch.
- Andrew Su
"It has been a mainstay of evolutionary theory since the 1970s. Natural selection acts purely on the level of the individual and any cooperation observed between organisms merely hides a selfish genetic motive. There have been two pioneering theories to explain cooperation in the natural world given this framework: the first was William Hamilton's (1964) theory of kin selection and the second was Robert Trivers' (1971) theory of reciprocal altruism. However, both of these scenarios break down where it comes to unicolonial ants. In a paper in the journal Trends in Ecology and Evolution (subscription required) Heikki Helantera, of the University of Sussex, and colleagues at Rice University have investigated how previous theories to explain cooperation don't apply for these unique supercolonies."
- Jamreilly
from Bookmarklet
But aren't they an individual? Just like we are super-organisms. Just because there is thin air between something, does it mean its two objects?
- Alexander Kruel
".. 'The extreme cooperation of unicolonial ants has been suggested to be an example of selection occurring on levels higher than the individual, such as the superorganism, group or even population.' ..Group selection is the idea that, under certain circumstances, genes will be selected for because they benefit the overall success of the group rather then simply the individual. While it...
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- Jamreilly
Often ant colonies differ from most multicellular organisms - since the workers and the queen are not 100% related.
- Tim Tyler
Good to see people taking the ethical side of this seriously. I'm less convinced about the value of specific rules and more by the idea that this should just be seen as bad behaviour but very glad to see people coming down on it like a ton of bricks. That's what will make people feel safe - not rules, not regulations, and not compulsions either, but very strong and public responses to breaches.
- Cameron Neylon
@Cameron +1 . But ideally some kind of consequences/punishment surely would be order as well, e.g. the authors responsible would not be kindly received next time they ask for ethical approval to access controlled-access data from NIH (or other) repositories. Some sort of blacklisting for 'repeat offenders'?
- 'Mummi' Thorisson
Not greatly in favour of blacklisting per se. I would say that it was a disciplinary offence though that ought to consider dismissal from post. Which really amounts to the same thing.
- Cameron Neylon
Please correct me if I'm wrong, but I thought the consequences ("punishment") was that their paper was retracted.
- Hilary
The paper was published Aug 31, retracted Sep 9, when all the authors had to do was to ask PNAS to publish it no earlier than Sep 23 to comply with the GENEVA data embargo policy. The closeness of all the dates suggests to me that it was more a serious messup than a malicious breach of policy. http://www.pnas.org/content...
- Iddo Friedberg
Hilary, I would say that the retraction is just the reversal of the act rather than punishment. Paper shouldn't have been published, therefore it was "unpublished". If (and there should definitely be a proper investigation) someone thought they could get away with playing outside the rules there should be punishment above and beyond simple reversal in my view. This is "conduct unbecoming..." etc. But as Iddo says, not clear from the dates whether it might just have been a screwup.
- Cameron Neylon
Cameron: a retraction is a very bad thing to have on your record. It is for all intents and purposes synonymous with"fraud".
- Iddo Friedberg
from Android
Without *knowing* the intent was malicious, forcing a retraction seems a bit harsh. If data is online it should be intended for use by the public. IMO this is just another argument for mandatory DOI's and better dataset citations. On the other hand, calling out a group for not having the courtesy or awareness to contact the originating lab is a good thing. Like Cameron said, the social norms are probably the best way to play this.
- Paul J. Davis
Also, don't physicists have a pretty good system for the whole idea of citing datasets? NCBI's ability to provide transparency in terms of what data came from where and when is pretty atrocious, so its a bit weird to consider for biology. But I thought I read that the LHC data was pretty much available for citation.
- Paul J. Davis
Iddo - I disagree on two counts with that. There are plenty of retractions out there that are honest mistakes or re-assessments. Embarrassing yes, emblematic of sloppy work yes, synonomous with fraud, nah. But more importantly if we take that kind of attitude then people will be too scared to correct things in the future - when we will (hopefully) have much more fine grained approaches...
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- Cameron Neylon
Paul - I think citing datasets at NCBI isn't so hard. I'm not sure that's really the problem in this case (if it is then it's a definite mark against the authors). The problem is the culture in biology that collecting the data isn't worth anything so having a highly cited dataset isn't useful on your CV - no matter how good or useful it is. Only the paper matters. I have to say I haven't actually had the time to look over this case in detail though.
- Cameron Neylon
This also raises issues of roles of journals, institution employing authors (often several, in different countries/legal systems, as papers now almost all multi-author), and funders in "policing" sci ethics. Lots of talk everywhere about this. Journals can publish policies and retract/correct (ensuring linking in A&I dbase searches etc) - but how can sci community deal with wider issues beyond the paper? (quite apart from the technical problems with enforcing eg "blacklisting")
- Maxine
Neil - in response to your Q above - v hard in practice to be perfect but from journal's perspective: (1) consult with relevant community and state policies for standards all agree and (2) the peer-review process (advice from reviewers on repeatability). Also, of course, journals can in general encourage authors to disclose more rather than less.
- Maxine
+1 Neil and Maxine. There is too much of an expection for "the journals" to sort this out. Publishers have an important role to play but we need to clean our own house. Or someone will do it for us. Probably the public. And probably by saying that they're not so interested in funding science any more.
- Cameron Neylon
Thanks, Cameron. I agree, journals can and should help but as part of a wider process that scientists themselves (as a profession) decide is "best practice". Neil - have had this "code" discussion with eds here before - one view is that the documentation better/more meaningful to scientists (who aren't programmers in the main) - also many programmes are not open-source. Probably other points which I don't immediately recall. Nature Biotech is running community consult at the moment on this, I think.
- Maxine
"Comparisons of Citations in Web of Science, Scopus, and Google Scholar for Articles Published in General Medical Journals" (JAMA 2009): http://jama.ama-assn.org/cgi...
Limitations: (1) 140 chars is too limited to accomodate a typical URI, (2) needs to be coupled to author ID, (3) only one rating dimension as of now.
- Daniel Mietchen
if we could aggregate a whole bunch of different comments from different sources and translate them automatically to fit? Or provide a link to the comment rather than the full text of the comment?
- Cameron Neylon
from twhirl
Ok, now I've looked properly. Would probably need to build a slightly more intelligent service but if you could parse links then there are two very nice things here. One is linking id, and review via URLs but the other is that this actually matches the PubSub-Syndicate mechanism that Jon Udell talk a lot about much better than commenting on websites (...now where is that half written blog post...?)
- Cameron Neylon
the comment text from people usually contains even more helpful information than rating metrics
- Mike Chelen
DOIs can still be very long - plus you'd probably want to give them in the http form so that makes them even longer. Mike, agree the text can be more useful but if it is held somewhere else then the tweet only needs to reference it via a shortened link was what I was thinking
- Cameron Neylon
The DOI problem could be solved if the @hreview service were to expand the shortened URL per default.
- Daniel Mietchen
Also, we need a URI scheme for anything on the web, from blog entries to wiki edits to @hreview ratings.
- Daniel Mietchen
Cameron:probably the posts could contain shortened DOI URLs that were expanded in the underlying hReview
- Mike Chelen
Daniel: can the hCard support be used to integrate with other author ID systems?
- Mike Chelen
CC-BY-ND certainly makes sense for the pure values (text or numbers) of the ratings, but isn't it too restrictive for reuse, e.g. aggregation?
- Daniel Mietchen
Daniel: there are clauses to specifically allow collections, but it's never been clear to me exactly how ND applies to subsets or programmatic reuse.
- Mike Chelen
Nor to me, Mike, but the opencritics are open to criticism (I had to bring that) and suggestions, and have lawyers to sort such things out properly. More to come on that by tomorrow - just had them on the phone.
- Daniel Mietchen
hmm, 140 characters won't work. We need an article social activity aggregation service, could then be mirrored onto twitter or where ever. Like stramosphere, but just for articles. Euan should write it.
- Ian Mulvany
Should note that CrossRef is thinking of creating alternative shortened DOIs that could address some of these problems. Working name is "toydoi". Advantage of CrossRef is we could avoid spam-plague faced by traditional URL shorteners. Would be good to hear from interested parties to understand use cases.
- Geoffrey Bilder
Ian, I think that "article social activity aggregation service" is a good description for what Mendeley are up to - still a bit rough a toy, but improving very fast.
- Daniel Mietchen
Geoffrey, good to read that. However, the length of DOI is just one problem, and more pressing from my point is to develop a DOI-like URI scheme for anything cited in a scientific context (and for anyone citing, too), e.g. via automatic deposit at places like Webcitation or Portico (and using some sort of author ID). And before going public with that working name, they might wish to invite comments from speakers of Vietnamese.
- Daniel Mietchen
So we've also been thinking a little bit about how to assign identifiers to new forms of scholarly communication- thinks like blogs, wikis, data sets, etc. Some background can be found here: http://tinyurl.com/m68jlq
- Geoffrey Bilder
Yes, that's useful background. Do you have an update on the current situation?
- Daniel Mietchen
hReview supports multiple rating dimensions if the site could use it
- Mike Chelen
Google are about to roll out what they call "Rich snippets" for selected sites, harvesting info provided via hreview, RDFa or similar: http://bit.ly/3bGVlE & http://bit.ly/SxWES . Would be nice to see this coupled (for scientists logged in with their author ID) with ratings like at PLoS ONE.
- Daniel Mietchen
Microformats for biological (and possibly even other, e.g. chemical) species ( http://microformats.org/wiki... ): "Imagine viewing a web page with a reference to a species - and being able to use an add-on to you browser to be taken directly to information about that species, on, say, Wikipedia, or Wikispecies, or Google Images, or another site, such as in an academic database, of your choosing."
- Daniel Mietchen
Thanks, Peter: Yes, EoL was in the mind of the writer of this phrase (he also quotes Wilson), but NameTag and the species microformat are two different approaches to this goal, and only the latter bears some resemblance to article-level metrics.
- Daniel Mietchen
Just got this link from Elsevier. Looked up some of the prices: First page of my article as a small poster: 25€+tax/shipping. Printed issue with my paper in it: 30€. 50 offprints of my article 300€. Checking the download stats of the article PDF on my homepage: priceless!
- Björn Brembs
from Bookmarklet
good for them! they figured out that a chunk of their customers are egomaniacs ;)
- Wladimir Labeikovsky