Daniel Mietchen - Comments

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Daniel Mietchen to Daniel's feed, Science 2.0, Science Online, Science in the long run

Fwd: Should you be tweeting? - http://www.hubmed.org/display... (via http://friendfeed.com/ff-for-...)

Sandeep Gautam, rowlikeagirl, Kubke and 19 other people liked this

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

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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... more... - 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

I gave it a start at http://etherpad.com/Microbl... - feel free to join in! - Daniel Mietchen

Added some stuff... - 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... more... - Björn Brembs

Correction: 660 words... :-) - Björn Brembs

See also Jean-Claude's stylesheet about FriendFeed + Science ? FFscience: https://spreadsheets.google.com/ccc... - Pierre Lindenbaum

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

Getting there ... >800 words. - Björn Brembs

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

@Daniel as a pseudonym, I suggest to use what Deepak calls the "BioGang" http://openwetware.org/wiki... http://www.linkedin.com/groups... - Pierre Lindenbaum

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

895 words... - 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

Björn - http://dx.doi.org/10... . - Daniel Mietchen

@Allyson: awesome! @daniel, sorry, meant this one: http://dx.doi.org/10...) - Björn Brembs

Added ref 4: the NAR paper ( http://tinyurl.com/mr5kvm ) - Pierre Lindenbaum

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

The DOI, if intact, should point to http://genomebiology.com/2009... , which is behind the paywall for me but perhaps Allyson can give us a hint ;-) - Daniel Mietchen

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

I'm about adding a ref to O'Reilly/"Beautiful Data". The collaboration for this book started here: http://friendfeed.com/fgibson... - Pierre Lindenbaum

@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

Cameron, do you have a reference for the second grant? I am only aware of http://www.labgrab.com/users... . - Daniel Mietchen

Added mention of polymath project. - Daniel Mietchen

Found reference mentioning both grants: http://www.nih.gov/news... . - Daniel Mietchen

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

Interesting turn: Etherpad will remain operative until at least when they release their source code. http://etherpad.com/ep... . - 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

@Daniel: DM was blocked (private). - 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... more... - 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... more... - 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... more... - 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... more... - 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... more... - 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

Bjoern, I will add that any librarians in this room (and I am not the only one) may have a professional interest in keeping mum. We are pathologically helpful folk, so it's hard to resist sending papers -- but we also belong to a profession that looks incredibly askance at even a HINT of copyright-related impropriety. Are you willing to lose me my job over this? Like Bill's, completely serious question. Remember also that my job is intimately OA-related. - D0r0th34

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

Just a couple of points. (1) I'd assumed that most or all contributors voted in good faith, i.e. once, on this issue. (2) Having read through the draft at etherpad, I think it reads as a good summary of the utility of FF, with or without the mention of RW room (which is only one small paragraph). Is this one aspect really so important, really such a major component of the FF science experience? I think our interactions and discussions are much more important and interesting. - Neil Saunders

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... more... - 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... more... - 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

Bjorn, you have lost my respect. I am blocking you and leaving this room. My email is findable if you care to apologize. - D0r0th34

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... more... - 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;... more... - 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... more... - 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

Just submitted. Latest version: http://etherpad.com/ep... . - 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

Article-level metrics

ResearchBlogging.org News » Blog Archive » ResearchBlogging.org ... - http://researchblogging.org/news...

December 17 from "article-level metrics" -... - Comment - Like - Share

Mr. Gunn, Duncan Hull, Björn Brembs and Daniel Mietchen liked this

Blogs offer another benefit over some other article-level metrics. As Cameron Neylon and Shirley Wu noted in an article in PLoS Biology, experts may be reluctant to offer comments directly on journal articles, because they often don't ...

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"PLoS offers bloggers the opportunity to see pre-release versions of its articles." - wasn't aware of this - how to apply? - Daniel Mietchen

Related post at http://everyone.plos.org/2009... . - Daniel Mietchen

Yes - see http://www.plos.org/journal... and follow the instructions for application. - Bora Zivkovic

Michael Nielsen

A guide to the day of big data : Nature - http://www.nature.com/nature...

December 16 from delicious - Comment - Like - Share

Dan Hagon, Duncan Hull, Eric Logan and 19 other people liked this

My review of "The Fourth Paradigm: Data-Intensive Scientific Discovery" - Michael Nielsen

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I appreciate the irony: a review of a Creative Commons licensed book, with a strong open data slant, behind a paywall. It's Nature's business model, and that's their choice, but it's a bit of a pity. I'll self-archive it when the time comes around. - Michael Nielsen

I was somewhat surprised that the book is freely-available; http://research.microsoft.com/en-us.... - Neil Saunders

Neil - it's under a CC license! Got to give Microsoft some kudos for that. - Michael Nielsen

I suppose so ;-) - Neil Saunders

Is this book available in dead-tree format? - Ricardo Vidal

Ricardo: Don't know - the review copy came printed on nice shiny electrons. - Michael Nielsen

Michael, thanks for sharing this. Great review. - Ricardo Vidal

Thanks, Ricardo! - Michael Nielsen

I was surprised about the footnote - is it really 2011? How many "notes added in proof" will this mean? - Daniel Mietchen

Daniel - The book doesn't focus on ephemera, insofar as it's possible to avoid, for the reason you mention. A few of the examples will date, but I expect the general argument to still be essentially correct decades from now. It's a book that's meant to help change hearts and minds through a powerful general argument, not TechCrunch for scientists, if that makes sense. - Michael Nielsen

Nice review, looking forward to your book Michael - Frank

The review now appears to be out from behind the paywall. It wasn't when I posted last night. I don't know why the change has happened. - Michael Nielsen

When did you drop the working title "The Future of Science"? This is the first time I've seen "Reinventing Discovery" and a publication timeline... - Bill Hooker

I changed the title a couple of months back - I like this one more, although it's still a working title. The timeline is tentative. - Michael Nielsen

Björn Brembs

Embedding 3D models of biological specimens in PDF publications - http://www.citeulike.org/user...

December 16 from CiteULike: brembs's library - Comment - Like - Share

Dan Hagon, Kubke, Mike Chelen and 5 other people liked this

Microscopy Research and Technique, Vol. 71, No. 11. (2008), pp. 778-786. By providing two examples, the option for embedding 3D models in electronic versions of life science publications is presented. These examples, presumably representing the first such models published, are developmental stages of an evertebrate (Patella caerulea, Mollusca) and a vertebrate species (Psetta maxima, Teleostei) obtained from histological section series reconstruction processed with the software package Amira. These surface rendering models are particularly suitable for a PDF file because they can easily be transformed to a file format required and components may be conveniently combined and hierarchically arranged. All methodological steps starting from specimen preparation until embedding of resulting models in PDF files with emphasis on conversion of Amira data to the appropriate 3D file format are explained. Usability of 3D models in PDF documents is exemplified and advantages over 2D illustrations... - Björn Brembs

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Awesome 3D models, rotatable, zoomable, everything within a PDF with no extra plug-ins! Amazing! - Björn Brembs

I think they should have mentioned some Open Source alternatives to Amira/Adobe, my favourites being http://rsbweb.nih.gov/ij/ and http://www.ctan.org/tex-arc... . For the fossil part, see also http://www.virtualpalaeo.org/ (summary in http://newsletter.palass-pubs.org/pdf... ). - Daniel Mietchen

+1 Björn - this is a most impressive piece of work !! @Daniel, I'll check those links out tomorrow. - Graham Steel

Now I need to find out how to get the 3D model of our experimental setup into our PDFs! - Björn Brembs

Daniel: how is imagej used to embed 3d models? - Mike Chelen

imagej produces the 3D models, animate the embedding. - Daniel Mietchen

That is a great link Bjorn. My student has been producing similar models of brain/brain regions that are extremely useful since one can rotate the brain, remove regions, or "slice" it at different angles (great when trying to interpret histology and also to calculate stereotaxic approaches for electrophysiology). But it never occured to me he could publish the dynamic pdf. - Kubke

Does anyone know if Osirix can do the pdf trick? http://www.osirix-viewer.com/index... - Kubke

Daniel Mietchen

Genome Desertification in Eutherians: Can Gene Deserts Explain the Uneven Distribution of Genes in Placental Mammalian Genomes? - http://www.springerlink.com/content...

December 17 from Bookmarklet - Comment - Like - Share

Posted it for the content, but it is also interesting in that it is labeled as "open access" but "contains supplementary material, which is available to authorized users." and because it was my first hit at the 500Mb upload limit at Mendeley (emptying the trash gave me a little more room again). - Daniel Mietchen

Research Funding 2.0

Peer review and 'openness'. - http://www.hubmed.org/display...

December 8 from HubMed - "peer review" - Comment - Like - Share

Eprint request sent - Daniel Mietchen

received - Daniel Mietchen

Daniel Mietchen to Daniel's feed, Environment, Going Green For The Planet!, Science in the long run

Petition to the 110 Presidents and Prime Ministers negotiating in Copenhagen: We call on each one of you to make the concessions necessary to meet your historic responsibility in this crisis. Rich countries must offer fair funding, and all countries must set ambitious targets on emissions. Do not leave Copenhagen without a fair, ambitious and... - http://www.avaaz.org/en...

December 17 from Bookmarklet - Comment - Like - Share

I've signed as # 11,110,748 some minutes ago, and now the counter is at 13,485,500 already - let's do at least this to tell the politicians they need to switch from bla to action. - Daniel Mietchen from Bookmarklet

Andrew Su to Andrew's feed, The Life Scientists

I'm getting frequent 503 errors on NCBI's eutils (retrieving PubMed entries). Anyone else notice that? Or am I getting throttled because I'm missing some usage limits?

December 15 - Comment - Like - Share

Mike Chelen and Peter Miller liked this

There are some usage limits, how hard are you hitting the server? - Paulo Nuin

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in my few automated runs, I've put in at least sleep(1), now sleep(5). But I'm getting it just from debugging my web app too (i.e., hitting refresh after a code change). Seems to have gotten worse later in the day... - Andrew Su

I've seen various errors using NCBI in the last couple of days (e.g. 404s and 502s using GEOquery via R). It seems better at certain times of day. Suspect general flakiness in their servers. - Neil Saunders

bummer, now I can barely get a good request to come back.... e.g., http://eutils.ncbi.nlm.nih.gov/entrez... must be all those Australians waking up and hitting NCBI... - Andrew Su

Sometimes they also block your IP for some amount of time if you tried to access their servers constantly. - Paulo Nuin

I've not been hitting the server hard - this has been happening on my first GEOquery call of the day, but then working a few minutes later. - Neil Saunders

any note on where I can find their usage guidelines? this search (http://www.google.com/search...) and variants didn't turn anything up... - Andrew Su

This is quite old but you get some ideas http://osdir.com/ml... - Paulo Nuin

Very helpful, thanks... Interesting though, since I'm running my stuff through Google App Engine, have I effectively blocked all other GAE users too? (Or, perhaps there are other eutils-consuming services there and we are collectively getting blocked...) - Andrew Su

Even manual queries (through links provided by HubMed rss feeds) have been causing errors about half of the time for the past few days for me. - Daniel Mietchen

you may want to subscribe to utilities-announce@ncbi.nlm.nih.gov and check out http://www.ncbi.nlm.nih.gov/mailman... - Mark A Jensen

Thanks Mark, good idea. (But now having done it, why does NCBI restrict viewing of the archives to only subscribers? Especially when there are only 3-4 email per year? grumble grumble...) Anyway, it did help highlight this section (http://eutils.ncbi.nlm.nih.gov/entrez...), which says "Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests..." - Andrew Su

(solidarity with your grumble-grumble!) - Mark A Jensen

fyi, I emailed their help desk last night, they replied today that they were "having issues" yesterday that was probably the root cause. Sure enough, things are running much smoother today... - Andrew Su

Science News: Ami Iida

Scientists decode memory-forming brain cell conversations http://www.physorg.com/news180...

December 16 - Comment - Like - Share

rowlikeagirl and RAPatton liked this

The conversations neurons have as they form and recall memories have been decoded by Medical College of Georgia scientists. - Ami Iida

Source: http://www.plosone.org/article... . - Daniel Mietchen

Thanks Daniel for the source. - Ami Iida

Daniel Lemire

versioned web-based text documents (via @hjarche) - http://writeboard.com/

December 15 from delicious - Comment - Like - Share

Peter Miller and Claudia Koltzenburg liked this

Seems to provide RSS feeds for notification of changes in the document - a feature long requested for Etherpad. - Daniel Mietchen

Science in the long run

Earth's Atmosphere (and Probably its Oceans) Came from Outer Space, Scientists Find - http://www.oceanleadership.org/2009...

December 15 from Consortium for Ocean... - Comment - Like - Share

The gases which formed the Earth's atmosphere -- and probably its oceans -- did not come from inside the Earth but from outer space, according to a study by University of Manchester and University of Houston scientists.

The abstract of the actual paper: "Noble gas isotopes are key tracers of both the origin of volatiles found within planets and the processes that control their eventual distribution between planetary interiors and atmospheres. Here, we report the discovery of primordial Kr in samples derived from Earth’s mantle and show it to be consistent with a meteorite or fractionated solar nebula... more... - Daniel Mietchen

Science in the long run

This is bigger than climate change. It is a battle to redefine humanity by George Monbiot - http://www.350resources.org.uk/2009...

December 15 from Resources for a sustainable... - Comment - Like - Share

Daniel Mietchen liked this

15/12/2009 Guardian This is the moment at which we turn and face ourselves.Here, in the plastic corridors and crowded stalls, among impenetrable texts and withering procedures, humankind decides what it is and what it will become. It chooses whether to continue living as it has done, until it must make a wasteland of its home, or to stop [...]

"We are the universal ape, equipped with the ingenuity and aggression to bring down prey much larger than itself, break into new lands, roar its defiance of natural constraints. Now we find ourselves hedged in by the consequences of our nature, living meekly on this crowded planet for fear of provoking or damaging others. We have the hearts of lions and live the lives of clerks." - Daniel Mietchen

"The summit’s premise is that the age of heroism is over. We have entered the age of accommodation. No longer may we live without restraint. No longer may we swing our fists regardless of whose nose might be in the way. In everything we do we must now be mindful of the lives of others, cautious, constrained, meticulous. We may no longer live in the moment, as if there were no tomorrow." - Daniel Mietchen

Science in the long run

Coconut-Carrying Octopus: Tool Use in an Invertebrate - http://www.oceanleadership.org/2009...

December 15 from Consortium for Ocean... - Comment - Like - Share

Daniel Mietchen liked this

Scientists once thought of tool use as a defining feature of humans. That's until examples of tool use came in from other primates, along with birds and an array of other mammals.

Seen it in various places already but it's still cool! - Daniel Mietchen

Science in the long run

'Cryo-egg' to Predict Sea Levels - http://www.oceanleadership.org/2009...

December 15 from Consortium for Ocean... - Comment - Like - Share

Daniel Mietchen liked this

A hi-tech "cryo-Egg", which will help predict sea levels changes, is to be created by experts at Bristol university.

"In addition to the need to survive crushing by ice and extreme cold, the probe must be able to communicate with scientists on the surface through kilometres of ice." - Daniel Mietchen

Shirley Wu

A co-worker mentioned to me yesterday that a colleague of his is thinking about starting an online journal club type website for scientists. The idea seems to be discussions about papers, data sets, and other web-publishable materials, from any source, in a central location. It would also have discussions about scientific culture, which made me...

October 22 from twhirl - Comment - Like - Share

Abhishek Tiwari, Anders Norgaard, suelibrarian and 15 other people liked this

It would be a place where people (students, junior faculty, etc) could learn the ropes of academia and science without the pain and misery that traditionally is required. The differences I can see from existing services is the focus on journal club-style discussions and maybe a low barrier to entry - Shirley Wu from twhirl

12 more comments

But obviously, whatever he ends up pursuing should learn from the trials and tribulations of the many related services out there (including services like FF, which is also discussion-oriented) - Shirley Wu from twhirl

It's easy to immediately discount any proposal that sounds like yet another facebook for scientists, but there are still some interesting and potentially good ideas out there. Unfortunately, people who aren't as familiar with the existence of these tools always think of facebook as the ideal and as a brand new idea if applied to the scientist community. Hopefully I convinced my co-worker otherwise, while still encouraging the more innovative aspects of the concept. <end rant> - Shirley Wu from twhirl

Thanks for doing that. - Mr. Gunn

AcaWiki is built around a very similar concept, and John Wilbanks makes an argument for bringing journal clubs online (cf. http://ff.im/airoV ). - Daniel Mietchen

Shirley, Besides AcaWiki (great place to have these discussions, but I'm biased! http://acawiki.org/ ) your colleague also might be interested in GradTurkey, a journal-club discussion wiki originally aimed at grad students: http://gradturkey.fastcoder.net/ - Jodi Schneider

can discussion on AcaWiki be linkable and embeddable for public like you can do on FF? If not, so why don't do journal club on FF? Can't get it - Alexey

I tried a site like this a few years ago. ResearchFire, or something like that? Never heard of it again. - Neil Saunders

my comments on the topic in 08/07 http://pimm.wordpress.com/2007... - Attila Csordas

Knol has many journal features built-in. Here is an example of a successful research journal on H1N1: http://knol.google.com/k... - Bill Strathearn

John Wilbanks mentioned doing journal clubs online in his talk here recently: http://bit.ly/3jxnxr - Walter Jessen

this topic came up during a discussion today with Mike Eisen of PLoS, re: why commenting hasn't really taken off - his thought is that people are more likely to comment if there's a central place to do it rather than individually at each journal website for each paper (how many of us access papers directly through journal websites except through PubMed anyway?). The whole time I was... more... - Shirley Wu from twhirl

can somebody point to the platform for journal club online better then blog post? It's combine everything - presentation (ppt embedded from SlideShare or Gdocs, video embedded from YouTube/Vimeo...) presenter's opinion, discussion section under the post, embedded comments from FF, ranking of the presentation and number of views. Importantly you don't need to register or get account for commenting, it's public and linkable, moderatable . Whole world can participate. What can be better? - Alexey

@Neil Saunders Were you thinking of JournalFire? We recently updated the site and are looking for feedback. I posted about it yesterday: http://friendfeed.com/the-lif... - John Delacruz

Michael Kuhn to Michael's feed, The Life Scientists, Allyson Lister, Roland Krause

How about trying to use Google Wave to cover a talk? - http://www.doodle.com/8zg76sy...

December 1 from Bookmarklet - Comment - Like - Share

Mike Chelen, Lucas Brouwers, François Dongier and 6 other people liked this

I'm thinking of trying to simulate covering a talk by simultaneously watching the same video, e.g. this one by Gary Bader: http://www.youtube.com/watch... Follow link above to a Doodle date finding poll - Michael Kuhn from Bookmarklet

16 more comments

I've proposed the afternoon in Europe, so that people from the US can join in the morning - Michael Kuhn

I've put in my availability. Should be interesting - we can compare (subjectively) the experience on that as compared with our known experiences on FF. Btw, if anyone wants a wave account, just let me know. We all have loads of invites now, it seems. - Allyson Lister

I've also put in my availability. - Graham Steel

thanks Allyson, Roland and Graham. I agree with Ally that we should compare Wave to FF, so I'd like to give priority to people who have covered ISMB. Also, I'm just curious to see how well Wave handles Ally's writing speed. :) - Michael Kuhn

I'll be covering the Recomb Satellite via FF for now; given the limited number of people who have access to it so far that seems to be the only venue. - Oliver Hofmann

I'm giving a talk on Wave in a few weeks - was thinking I might put the slides in as images, then work through them using the slideshow function - if I can stream audio out and people could leave comments on the slides as we go...but collaborative note taking with a relatively small number of people seems to work really well - if you can pull the video/slides in even better. - Cameron Neylon

The talk is supposed to be 3:30 on Tuesday 15th but is late in the day so would probably be later. Will looking into what networks facilities are available... - Cameron Neylon

@Michael, nothing can handle Ally's writing speed :D - Benjamin Tseng

@Cameron, forgive me if this is a dumb question, but how would a talk like that work? would you interrupt it to answer comments/questions as they came in? - Benjamin Tseng

@Michael, @Benjamin - you're really bigging me up there! :) FF seemed to be able to keep up, so hopefully so will Wave :) - Allyson Lister

@Benjamin - thinking I would have the slides in a Wave, webcast video, people could comment next to the slides as appropriate (or inappropriate) and then at the end you have an annotated version of the talk as it happened. Could certainly answer questions - people often interrupt inside the room anyway - but there wouldn't be a simple mechanism to get speakers attention. Anyway I don't... more... - Cameron Neylon

looks like Wed, Dec 16 at 4 pm UT / 5 pm CET will be it. (Sorry Roland.) Any other nominations than for what to watch instead of Gary Bader: Predicting Protein Interaction from the Genome, http://www.youtube.com/watch... ? - Michael Kuhn

@Cameron: I also think having slides and comments in the same Wave is a separate experiment, also streaming live can have its own problems. so let's keep this one simple :) - Michael Kuhn

Yep, that's cool. I should be available on 16th as well anyway - Cameron Neylon

Just saw this thread and plan to be there on 16th. My suggestions for videos to watch are at http://en.citizendium.org/wiki... . Alternatively, we could also go for 2-3 TED talks where the change of subject may provide for additional testing functionality. - Daniel Mietchen

A further suggestion would be to go for Michael Nielsen's talk at http://www.youtube.com/watch... . - Daniel Mietchen

*bump* I've created a Wave with those that entered their times on Doodle. Could you guys please check and vote for a talk? - Michael Kuhn

References Wanted: Graham Steel

POLL. As a direct result of this FF thread http://friendfeed.com/science... I've created a one question poll. The question is "Is it appropriate to raise the visibility of the References Wanted room outwith FriendFeed?". The possible answers are "yes", "no", or "unsure". I would be really grateful if subscribers to this room would participate.

December 8 - Comment - Like - Share

Sandeep Gautam, Kubke, Joe and 7 other people liked this

Poll is here:- http://www.micropoll.com/akira... Thank you in advance. - Graham Steel

39 more comments

Just to expand briefly on Graham's intro: I think the RW room is covered by Fair Use (nota bene, ianal). Nonetheless, the likely result of any legal challenge by publishers would be that FF would shut the room down as a precaution, and we'd have to fight to re-open it. I doubt we have the resources for that fight, so as a matter of realpolitik I'm voting to continue to fly under the... more... - Bill Hooker

^^What Bill said. Yes, the world absolutely needs access to the scientific literature, but we need to work to reform the publishing process and the laws. All things considered, this is a very small room, which is why it hasn't attracted the ire of the publishers. If we advertise and it gets large, the industry will start playing the same whack-a-mole lawsuit game that they do with music or movie sites. - Chris Miller

I voted "No" - Pierre Lindenbaum

Please keep voting folks. A dozen in so far, thanks. - Graham Steel

The referenced thread is about a letter to the journal Cell in which we promote FriendFeed. The RW room will be the single most attractive feature for people who have never used social media. I also think it helps to show a large readership what kinds of hoops we will jump through to get access - and the RW has a great record of people not having access. So in the end, all publicity... more... - Björn Brembs

I'd love to read that Cell paper if possible! http://is.gd/5fQ0D I voted 'unsure' on the poll, perhaps not very helpful, but I thought that my 'yes' might not be as strong as the poll's yes might be demanding. I would like more people to be aware of this helpful service, but to hear of it as word of mouth rather than a 'one to many' broadcast in a journal article. I suppose I'm voting for the status quo (of this room), but with gradual increases in numbers. #fencesitting ;) - Jo Brodie

I would be more concerned about publishers cutting off access to individuals known to be supplying papers in the room for breech of TOS. It has happened to one of our researchers but for other reasons. - suelibrarian from iPhone

Here is the draft of the letter: http://etherpad.com/Microbl... Note that we do not need to spell out the name of the room in the letter, as we do now, just the functionality. I can only re-word my argument from above: cowering before the possible reprisals of 'big publishers' is definitely not the best way to change the current publishing model. In fact, anybody who... more... - Björn Brembs

I voted no. As I see it, the role of RW is to provide a service, not to instigate a revolution or provide a soapbox for change in the publishing industry. I don't think it's fair to create the potential for unpleasant repercussions through wider publicity for a "cause", certainly not without the full knowledge and agreement of everyone who has ever used the room. - Neil Saunders

@Bjoern, it's not "no big deal" to open another room -- that simply won't work, corporate copyright lawyers are quite good at whack-a-mole and we cannot expect FriendFeed to fight our Death To Toll Access battle with us. As I said above, the fight you are spoiling for is worth having, but I don't want to pick it and then get my ass kicked. If you really want people to fight, you'll need... more... - Bill Hooker

The purpose of the room is explicitly "to document the harm caused by closed/toll-access publication". What's the purpose of collecting this data if we're not going to publish it? Voted yes, apparently against the consensus, whose arguments I'm sympathetic to, but it seems to me like even if we did mention the RW room in a letter it would still only have visibility to a quite small audience. Perhaps the poll choices should have been "yes, publish the RW room/No, don't publish yet"? - Mr. Gunn

28 votes so far, with "no" currently in the lead. - Bill Hooker

What about mentioning the functionality but not the room? If we include a link to the etherpad in which the letter has been prepared, interested people would find the information. - Daniel Mietchen

A few thoughts. 1) It is possible to vote multiple times, I noticed. 2) @Neil: as Mr. Gunn pointed out, the explicit purpose of the room is to document, not to provide a service. What's the point to document, when the document remains secret? 3) @Bill: point taken. However, the mere fact of multi-billion dollar corporations (who, unlike the RIAA, make their money from tax-dollars!!)... more... - Björn Brembs

Also unlike the music industry, the three major publishers have had increasing profits for at least the last five years, with 2008 (of all years!) being a record year with double-digit growth rates for some and a total of almost 5 billion dollars in profits for the three largest corporations alone - and that when other large publishing businesses seem not to have such a great time... more... - Björn Brembs

Couple things. 1) researchers are not the only people here; publishers have shown no compunction in going after librarians. 2) in the library literature, it's fairly well-established that researchers are asking other researchers for copies of articles, rather than (sometimes in addition to) going through ILL and document-delivery services. - D0r0th34

I don't know if this has been studied, but the reasons for that, D0r0th34, have to do with the overhead. To ask a colleague, all you have to do is send them an email. ILL requires forms and accounts and waiting periods and follow-up and so on. - Mr. Gunn

yes, that's the usual reason given :) - D0r0th34

Procedural suggestion - I don't use the RW room for reasons I can go into elsewhere but I voted I don't know because I didn't. I actually take Bjorn's point though - what is the point if it doesn't change things? Anyway the suggestion - rather than people posting that they've sent stuff I suggest people post when they receive a copy. It would even be possible to set up a dead letter... more... - Cameron Neylon

I am behind Bjørn on this, I voted yes and at the time the yes -side was winning. In my opinion, this is a fight worth taking and if that happens, worth loosing. - Nils Reinton

+1 Neil and +1 Cameron. A simple change in the etiquette of the room would protect those sending papers from liability. To fully protect them, though, you'd also have to scrub the archives, something that isn't easy to do on the internet. - Chris Miller

Changing the etiquette in that way is a tacit admission that we are doing something wrong, OR that we are doing something we don't believe is either wrong or illegal but that we fully expect we could be punished for anyway (because the system is unjust). If we are going to fight the good fight as above, we would be better off not handing our opponents the opportunity to argue for the... more... - Bill Hooker

I'll admit to not following the 'fair use' argument very closely, but I'm under the impression that sharing such articles is a clear violation of an institution's TOS with the publisher. I'll readily agree that something can be just but illegal, but that doesn't change the fact that there could be repercussions against those providing articles. Every movement needs its zealots, but I'm more of a casual supporter, and certainly am not willing to go down for the cause. I suspect there are many others like me. - Chris Miller

Chris, it does appear that our use of References Wanted falls under fair use as I figure it: http://www.utsystem.edu/OGC... - Mr. Gunn

Yes, I also think it is fair use, though I am aware that just the suspicion of this not being the case may be enough to shut down the room. Besides, we have Harvard law professor Lawrence Lessig on our sides: http://ff.im/9xiRN . - Daniel Mietchen

Chris's point is a good one - fair use is one thing but its definitely a technical violation of most TOS. On the other hand its not clear that library users sign up to the TOS, the librarians do, which takes us back to Dorothea's point. I take Bill's point though. If you think its a fight worth fighting then it should be done out in the open. The question is both strategic and tactical.... more... - Cameron Neylon

A very kind person sent me a copy of the letter to Cell - unfortunately it was picked up by my mail system's quarantine and instead of rerouteing it safely to my inbox I have to admit I pressed the wrong button and deleted it. Might I trouble them to resend it to me? http://is.gd/5fQ0D <embarassed> - Jo Brodie

http://friendfeed-media.com/50c126f... - Björn Brembs

Given that you can vote multiple times and only 40 votes have been cast, does that mean that about 75% of the subscribers to this room don't care enough to vote? - Björn Brembs

well, you have to figure on some attention attrition, there -- I have a lot of FFeeps who don't seem to actually use the service - D0r0th34

Jo, in case it wasn't clear -- that link from Bjoern goes to the Cell letter. - Bill Hooker

@Björn, that was only the second online poll that I've created and realised shortly after creating it that there _might_ be a potential issue with multiple votes. Can't drill the stats so will have to work on trust. Many of the subscribers to RW don't frequent that often in terms of posting, so I think it's unlikely that the "n" of 40 on the poll is likely to increase much further than as it stands. Moving forward, I guess we'll have to rely on the stats of 57% no 30% yes and 13% unsure. - Graham Steel

Sorry for just posting the link, was in a hurry! - Björn Brembs

@Graham: The question now is, what do we do with the poll? I don't think it really tells us all that much. Moreover, I think none of the arguments for publishing have seen any serious refutation. On the other hand, I don't want to dismiss the counter arguments completely. I suggest we go ahead and describe the functionality without mentioning the room name, even though I think it would be much more effective to mention it explicitly. Any comments/suggestions? - Björn Brembs

I for one agree with that suggestion. What do others think... - Graham Steel

I voted to mention the name but since the majority of votes are against I think Bjorn s suggestion is a good balance. - Pedro Beltrao

+1 Pedro - Nils Reinton

Presumably the letter's authors will give links to their FF accounts, then it's just a matter of scrolling through their posts until, aha!, "Refs Wanted" must be the room they were talking about. So is there really much difference between describing and naming the room? - Bill Hooker

@Bill: You're right, of course, in that it is more a token of appreciation of the other arguments than an effective step towards concealing the room. Alas, it is the only 'middle ground' I could think of. - Björn Brembs

Thank you Björn and Bill :) - Jo Brodie

Ruchira S. Datta

Creativity: A Crime of Passion http://www.scientificblogging.com/rogue_n...

December 13 - Comment - Like - Share

Meryn Stol, Daniel Mietchen, Khader Shameer and 2 other people liked this

"What society claims to want and what is actually rewarded in practice are two different things. We claim to want innovation, but are innovation and creativity actually encouraged, or even allowed in most environments? What types of creative behaviors are rewarded by society, and what types are punished?" - Ruchira S. Datta

3 more comments

It is hard scientific expert blogs,I reference it. - Ami Iida

"it is selective and purposeful rule-breaking that serves to advance ideas or thinking about a situation, in order to come up with a new solution to a persisting problem. There is a difference between rule-breaking for selfish purpose (illegal motive) and rule-breaking for creative purpose (idea advancement)." - Daniel Mietchen

I would add that creativity is not just about consciously breaking rules but very frequently about exploring areas not yet penetrated by human-made rules. And there are some who manage to be creative fully within the rules... - Daniel Mietchen

Ami, thanks. - Ruchira S. Datta

Daniel Mietchen

Amazing Animated Optical Illusions! - http://www.youtube.com/watch...

December 14 from YouTube favorites - Comment - Like - Share

Jan Wessnitzer, Pierre Lindenbaum, Björn Brembs and 2 other people liked this

nice find Daniel - Andrew Lang

Andrew: got it from http://feeds.feedburner.com/Optical... - Daniel Mietchen

Daniel Mietchen

What would research funding look like if it were invented today? Let's start collecting materials. (via http://friendfeed.com/danielm... ).

October 15 - Comment - Like - Share

joergkurtwegner, suze, Meryn Stol and 7 other people liked this

The basic structure for this part iii of the "what would X look like if invented today" series is in the mind map at http://www.mindmeister.com/3016825... , with background via http://friendfeed.com/search... . Main points: More flexibility in the models of funding, more attention to technological shifts in the way people (including scientists) communicate. Such has also been argued at http://ff.im/9GGRn and http://2020science.org/2009... . - Daniel Mietchen

18 more comments

Just noticed that we used different notions of "public funding environments" in the mind map so far. What I had in mind was to have "funding environments" in public, much like what fundscience.org plan to do. Some of the added comments seem to have used the term in the sense of environments for "public funding". Both notions are certainly valid, and we should think of ways to keep them apart. - Daniel Mietchen

good point re making this difference clear(er) in the map - Claudia Koltzenburg

I would like to see a lot more funding of contests - Jean-Claude Bradley

Yes, Jean-Claude, contests and prizes with a competitive element are definitely on the list. If you have good examples from the recent past, please post them here. - Daniel Mietchen

"More money for science is always good. Or is it? Six experts tell Nature what concerns them most about the US stimulus spending and suggest ways to ensure that it benefits research and society in the long term." - http://www.nature.com/nature... - Daniel Mietchen

Daniel -for a recent example of a contest for research: http://onschallenge.wikispaces.com/ - Jean-Claude Bradley

Thanks, Jean-Claude. It is noted along with http://www.claymath.org/millenn... and http://www.xprize.org/ as an effort to make the chain from achievement to award both shorter and more transparent than currently usual. - Daniel Mietchen

Daniel - the thing I like about contests is that barrier to participation is orders of magnitude lower than traditional funding - there is no need to convince anyone that what you are attempting will actually work before doing anything. Of course this limits the type of projects that can be run but it still applies to a large number. - Jean-Claude Bradley

Has there been any recent follow-up study to "Activities, costs and funding flows in the scholarly communications system" at http://www.rin.ac.uk/our-wor... ? - Daniel Mietchen

The Wellcome Trust weighs in on reforming science funding: http://www.timeshighereducation.co.uk/story... - see also http://ff.im/bljS1 . - Daniel Mietchen

thanks for the pointer, Daniel - Claudia Koltzenburg

Let's not forget that http://www.submeta.org/ provided funding for http://onschallenge.wikispaces.com/ - certainly a "basic research" funding model that looks promising - Daniel Mietchen

One more: http://ff.im/cHoa5 on HHMI's focus on "people, not projects" - http://pazoulay.scripts.mit.edu/docs... . - Daniel Mietchen

Daniel, not that I have anything against HHMI, but that mantra is not exclusive to them. For example Max-Planck Society has exactly the same approach (and I would say that at 10% of HHMI's budget and having twice as much Nobel prize winners, MPG looks a bit more effective ;) ). - Pawel Szczesny

Didn't mean this to be exclusive, and I am well aware of MPG approaches (been there for a while). - Daniel Mietchen

"I wish there was a universal format for submitting grant proposals; authors could post proposals (once!) & then the funders bid on them." (rephrased from http://ff.im/5VwEI ). I would add that the process should be public. fundscience.org plan to go this way. - Daniel Mietchen

How do funders and scientists rank "more attention to technological shifts" against the "scientific expertise they have"? One says "change" the other "keep doing what you know"! Are those two things not disagreeing each other? In other words, who would you fund first, the "crazy new idea" or the "conservative stuff"? - joergkurtwegner

I would think funders should have (as they do now) the liberty of choosing their priorities, and in many cases this will be a mixture of many incremental projects and some revolutionary ones. The main shift in the system would thus be to have just ONE avenue for proposals, and to make it public. - Daniel Mietchen

On the role of rules in creativity and innovation: http://ff.im/cRs7K . - Daniel Mietchen

Daniel Mietchen

APOD: 2009 December 13 - Crescent Neptune and Triton - http://antwrp.gsfc.nasa.gov/apod...

December 14 from Bookmarklet - Comment - Like - Share

" Explanation: Gliding silently through the outer Solar System, the Voyager 2 spacecraft camera captured Neptune and Triton together in crescent phase in 1989. The above picture of the gas giant planet and its cloudy moon was taken from behind just after closest approach. It could not have been taken from Earth because Neptune never shows a crescent phase to sunward Earth. The unusual vantage point also robs Neptune of its familiar blue hue, as sunlight seen from here is scattered forward, and so is reddened like the setting Sun. Neptune is smaller but more massive than Uranus, has several dark rings, and emits more light than it receives from the Sun. " - Daniel Mietchen from Bookmarklet

Duncan Hull

The invited review - or, my field, from my standpoint, written by me using only my data and my ideas, and citing only my publications. - http://www.citeulike.org/user...

December 10 from CiteULike: dullhunk's library - Comment - Like - Share

Khader Shameer, Daniel Mietchen, Frank and Egon Willighagen liked this

Do you feel scientifically isolated? Do you find yourself sitting on the side-line while others take the field by the nose and lead it? Are you unable to publish a model that summarizes your data and ideas because reviewers label it as being too speculative and unsupported? Can't get those experiments published in any regular journal? Do you find that nobody is citing your papers? Haven't published in your field for some time, but want to show that you are still a player? Well, no need to worry! There is a special category of publication for you, 'the invited review', and even specialized journals, the 'review journals', that cater to every part of your neurosis. - Duncan Hull

I still think stand-alone reviews should be abandoned in favour of collaboratively written updatable documents (who said wiki?). - Daniel Mietchen

Article-level metrics: Peter Binfield

Powerpoint and Audio for the PLoS Article Level Metrics program http://www.myplick.com/view...

November 20 - Comment - Like - Share

Mike Chelen and Daniel Mietchen liked this

Does not mention whether you have any plans on agreggating contributions by author. Are there any? - Daniel Mietchen

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Plans: not yet. Desires: yes - Peter Binfield

There may well be a Drupal module that allows this. Will have to check. - Daniel Mietchen

Daniel: maybe the aggregator in core or http://drupal.org/project... would work? - Mike Chelen

Thanks, Mike - will take a look; definitely haven't found anything more likely to work so far. - Daniel Mietchen

I now had a look at FeedAPI and do not think it does what we are after. However, a successor module, Feeds, has been released last month, and its description at http://developmentseed.org/blog... looks promising. - Daniel Mietchen

Another interesting module, probably even closer to the target, is http://drupal.org/project... : "Heartbeat displays user activity on a website. This module fungates as API to log message structures, attributes and variables. Once they exist in the database, the activity messages together with their messages templates will form the streams." - Daniel Mietchen

Daniel Mietchen

The Neurocritic: Spindle Neurons in Elephants and Dolphins: Convergent Evolution/ Deep Homology in Large-Brained Mammals? - http://neurocritic.blogspot.com/2009...

December 14 from Bookmarklet - Comment - Like - Share

"Fig. 5 (Hakeem et al., 2009). The phylogenetic distribution of the VENs. Species in which VENs have been observed are indicated by underlines; species which have been examined and found to possess no VENs are indicated by italics. Note that while the African and Indian elephants have VENs, they share this trait only with other large-brained groups (the cetaceans and humans/great apes) and not with their nearest relatives, the rock hyrax, manatee, giant elephant shrew, and tenrecs." - Daniel Mietchen from Bookmarklet

Daniel Mietchen

Scientists doing great work seldom look like Great Scientists. - http://metamodern.com/2009...

December 9 from Bookmarklet - Comment - Like - Share

Richard Akerman, Chad Orzel, Konrad Förstner and 7 other people liked this

Yes! At the Beagle Project we're always harping on this - it's a big problem - the 'icons' make people feel disconnected from the possibility of genius and alienate young would-be scientists. - Karen James

The reverse also seems to be true - grant reviewers being alienated by the young guys' ideas. - Daniel Mietchen

Daniel Mietchen

Open Recherche policies - http://www.backtype.com/url...

December 13 from Comments by... - Comment - Like - Share

Bonne idée! En fait, on est en train d'écrire une charte à http://en.citizendium.org/wiki... qui est assez proche.Quelques coquilles:# Créer des outils pour partager des méthodes et des résultats.# Faciliter l’accès aux logiciels libres. Read more comments by Daniel Mietchen - Daniel Mietchen

Daniel Mietchen to Daniel's feed, Science in the long run

Open Recherche serait un environement international de travail scientifique intégrant les avantages deWikipédia, de Google Code, d’ArXiv, de CiteULike et de systèmes d’Open Peer Review. Il n’encouragerait pas la course à la publication mais encouragerait les utilisateurs à mettre à jour les articles existants, que d’autres pourront utiliser... - http://ths1104.wordpress.com/

December 13 from Bookmarklet - Comment - Like - Share

Jean-Claude Bradley and Kubke liked this

"Il permettrait, grâce au partage massif et structuré des données, d’arrêter d’inventer la roue. Il permettrait à chacun de rejoindre un projet personnel simple ou un projet interdisciplinaire complexe. Il permettrait à Mr Curieux d’apprendre ce que Mme Catastrophe fait dans son garage et de lui dire qu’elle le fait mal. Il permettrait peut-être même d’ouvrir les yeux et réfléchir un peu…" - Daniel Mietchen from Bookmarklet

Open Recherche policies: http://ths1104.wordpress.com/open-re... - Daniel Mietchen

Science in the long run

Climate vs. Tobacco - http://rs.resalliance.org/2009...

December 13 from Resilience Science - Comment - Like - Share

Daniel Mietchen and Ruchira S. Datta liked this

Tobacco and public health researcher Maria Nilsson and others have a Comment in the Lancet Climate policy: lessons from tobacco control (doi:10.1016/S0140-6736(09)61959-0) in which they compare the policy response to the public health problems of tobacco to climate policy: Controlling tobacco use is the highest immediate priority for global health, while climate change is the biggest [...]

"Climate change can be compared to passive smoking because those who generate the damage are not the same [...] as those who suffer" - Daniel Mietchen

Daniel Mietchen

Three days left to vote on Open Science Breakthrough 2009 - http://ways.org/en...

December 13 from daniel's blog - Comment - Like - Share

Direct link to poll: http://bit.ly/77Ua4Q . - Daniel Mietchen

Brian Haugen

Not Much "Novel" Under the Sun -- http://www.sciencemag.org/cgi...

December 11 from Twitter - Comment - Like - Share

Neil Saunders liked this

"In 1970, we saw one “novel” discovery for every 50 “new” ones. By 2007, that ratio had changed so that a “novel” discovery came along for every 1.45 “new” discoveries. " - Daniel Mietchen

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"What should we make of the steady rise in “novel” papers? We suggest that the trend represents two things. First, the growing ties between scientific and financial endeavors offer some explanation." - Daniel Mietchen

"The second likely explanation has been an increase in the degree to which authors of scientific papers resort to self-promotion and hyperbole in the effort to publish papers that will be noticed." - Daniel Mietchen

"When scientists feel the need to resort to novel ways of saying “new,” even at the price of misrepresenting their meaning, the effect is to diminish the standing of their work." - Daniel Mietchen

That's exactly the sort of behavior you'd expect to see from individuals who must use article publications to compete for ever-diminishing amounts of post-doc positions. - Naomi Most

Very little is truly "novel". Which is not to say that it isn't interesting, clever, useful, "new" and so on. - Neil Saunders

Daniel Mietchen › Comments