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Alex Holcombe › Likes

Michael Nielsen
Sugata Mitra: The child-driven education | Video on TED.com - http://www.ted.com/talks...
Fascinating. A very related post by Daniel Lemire: http://friendfeed.com/lemire... - Jan Jensen
Cameron Neylon
Public Availability of Published Research Data in High-Impact Journals - http://www.citeulike.org/user...
Kubke
Times Higher Education - A footnote - Far from it, publishers are key in advancing scholarship - http://www.timeshighereducation.co.uk/story...
"We evolve scalable, sustainable enterprises that enable intellectual freedom and the flow of culture and scholarship. Beyond a copyright framework to protect our investments, we strive for the widest distribution and access to our publishing that we can achieve." - Kubke from Bookmarklet
"Publishers are needed to maintain quality standards, build brands, enhance discovery, enable access, fund the supply chain, invest for the future, and nurture the authors who express our culture. Without us, there is the "information superhighway" to fall back on, but soon enough that would become an unmanageable "digital deluge"." - Kubke
The comment by Herbert on the article is very nicely put - Alex Holcombe
Johnstone's comments are not far off the mark either.... - Kubke
Michael Nielsen
Why Education Startups Do Not Succeed « Avichal's Blog - http://avichal.wordpress.com/2011...
Michael Nielsen
My new book on open science and related topics has just come out. It's currently available in hardcover from Amazon.com, and should by Oct 21 become available for Kindle, and from other booksellers (when it's not already). - Michael Nielsen
Server looks down. - Daniel Mietchen
Daniel: yes. I've had very few problems with my host (Dreamhost), but today the machine my blog is hosted on had filesystem problems. It should be up again very soon. - Michael Nielsen
And it's still not back up :-( - Michael Nielsen
Now back up :-) - Michael Nielsen
Cameron Neylon
Everything’s fine with peer review- if there are any flaws, they’ll be taken care of by evolution? - http://alexholcombe.wordpress.com/2011...
Michael Nielsen
Doing Science in the Open | Jonas Kubilius on neuroscience - http://neuromokslai.wordpress.com/2011...
Some thoughtful practical remarks about open science from neuroscientist Jonas Kubilius - Michael Nielsen
Kubke
Times Higher Education - Peers, review your actions - http://www.timeshighereducation.co.uk/story...
"But what's truly mind-boggling is that we also review and edit for these corporations. For free. It's the editorial and review process that gives the crucial stamp of approval to research. But publishers don't provide this: it's one more thing that we give them. We feel obliged to contribute our time, effort and expertise because reviewing is seen as a service to the community. But it's become a service to corporations." - Kubke from Bookmarklet
Michael Nielsen
Open research casts doubt on arsenic life - http://www.nature.com/news...
Michael Nielsen
Coaching a Surgeon: What Makes Top Performers Better? | The New Yorker - http://www.newyorker.com/reporti...
Wonderful essay on whether coaching can help in areas where we don't traditionally have coaches. - Michael Nielsen
Wondering how science coaching would look like. Certainly room for improvement at all stages of what formerly was called a "career" in science. - Daniel Mietchen
Michael Nielsen
Radiolab: An Appreciation by Ira Glass - http://transom.org/?p=20139
A wonderful detailed appreciation of RadioLab, by Ira Glass. - Michael Nielsen
Michael Nielsen
The Necessity of Funding Failure | Wired Science | Wired.com - http://www.wired.com/wiredsc...
Wouldn't have hurt to cite the HHMI vs. NIH study: http://papers.ssrn.com/sol3... . - Daniel Mietchen
oatp
Open science is a research accelerator - http://www.nature.com/nchem...
"An open-source approach to the problem of producing an off-patent drug in enantiopure form serves as an example of how academic and industrial researchers can join forces to make new scientific discoveries that could have a huge impact on human health." Posted by stevehit to pep.opendata oa.new on Fri Sep 23 2011
"For people to actually take part, we found two things to be crucial. The first is that there must be a kernel of data or activity with which people can become involved. Without a starting point, people have little to go on and no incentive to contribute. Second, the barrier to entry must be low. Thus it is essential that project summaries are up to date, and that what is required from the community is clear. It is also important that the technology and software people use to contribute is simple." - Daniel Mietchen
"Participation in open projects allows companies to demonstrate a commitment to worthy causes for public-relations reasons." - Daniel Mietchen
"having effective means of sharing research data in full stimulated a distribution of the real, experimental lab work. With advances in technology, it will only become easier to collaborate in this way." - Daniel Mietchen
"The crucial message of the open project is this: the research was accelerated by being open." - Daniel Mietchen
"in open projects everything is available on the web; the project need not cease with the graduation of students, the termination of a grant or the demise of a principle investigator." - Daniel Mietchen
"Funding for the kernel effort of such a project, crucial in generating activity to which others may respond, can leverage extra input that is unfunded, and this should be attractive for funding agencies keen to maximize the impact of the relevant science." - Daniel Mietchen
"Open science is subject to the most rigorous peer review because the review process never ends, essentially because there will always be a commenting function on results, and a mechanism for the community to police those comments." - Daniel Mietchen
"what about open-source drug discovery?" - "That the answer is unclear makes it worth trying." - Daniel Mietchen
A great piece - should be required reading for anyone doing, managing, financing, publishing, teaching, learning or reusing science. - Daniel Mietchen
Thanks, Daniel. - Matthew Todd
Bill Hooker
Resharing because the end of the month is looming: http://friendfeed.com/science.... There have been many conversations in this space concerning the value to Open Science of having people on the inside -- able to move up the traditional tenure foodchain and still advocate for openness. Please consider helping Steve Koch become one of those people.
You'll need to go to the linked post for full context; briefly, there's a draft letter in support of Steve's tenure case here (http://piratepad.net/DpuxZJT...) that his Open Science peeps can sign. This is not a substitute for the traditional individual letters of support, but an entirely appropriate supplement to same given that Steve is making Open Science a big part of his case. - Bill Hooker
thanks for posting this, i lost track of it and i never saw the actual letter. - Christina Pikas
Made some mods and signed the letter. Not sure whether adding additional positions helps much? - Cameron Neylon
Thanks Cameron! I like the mods you made. - Bill Hooker
signed! - Björn Brembs
(Thought I had already done so) - Signed. - Graham Steel
Added a sentence and signed. Apologies for the delay. Lending one's signature to something like this is no small thing, and I just had to find a few minutes to check the text of the letter, which I think is good. The very best of luck, Steve. - Matthew Todd
Signed. Good luck, Steve! - Michael Nielsen
Just saw this thread. Thank you everyone! - Steve Koch
Matthew Todd
Our commentary on open science is out in Nature Chem http://www.nature.com/nchem...
Thanx for citing the Blue Obelisk paper! - Egon Willighagen
Of course! - Matthew Todd
Kubke
"It is said that peer review is like democracy: it's not the best but it's the best we know. But science is not democratic. One doubtful scientist can be right while 100 convinced colleagues can be wrong. Indeed, the physicist Richard Feynman once defined science as "the belief in the ignorance of experts". Specifically, peer review of grant applications, or peer "preview", is inimical to radically new ideas. Today, however, the all-powerful peer-preview bureaucracy is the determinant of excellence. It is taboo even to criticise it. So the natural inclination to oppose major challenges to the status quo has become institutionalised. For radical research, one can argue that "the best we know" has become the worst." - Kubke
hm. taboo to criticize where? 'cause we sure do in STS. We also talk about its conservative nature. - Christina Pikas
@Christina you should meet the crowd that surrounds me - even open access is sometimes a bad word :) - Kubke
Peer review can indeed be a total shambles. But I worry that without it science would be littered with total cranks chasing their own crazy 'science' ideas eg. http://maya12-21-2012.com/2012for... OK - even more total cranks than we already have. - Paul Gardner
I don't think there is anything intrinsically wrong with peer review - it is the 'x number of dudes/dudettes to remain undisclosed whose names will never be made public and whose opinions will never be publicly visible will decide in the name of the entire community what is valuable and what isn't what is correct and what isn't and if you happen to have a different opinion I will not make a space available for you to share it" that I think is wrong - Kubke
Joe
Fwd: http://scitech.sla.org/2011... Please join us on Monday, October 24th for a free online seminar devoted to a discussion of the changing landscape of scholarly communication and scientific publishing. The speakers (John Wilbanks, Heather Piwowar, and Molly Keener) will address what STM...
Pawel Szczesny
Science Commons is closed and it seems that the focus of that part of Creative Commons shifts from (open) science to (open) educational resources.
I have an impression that it will disconnect scientific community from important discussions again. - Pawel Szczesny from iPhone
John had reassuring thing to say about CC's continuing role in science: http://del-fi.org/post... - Bill Hooker
CC community at the CC global summit (last weekend) remained unconvinced. We'll see. - Pawel Szczesny from iPhone
Michael Nielsen
Daniel Mietchen
Scientific research is a process concerned with the creation, collective accumulation, contextualization, updating and maintenance of knowledge. Wikis provide an environment that allows to collectively accumulate, contextualize, update and maintain knowledge in a coherent and transparent fashion. Here, we examine the potential of wikis as platforms for scholarly publishing. In the hope to stimulate further discussion, the article itself was drafted on Species-ID – a wiki that hosts a prototype for wiki-based scholarly publishing – where it can be updated, expanded or otherwise improved. - Daniel Mietchen
"RT @GigaScience Article even editable: http://bit.ly/i3Fu10 RT @OAgeek Wikis in scholarly publishing http://bit.ly/fSHmy0" http://twitter.com/#!... - Claudia Koltzenburg
see entry for this article on p2pfoundation wiki http://p2pfoundation.net/Categor... - Claudia Koltzenburg
Strange to have a non-editable (PDF) proof of an article drafted entirely on-wiki. Always looking for the edit button. - Daniel Mietchen
:-) -- well, actually it produces extra work, hence extra costs... - Claudia Koltzenburg
The paper is out - http://dx.doi.org/10... . Editing continues at http://species-id.net/wiki... . For instance, ideas for images and multimedia are always welcome, and of course updates, examples. - Daniel Mietchen
Björn Brembs
Peer reviews: make them public - http://www.nature.com/nature...
I've thought about including reviewers' comments in "behind the scenes" blog posts about my papers, as a step towards transparency. I'd certainly be interested in reading peer reviews of papers I've liked (or not liked). But on a broader scale, I wonder if institutionalizing this process would be a more feasible step towards reforming peer review as compared to, say, completely open/signed reviews (as Daniel alludes in his first sentence). - Jason Snyder
There are a couple of journals now that publish the referee reports along with paper (ex. EMBO J and Mol Sys Bio). I think it is interesting to be able to go read them for those cases where you want a lot of detail. - Pedro Beltrao
Starting to publish reviews along with the accepted papers is a good initial step, yet qualitative change is more likely to happen when reviews of rejected papers (or grants, for that matter) are likewise being made available. - Daniel Mietchen
The medical BMC-series journals have been doing this for a decade due to Fiona Godlee's influence. All articles versions and reviews complete with the reviewer names are available to the readers. They don't shout about it much so hardly anyone seems to know about it. People still talk about open peer review as a wholly hypothetical thing. - Matt Hodgkinson
Yes, BMC is ahead of the crowd in this regard, but they lose interactivity by publishing the review process only after (and only if) the paper has been accepted. The two-step process in use at EGU journals (where the submitted manuscript is public, as are the reviews and comments) is more inviting to community participation (about 25% of their articles receive comments from beyond the... more... - Daniel Mietchen
You're right on that distinction. I call non-anonymous review "Open peer review" and public/volunteer peer review "Community peer review" (http://journalology.blogspot.com/2007...). EGU's discussions are a little hidden away, two clicks from the abstract. EGU has "service charges" for papers to appear in the discussion forum - essentially a... more... - Matt Hodgkinson
Submission fees do indeed not feature prominently in the discourse, and I agree that they merit more attention. - Daniel Mietchen
I like how Friendfeed's email updates for this discussion are delayed by 3.5 weeks... - Jason Snyder
Do any journals have policies about whether it's ok for authors to publish reviewers' comments (on a blog, for example)? Could get in trouble for doing it? - Jason Snyder
Good question. I"ve published reviews on my blog, but mainly grant application reviews. - Björn Brembs
Jason++ (interesting question!) - Egon Willighagen
Jason, I don't think it would be big trouble, I think they'd just ask you to take them down as a first step, if they care. Seems a worthwhile place to ask for forgiveness rather than permission. I'm planning on posting some conference reviews I've received this way, shortly... in addition to all the other good reasons, very helpful for newbie submitters and reviewers to see more examples, I think. - Heather Piwowar
Thanks for the feedback. We just had a paper accepted to Nature and, Heather, as you suggest I would like to provide an example. After hearing so many discouraging, through-the-grapevine stories I feel like sharing my experience could be helpful and encouraging for others. Whether or not my PI is game is another question... - Jason Snyder
I am planning an ESOF session on peer review for newbies - anyone game to get involved? http://en.wikiversity.org/wiki... - Daniel Mietchen
Heather Piwowar
Pitching "research for more effective research" conference idea to o'reilly, with others. Sponsor+attendee list ideas? #scifoo
unconference, you must mean - Matthew Todd
Heather Piwowar
Just finished great session on open data. Had to get after conversations kicked out of room: good sign #scifoo
Cameron Neylon
(#ESA11) rOpenSci: a collaborative effort to develop R-based tools for facilitating Open Science - http://feedproxy.google.com/~r...
Heather Piwowar
28% of articles deposited in PubMed in 2009 are now freely available. http://t.co/DY3GMWc
Pawel Szczesny
Daniel becomes Wikimedian in Residence on Open Science. http://blog.wikimedia.org/2011...
Happy days. - science3point0
W00t! - Björn Brembs
This means that there will be a need for reviewers of existing content, and for suggestions on topics that are not yet covered. I take the above as applications for at least one of these two options :-) - Daniel Mietchen
Obviously! - Björn Brembs from iPhone
This is great news! Congratulations. - Marcus D. Hanwell
Daniel Mietchen
Getting scooped for being open - time to set the norms straight - http://www.nature.com/news...
""The crowd-sourcing efforts arrived at almost all of the scientific conclusions about the strain comparisons first," says Mark Pallen from the University of Birmingham, UK, "so we're surprised and disappointed that these findings are not referred to in these papers."" - Daniel Mietchen from Bookmarklet
To me, this is another strong argument for doing peer review in public - not sure how the reviewers for the Archives of Microbiology paper could have missed the missing reference to the GitHub repository, but with review in public mode, someone would certainly have told them quickly. - Daniel Mietchen
Björn Brembs
Why would you pay to get published? - http://onlinelibrary.wiley.com/resolve...
Hahahaha... funny story! - Egon Willighagen
Don't feed the trolls. - Noel O'Boyle
I was going to make a sarky comment given I can't access it but I did wonder whether there was more to article than just a disingenous claim that publishing with them was "free" or whether there was a joke buried in there somewhere? - Cameron Neylon
Good quote: "It seems doubtful that lack of access to their articles represents a sufficiently widespread concern to motivate authors publishing in OA journals" - Jason Snyder
What happens when everyone has gone open access but there's still all that good, old research published in subscription journals? Can libraries download entire digital archives prior to ending their subscriptions and make them available once they no longer pay the bill? Or might for-profit publishers continue to attract subscriptions long after they've become unpopular, just because people want/need access to the classic papers? - Jason Snyder
Email the author and ask for a reprint? - Egon Willighagen
wow... - Kubke
I'd love to see libraries get together and collaboratively write an application that downloads every single article each library has access to and build a large database of the scientific literature. - Björn Brembs
+100 Björn - Graham Steel
Jason - it depends on the subscription. Some licenses allow us to keep locally owned copies of content. Also anything that's in the public domain can be digitized and hosted. Bjorn - I doubt we (libraries) could write an application like you decribe for collecting journal article content. LOCKSS is a network that allows people to share (sort of) and Hathitrust has collected digital... more... - Elizabeth Brown
@Elizabeth: I think starting with the content where local copies are allowed by the license would be a good start. That should include all print subscriptions, be definition. One may successively widen the scope of such a database using fair-use and trying to create precedent as well as by support from science funders and eventually legislation. Creating awareness of the problem and initiating action would already go a long way, as far as I'm concerned. - Björn Brembs
Bjorn, thanks for responding. The problem is that the print content is part of the electronic license, so it can't be treated separately. Most, if not all of those articles are owned by the publishers. We can lend a print copy by ILL (using the first sale doctrine) but we don't have the same first-sale rights for electronic materials. I'm refering to US copyright law which is different... more... - Elizabeth Brown
Am halfway through with your post but need to run. Real quick: I was trying to say that libraries which have a print copy, already have a local copy. It will be hard to argue against local digital copies. - Björn Brembs
Ontario has done more-or-less what Bjorn is suggesting with our Scholars Portal Journals database. It has 20+ million article and is very easy to use. We've essentially negotiated our licenses with publishers to allow us to own and locally host the database. The good news is that it's an amazing resource, particularly for ugrads looking for "good enough." The bad news is that it leaves... more... - John Dupuis
Thanks for mentioning initiatives in Canada. In the US most licenses are negotiated at the campus (sometimes system level), and it seems to be harder to negotiate the access you describe. Another major licensing issue that comes up is ILL use - some of the ebook and e-journal licenses don't allow for ILL lending. Once this use is prohibited it's hard to negotiate back into a contract. - Elizabeth Brown
That's excellent, John! Now other libraries would have to do similar things and (as much as legally possible) get the databases interoperable. The proof of concept would already be enough to push for next steps, IMHO. - Björn Brembs
I agree with you Bjorn that the database interoperabilty should come soon. The biggest roadblock is getting standards in place and persuading publishers it's OK to do this. I still see the silo mentality in full force. - Elizabeth Brown
Bjoern Have quoted you in my blog http://blogs.ch.cam.ac.uk/pmr... . Do you have a formal reference about publishers negotiating impact factors? - peter murray-rust
@brembs Fantastic dissection, give us more of the same plz. - 'Mummi' Thorisson
@peter: the PLoS Medicine reference in the talk is as formal as it gets. The Current Biology example is just pulled from the ISI website. - Björn Brembs
speaking of downloading every single article a library has a subscription to, check out what can go wrong: http://kottke.org/11... - Jason Snyder
Michael Nielsen
Civic hacking: a new agenda for e-democracy | openDemocracy - http://www.opendemocracy.net/media-e...
A nice post about open governance: it's not the same as open government. Perhaps the main impact is to shift the locus of collective action away from government and toward citizen groups. In other words: is open government really about government? Or is it about something completely different? - Michael Nielsen
Kubke
Times Higher Education - A class half full: Australia's missing indigenous scholars - http://www.timeshighereducation.co.uk/story...
"According to a report for Universities Australia by the Centre for the Study of Higher Education at the University of Melbourne, published in 2008, indigenous people participate in higher education at less than half the national average rate. By 2006, indigenous people made up 2.4 per cent of the Australian population. However, only 1.25 per cent of Australians commencing university study were Aboriginal." - Kubke from Bookmarklet
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