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Steve Koch
Rob Olendorf has begun some calculations to frame "open" versus "closed" science in game theory context. Even the basic analysis, considering "defect" versus "tit for tat" strategies gives some illumination on the landscape for open science incentives. He and I have decided to do the work as "open science," hosted on github....
Annotated pdmatrix for friendfeed.png
Annotated temptationtodefect figure for friendfeed.png
Whoops. Github link was truncated - Steve Koch
This presumes fixed strategies and rational decisions I presume? So there are also marketing effects in here as well? Not just what are the percentage of players in each camp but the perceived percentage? - Cameron Neylon
Important theory... now many tend to think that Closed Science only takes advantage of Open Science... game theory can provide some (theoretical) evidence for that.... interesting! - Egon Willighagen
Open science has many "players". Do the arguments hold if I am Player 1 and the crowd is Player 2? - Matthew Todd
If you haven't already, you should check the literature on game theory and collective action problems (e.g., ) Open science is an example of a collective action problem. - Michael Nielsen
@Michael, I haven't read any background yet. Rob has, I'm sure, as he used this in his Ph.D. research in evolutionary biology (experiment + modeling/theory). I'm hoping I can get his attention / contribution on this thread soon! I don't have any background in game theory. But, as far as I understand, the analysis Rob's done so far is the most basic first step, and tit for tat (TFT)... more... - Steve Koch
@Mat I am not sure. I'm going to see if I can get Rob to chime in here! - Steve Koch
@Cameron, I think this starting point is fixed strategies, either "defect" or "tit for tat." Like I said in one legend, I can't remember what "temptation to defect" means exactly. I don't think perception is modeled in this basic starting point. I sent an email to Rob urging him to chime in on this thread, so I hope he can! - Steve Koch
Good to see this being tackled in a more formal way, but sure, the simple 2x2 matrix is only the first step. For instance, collaboration can well occur behind closed doors. - Daniel Mietchen
Side issue: Wouldn't something like Octave or R be a better fit to an open project than MATLAB? - Daniel Mietchen
Totally agree open coding platform would be better. Right now there's not much code at all, since it's analytical that Rob did. (Rob, can you post snapshot images of your calculations, if any?) Since right now it's just plotting, R would be good. (I added the text to his images via powerpoint, just for convenience.) I am tempted later tonight to make the pots in R. A further aside: I... more... - Steve Koch
A somewhat related project is Lee Worden's "Mathematics of Direct Democracy" at (or, more detailed, at ) - see also on link to collective action problems. - Daniel Mietchen
Rob posted some thoughts / responses on the github wiki: - Steve Koch
Infinite Stupidity. Social evolution may have sculpted us not to be innovators and creators as much as to be copiers | Edge -
Infinite Stupidity. Social evolution may have sculpted us not to be innovators and creators as much as to be copiers | Edge
"If we think that humans have evolved as social learners, we might be surprised to find out that being social learners has made us less intelligent than we might like to think we are. And here’s the reason why. (...) I can choose among the best of those ideas, without having to go through the process of innovation myself. So, for example, if I’m trying to make a better spear, I really have no idea how to make that better spear. But if I notice that somebody else in my society has made a very good spear, I can simply copy him without having to understand why. (...) We like to think we’re a highly inventive, innovative species. But social learning means that most of us can make use of what other people do, and not have to invest the time and energy in innovation ourselves. (...) As our societies get larger and larger, there’s no need, in fact, there’s even less of a need for any one of us to be an innovator, whereas there is a great advantage for most of us to be copiers, or followers.... more... - Amira from Bookmarklet
"I want to go further, and suggest that our mechanism for generating ideas maybe couldn’t even be much better than random itself. And this really gives us a different view of ourselves as intelligent organisms. Rather than thinking that we know the answers to everything, could it be the case that the mechanism that our brain uses for coming up with new ideas is a little bit like the... more... - Amira
Very culturally specific though - varies between countries - Winckel from iPod
"Maybe curiosity means trying out all sorts of ideas in your mind. Maybe curiosity is a passion for trying out ideas. Maybe Einstein’s ideas were just as random as everybody else’s, but he kept persisting at them. (...) We might even wonder if the people in our history and in our lives that we say are the great innovators really are more innovative, or are just lucky." - Amira
This notion has been thoroughly explored in Dean K. Simonton's _Origins of Genius_. - Ruchira S. Datta
Thanks for pointing this book, Ruchira! I still have in mind Malcolm Gladwell's "Outliers" - an interesting study of what determines the "success" and redefines the word "genius" (from a more sociological context). - Amira
Bruno C. Vellutini
Welcome to the Nanopub, a friendly place serving up nanopublications to critique, customize and share. This site was established to host the very first collection of nanopublications. - Bruno C. Vellutini
Science in the long run
Surviving the atemporality of internet technology by becoming multi-temporal -
Becoming ‘multi-temporal’, rather than multi-cultural: it used to be a very big problem for historians that they supposedly could not divide themselves from the outlooks and interests of their own age. I think we are approaching a situation where the outlooks and interests of our own age make very little sense. They just don’t bind [...]
Identification and correction of systematic error in high-throughput sequence data -
Background: A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads. The implications of such errors are application specific, ranging from minor informatics nuisances to major problems affecting biological inferences. Recently developed ``next-gen'' sequencing technologies have greatly reduced the cost of sequencing, but have been shown to be more error prone than previous technologies. Both position specific (depending on the location in the read) and sequence specific (depending on the sequence in the read) errors have been identified in Illumina and Life Technology sequencing platforms. We describe a new type of systematic error that manifests as statistically unlikely accumulations of errors at specific genome (or transcriptome) locations. Results: We characterize and describe systematic errors using overlapping paired reads form high-coverage data. We show that such errors occur in approximately 1 in 1000 base pairs, and... - bioinffeed
Michael Kuhn
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. -
“For the last year, my colleagues and I at Institute for the Future have been researching the future of science to identify big areas of science we think will have a transformative impact over the next decade. We read a lot of papers, conducted interviews, hosted an Open Science unconference, held an expert workshop with researchers from UC Berkeley, Stanford, UC Santa Cruz, Scripps Research Institute, SETI, and private industry, and spent many weeks synthesizing what we learned. (...) The map focuses on six big stories of science that will play out over the next decade: Decrypting the Brain, Hacking Space, Massively Multiplayer Data, Sea the Future, Strange Matter, and Engineered Evolution. Those stories are emerging from a new ecology of science shifting toward openness, collaboration, reuse, and increased citizen engagement in scientific research. (...) Every forecast could be rephrased as a “what if” question. What if you could record your dreams? What if you could design a life... more... - Amira from Bookmarklet
Michael Nielsen
Paris Review - The Art of Fiction No. 211, William Gibson -
Thought-provoking throughout. - Michael Nielsen
Daniel Mietchen
"There should be only one repository of art in the world, to which the artist would donate his works to take what he would need" -
"There should be only one repository of art in the world, to which the artist would donate his works to take what he would need"
Such wrote Beethoven in 1801 as a postscript to financial negotiations. With , we are aiming at a science version of such a repository (keeping in mind that it may well be distributed). UPDATE Nov 2011: The project is now up for crowdfunding via . - Daniel Mietchen from Bookmarklet
"Nun waere das saure Geschaeft vollendet, ich nenne das so weil ich wuenschte dass es anders in der Welt sein koennte. Es sollte nur ein Magazin der Kunst in der Welt sein wo der Kuenstler seine Kunstwerke nur hinzugeben haette um zu nehmen was er brauchte; so muss man noch ein halber Handelsmann dabei sein und wie findet man sich darein -- du lieber Gott -- das nenne ich noch einmal sauer." - Bill Hooker
Possibly bad translation: "Now let the sour business be finished; I call it so because I wish it could be otherwise in the world. There should be only one Repository of art in the world, to which the artist need only donate his work in order to take what he needed. That one must be half a merchant into the bargain, and how to find oneself in it -- dear God! -- that is what I call again sour." - Bill Hooker
If I have the translation even close, then Ludwig is complaining not just about the absence of a single repository and reciprocal access rights for depositors, but also about search! :-) - Bill Hooker
A video on Beethoven's repository is now up: . - Daniel Mietchen
Fascinating bit of history. I'll be giving a talk on open science in the city of Beethoven's birth (Bonn) later this month and it'll be fun to riff on this. - Todd Vision
Thanks Dan for the link to the Google Books transcription. I found a facsimile of the letter itself here: - Todd Vision
Thanks - I cropped the relevant passage to . When will the talk be? - Daniel Mietchen
Pierre Lindenbaum
The paper about BioStar has been published in "PLoS Computational Biology" -
Christina Pikas
OT: New project for the spring -
Woohoo! - Marie
Mega congrats - suelibrarian
Congrats!!! - Katy S
Congratulations! - Björn Brembs
thank you all! - Christina Pikas
Simon Cockell
Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data. -
Bioinformatics (Oxford, England) (12 October 2011) MOTIVATION: High-Throughput Sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein-DNA and protein-RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing-depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing. RESULTS: We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq, and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics.... - Simon Cockell
Daniel Mietchen
Thanks! I have also uploaded it to and . We have the audio and video files separately, so if anyone would like to go for a translation or other modification, that should be facilitated. Just looking for a good place where to put these additional files. - Daniel Mietchen
So cool! - Björn Brembs
Einstein quote, great. Video, super. - Anthony Sebastian
It's actually a Beethoven quote: . - Daniel Mietchen
Michael Nielsen
My new book on open science and related topics has just come out. It's currently available in hardcover from, 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
Egon Willighagen
ha! in just 5 months, our HLCS LODD paper on linked open drug data made the top 10 of jcheminf *all time*!
Ruchira S. Datta
I'm really excited to join Prof. Carlo Maley's lab in the Center for Evolution and Cancer in the UCSF Medical Center at Mt. Zion as a research specialist on Monday.
Congratulations! - imabonehead
We'll be researching how precancerous cells progress to cancer, and how cancer develops resistance to chemotherapy, leading to difficult-to-treat relapses. - Ruchira S. Datta
imabonehead, thanks so much! :-) - Ruchira S. Datta
Wow, you guys are quick. I posted on Google+ first, but still haven't gotten any response, whereas here I have 4 likes and 1 comment. FriendFeed lives! :-) - Ruchira S. Datta
Congrats, Ruchira. - OCoG of FF, Jimminy
Thanks, Jimminy! :-) - Ruchira S. Datta
Ruchira, well that definitely tells you something about FriendFeed versus Google+ :D - imabonehead
Congrats! - Anne Bouey
Very cool; congratulations! - Jenny from Android
Thanks, Anne and Jenny! - Ruchira S. Datta
Congrats! - Spidra Webster
Congratulations, Ruchira! - Victor Ganata
Thanks, Spidra and Victor! imabonehead, at this point I have 9 likes here, and still the only response I have on Google+ is a +1 from Anne. - Ruchira S. Datta
That +1 actually came before I saw it here. - Anne Bouey
Thanks, Anne! Now chaz2b has +1ed it there too (thanks!), and I have another +1 from my friend Monica Anderson--the first response on Google+ that isn't also here. Interesting and somewhat surprising. - Ruchira S. Datta
thank you for sharing this great news with us, :) - chaz2b
Deepak Singh
Getting kids on the right track with early science education -
Of course, pre-schoolers are ready. I got my introduction well before I was 5 and really got interested between 5 and 8 - Deepak Singh
Yann Abraham
Identification of Human Housekeeping Genes and Tissue-Selective Genes by Microarray Meta-Analysis -
PLoS ONE, Vol. 6, No. 7. (27 July 2011), e22859. The results indicate that sufficient samples have improved the identification of protein-encoding transcriptome of a tissue. Comprehensive meta-analysis has proved the high quality of our identified HK and TS genes. These results could offer a useful resource for future research on functional and genomic features of HK and TS genes. Cheng-Wei Chang, Wei-Chung Cheng, Chaang-Ray Chen, Wun-Yi Shu, Min-Lung Tsai, Ching-Lung Huang, Ian Hsu - Yann Abraham
Bill Hooker
50_tipsPoynter.pdf (application/pdf Object) -
Tags: tools writing spouse - Bill Hooker
Pedro Beltrao
RT @gepasi: Lots of #sysbio & modelling success stories in a huge survey of the literature of last 10 years by Hübner et al.
Michael Nielsen
‪Steve Yegge, "What Would You Do With Your Own Google?"‬‏ - YouTube -
‪Steve Yegge, "What Would You Do With Your Own Google?"‬‏ - YouTube
I love the concept of making money with principles -- I can buy that, and sell that personally as well. - Mickey Schafer
love the idea: medicine is a generalists profession -- or something like that! - Mickey Schafer
LOVE THIS: not once did he mention "external funding" -- it was all about individuals making principled decisions about how to invest their intelligence. What an awesome way to start the morning:-). - Mickey Schafer
Björn Brembs
Why I will never pursue cheating again - A Computer Scientist in a Business School - http://behind-the-enemy-lines....
Why I will never pursue cheating again - A Computer Scientist in a Business School
"After spending a tremendous amount of time fighting and pursuing all the cheating cases, I decided that it makes no sense to fight it. The incentive structures simply do not reward such efforts. The Nash equilibrium is to let the students cheat and "perform well"; in exchange, I get back great evaluations." - Björn Brembs from Bookmarklet
Weird -- I cannot get to the link. - Mickey Schafer
Thank the FSM for content scrapers: - John Dupuis
Maybe the problem is in the creating of assignments for which it is so easy to cheat? - Todd Hoff
This is exactly what I find, too: "One interesting observation: Almost all cheating happened within groups with cultural ties. Koreans copy from Koreans. Indians from Indians. Greeks from Greeks. Jews from Jews. Chinese from Chinese. Not just in international students (we do not have that many in the undergrad program), but within US-born students. A result of socializing in similar... more... - Mickey Schafer
Todd -- that is a lovely idea, and certainly we can work on making assignments more difficult to cheat on, but it is also impractical. First, if a student is going to learn to write a science paper, then s/he has to write a science paper. Learning about the process doesn't work; the student must write. Second, there's good evidence that writing about something increases understanding --... more... - Mickey Schafer
And the extra prep still cannot resolve the problem that Turnitin cannot address: that in the sciences, technical jargon has no synonyms, quoting is discouraged/avoided, grammatical paraphrasing is so limited as to be worthless, meaning that students cannot merely be taught not to plagiarize: they have to be taught how to deal with information like a practicing scientist deals with... more... - Mickey Schafer
@John -- thanks for the working link! - Mickey Schafer
I cached a copy as well: - Chris Miller
Yes, I was quite surprised when I went back to it the next day and it wasn't there... does anyone know why he took it down? - Allyson Lister
Very strange indeed - and such a useful post. One can only assume the university asked him to? Mickey raises the exact points I was thinking about when reading the post. There is definitely room for improvement in terms of making plagiarism more difficult, but it's impossible to avoid it completely. - Björn Brembs
Follow up about the issue, here: And yes, he was pressured to take down the post. - John Dupuis
I'm astonished that anyone is surprised the post disappeared. My first thought on reading it was, he'll get fired for this. It's probably too public now for him to lose his job, but I expect him to face more punishment/reprisal of the invidious sort that he described in the post. Make no mistake, universities are businesses now, the students are customers, and they are buying imprimatur, NOT education. - Bill Hooker
I predict that he'll ultimately restore the post but modified so it'll be harder to identify individual students. Not that I thought it was that easy to do that before, but I think that'll be the thing they'll make him do. - John Dupuis
That's the (bogus) hook on which they are hanging the legal threat, certainly. I doubt the post will go back up, because no one actually cares about violations of student privacy (even if they did happen in that post, which they didn't). The university admin cares about the blot on its public copybook, the open airing of one of its dirty little DADT secrets. It's no surprise to anyone... more... - Bill Hooker
Thank you Chris Miller for the link to your cache of the original posting. As the reaction was coming out I was sharing it with members of the Fac Sen Council here at NYU, as well as others. Almost all found it a compelling read. Speaking for myself I hope it might engender a wider and constructive discussion here. I am chagrined at the takedown of the post. - carolh
I am likewise distressed by the higher ed post linked by John. We've had a special task force at UF looking at cheating in general; I was in one of the focus groups. My impression was that cheating was well-known, actively despised, but the solutions come up against the most precious resource: time. Research profs, particularly those at the beginning of their careers, were overwhelmed... more... - Mickey Schafer
Pedro Beltrao
Sequence, structure, and network evolution of protein phosphorylation. -
Daniel Mietchen
A wiki approach to Open Access and Open Science -
This blog is dedicated to documenting the progress of the Wikimedian in residence on Open Science project – with an initial focus on Open Access - funded by the Open Society Foundations Information Program and hosted by the Open Knowledge Foundation Germany… Continue reading → - Daniel Mietchen
Deepak Singh
Network neighbors of drug targets contribute to drug side-effect similarity. -
Cameron Neylon
Audio from my talk at the OAI7 meeting in Geneva: Cultural infrastructure for Open Research
Cameron Neylon
Wears the passion? Yes it does rather… -
Quite some months ago an article in Cancer Therapy and Biology by Scott Kern of Johns Hopkins kicked up an almighty online stink. The article entitled "Where's the passion" bemoaned the lack of hard core dedication amongst the younger researchers that the author saw around him. This article got a lot of people very ... - Cameron Neylon
Cameron Neylon
Tried to condense all of my views around schol comms into one (rather long) document. Comments welcome:
Matthew Todd
‪TEDxBoston - Dr Jay Bradner - Opensource Drug Discovery‬‏ - YouTube -
‪TEDxBoston - Dr Jay Bradner - Opensource Drug Discovery‬‏ - YouTube
Bradner appealing for open source style help with drug optimization. - Matthew Todd from Bookmarklet
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