Biweekly links for 05/29/2009

  • Understanding Consistent Hashing |
    • Nice basic explanation of consistent hashing.
  • Server Fault
    • StackOverflow for SysAdmins
  • The New Socialism: Global Collectivist Society Is Coming Online
  • 1984: The masterpiece that killed George Orwell | Books | The Observer
  • [0903.3971] Astronomical Software Wants To Be Free: A Manifesto
    • “Astronomical software is now a fact of daily life for all hands-on members of our community. Purpose-built software for data reduction and modeling tasks becomes ever more critical as we handle larger amounts of data and simulations. However, the writing of astronomical software is unglamorous, the rewards are not always clear, and there are structural disincentives to releasing software publicly and to embedding it in the scientific literature, which can lead to significant duplication of effort and an incomplete scientific record. We identify some of these structural disincentives and suggest a variety of approaches to address them, with the goals of raising the quality of astronomical software, improving the lot of scientist-authors, and providing benefits to the entire community, analogous to the benefits provided by open access to large survey and simulation datasets. Our aim is to open a conversation on how to move forward. We advocate that […]”
  • Human Genome Project: Genetics and Patenting
    • “Currently over three million genome-related patent applications have been filed. U.S. patent applications are confidential until a patent is issued, so determining which sequences are the subject of patent applications is impossible. Those who use sequences from public databases today risk facing a future injunction if those sequences turn out to be patented by a private company on the basis of previously filed patent applications.”
  • Diamond v. Chakrabarty – Wikipedia, the free encyclopedia
    • 1980 test case where the US Supreme Court decided that genetically modified micro-organisms can be patented. At the time, the law said that living organisms were not patentable. A genetic engineer working for GE had a patent application turned down for a bacterium capable of breaking down crude oil. He appealed, and the case ultimately went to the Supreme Court, which ruled 5-4 that a human-made micro-organism is patentable. Both the majority decision and the dissent are fascinating.
  • Pslc Wiki
    • A well-tended wiki containing a lot of material about learning: how we do it, what the best strategies are, and so on. Interesting, definitely. What fraction of the ideas are correct? Hmm.
  • Books, papers, sites, and software for learning about Web search and related areas – Quinn Slack
  • Michael Mitzenmacher: Algorithms at the End of the Wire
    • Course page for Michael Mitzenmacher’s course on algorithms. Links to many classic papers on web search, data mining, recommendation algorithms, and so on.
  • Statistical Data Mining Tutorials
    • Tutorials on many aspects of data mining.
  • Yury Lifshits | A Guide to Web Research
    • Links to many classic papers on graph algorithms, advertising, data mining, and so on.
  • Distributed systems primer :: snax
    • Classic papers on distributed systems.
  • xkcd as a text on algorithms
    • A useful piece of code that uses xkcd as its sole algorithmic reference.
  • The open, social web | FactoryCity
    • “a few concepts […] necessary to defeat monopolies in social networks and cloud-based markets:
      data portability: related to switching costs; an example of this is phone number portability (which require government intervention to achieve); multi-homing: increasing reliability through parallelization; the example I used was, which allows you to publish content simultaneously to multiple destinations, thereby defeating network exclusivity and lock-in; roaming: have access to and using other people’s networks; I showed a text message that I received from AT&T explaining how they wanted to charge me $20/MB while roaming in Europe. Clearly networks don’t like it when their customers roam! disaggregation: service substitutability; in this case the photo-editing service Picnik imports photos from a multitude of sources, avoiding tightly coupling itself an any one particular service, unlike Facebook’s photo-sharing service, which can only be used and accessed on”

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Biweekly links for 05/22/2009

  • A solution to an exposition problem « Gowers’s Weblog
    • “Let me explain the title of this post by quoting from Timothy Chow’s highly recommended expository article A beginner’s guide to forcing: “All mathematicians are familiar with the concept of an open research problem. I propose the less familiar concept of an open exposition problem. Solving an open exposition problem means explaining a mathematical subject in a way that renders it totally perspicuous. Every step should be motivated and clear; ideally, students should feel that they could have arrived at the results themselves.””
  • Seb’s Open Research: Stocks, Flows, and Upkeep in Social Media
    • Seb Paquet’s exegesis of an experiment in mass collaborative drawing. Vandalism, designing good social media, persistent social structures, and many other topics…
  • ICML Discussion Site [ICML Discussion]
    • “The aim of this site is to enable the research community to discuss papers accepted to ICML [International Conference on Machine Learning]. Each paper accepted to ICML 2008 has a page on this site. Each page has details of the paper and a discussion thread. “
  • Meatball Wiki: WikiLifeCycle
  • CiteULike: Group on Statistical Machine Learning
  • Life on the lattice: Openness >> fraud
    • “Schön’s deception was only possible because the researchers who tried and failed to replicate his results didn’t have access to his primary data. Once doubts had been raised over the appearance of two completely identical graphs supposedly representing two completely different sets of experimental data, Schön’s primary data were subjected to close scrutiny and were found to be non-existent — his labbooks had been destroyed, and his samples were damaged beyond recovery. This raises the question whether it would have been possible to even contemplate such a fraud in an environment where scientists are genuinely expected to hide nothing, and in particular to make their primary data publicly available after publication.”

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Biweekly links for 05/15/2009

  • Grand Text Auto » Blog-Based Peer Review: Four Surprises
    • “But we decided to do something different with Expressive Processing: we asked the community around an academic blog — Grand Text Auto — to participate in an open, blog-based peer review at the same time as the anonymous review.”
  • Quantiki Video Abstracts | Quantiki
    • “The purpose of the video abstracts is to provide brief video abstracts to recent papers on the arXiv. The abstracts provide a “teaser” for the paper and should guide the audience into your work, emphazising what you think is the most important result. Everybody is welcome to contribute – just take out your webcam and upload a new video!”
  • ACLU sues over patents on breast cancer genes –
    • “Patents on two human genes linked to breast and ovarian cancers are being challenged in court by the American Civil Liberties Union, which argues that patenting pure genes is unconstitutional and hinders research for a cancer cure.

      “Knowledge about our own bodies and the ability to make decisions about our health care are some of our most personal and fundamental rights,” said ACLU Executive Director Anthony D. Romero. “The government should not be granting private entities control over something as personal and basic to who we are as our genes.””

  • The Camera that Changed the Universe: Part 1 : Starts With A Bang
    • Wonderful post about the Hubble telescope, incidentally telling you how to figure out roughly how many galaxies there are in the Universe.
  • Tweeting from space: Mike Massimino: From orbit: Launch was awe …
    • From orbit: Launch was awesome!! I am feeling great, working hard, & enjoying the magnificent views, the adventure of a lifetime has begun!
  • Gamers Unravel the Secret Life of Protein: Wired
    • Wired story about Foldit, the protein folding game.
  • Drawball: from Chaos to Community
  • Smart Mobs » Blog Archive » Drawball, collaborative web graffiti
    • “In January and February 2006, a large South Korean flag was constructed on the Drawball by members of several Internet forums (or many South Korean people). The flag was constantly expanded and repaired, and as the first of many logos to come, it was quite noticeable from the ball.

      Members of various communities colluded to vandalize the Korean flag. On February 27, 2006, the flag was turned almost entirely neon green. It was because of this large attack that Drawball gained its current presence. The website became so flooded that hundreds of people at a time were put in queue before being able to access the Drawball. After extensive attack, the center of the flag was eventually converted into a Pepsi logo, and, like all Drawball drawings, the space was eventually reclaimed by other users.”

  • Making Light: Virtual panel participation
    • This is a canonical short text I recommend to people wanting something to read about online communities. Expanded a bit it’d make a nice short book.
  • Seb’s Open Research: SciBarCamp II, Toronto
    • Seb’s summing up of SciBarCamp II.
  • Drawball
    • An experiment in mass artistic collaboration. The link is to a playback showing the entire collaboration; you can also participate if you wish.

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Biweekly links for 05/11/2009

  • Natalie MacMaster and Thomas Dolby: Blue is a River
    • A moving duet between Natalie MacMaster and Thomas Dolby. Blends MacMaster’s folksy fiddling, Scotts highland dancing, and Dolby’s electronica. The song is the story of the exile of displaced Scotts, forced to move to Newfoundland. There’s much more at Dolby’s blog –
  • Useful Chemistry: Leaders and Pushers in Open Science projects
    • “People often think that successful leaders attract followers – people who are subservient. In my experience successful projects result from a collaboration of colleagues who share common values.”
  • Frank Rich: The American Press on Suicide Watch –
    • Better than most of the knee-jerk writing on this (albeit that’s a very low bar to clear): “That’s why the debate among journalists about possible forms of payment (subscriptions, NPR-style donations, iTunes-style micropayments, foundation grants) is inside baseball. So is the acrimonious sniping between old media and new. The real question is for the public, not journalists: Does it want to pony up for news, whatever the media that prevail?”
  • Selfish Scientists Won’t Share New Findings | The Onion
  • The danger of drugs … and data | Ben Goldacre | Comment is free | The Guardian
    • “It turns out that Elsevier put out six such journals, sponsored by industry. The Elsevier chief executive, Michael Hansen, has now admitted that they were made to look like journals, and lacked proper disclosure. “This was an unacceptable practice and we regret that it took place,” he said.”
  • Elsevier’s Medica Communications imprint
    • This is worth looking into more, and I hope Elsevier responds.
  • On Blogging | Serendipity
    • “blogging is time consuming. Several people have told me this is why they don’t blog. But actually, this doesn’t seem to be an issue for me – each blog post represents a small chunk of research that I would do anyway – the only difference is that now I’m sharing my notes in the blog, rather than keeping them to myself. One of the hardest parts of doing research is that its very easy to let the “playing with ideas” part get endlessly encroached by things that have short term deadlines. The discipline of blogging daily means I then don’t let this happen. “
  • Doing science in the open: Physics World

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Biweekly links for 05/08/2009

  • Clocks, Kids and General Relativity on Mt Rainier
    • “In September 2005… we took several cesium clocks on a road trip to Mt Rainier; a family science experiment unlike anything you’ve seen before. By keeping the clocks at altitude for a weekend we
      were able to detect and measure the effects of relativistic time dilation compared to atomic clocks we left at home. The amazing thing is that the experiment worked! The predicted and measured effect was just over 20 nanoseconds…. Waiting as cesium clocks undergo time dilation is much worse than watching a kettle boil.”
  • The Top 10 Most Extreme Office Chair Videos | Sitbetter Office Chairs
    • I appreciated the fact that this is from the website of a company that sells chairs: “The ingenuity and creative spirit of the overly bored individual should never be underestimated. It truly is amazing. For most, boredom leads to lounging around and, ultimately, to more boredom. But for a few brave souls, this time of ennui is channeled into something much bigger than the rest of us could fathom. When a lazy afternoon leaves you only with a leather office chair, an overactive imagination, and a desire to be extreme, anything can happen. Here is the list of the top 10 extreme office chair videos floating around the web”
  • Roy Fielding Dissertation: CHAPTER 5: Representational State Transfer (REST)
    • The original description of the RESTful approach to web services.
  • Student’s Wikipedia hoax quote used worldwide in newspaper obituaries – The Irish Times
    • “A WIKIPEDIA hoax by a 22-year-old Dublin student resulted in a fake quote being published in newspaper obituaries around the world.

      The quote was attributed to French composer Maurice Jarre who died at the end of March.

      It was posted on the online encyclopedia shortly after his death and later appeared in obituaries published in the Guardian, the London Independent, on the BBC Music Magazine website and in Indian and Australian newspapers.”

  • Larry Page’s commencement speech at the University of Michigan
    • “I think it is often easier to make progress on mega-ambitious dreams. I know that sounds completely nuts. But, since no one else is crazy enough to do it, you have little competition… The best people want to work the big challenges. That is what happened with Google. Our mission is to organize the world’s information and make it universally accessible and useful. How can that not get you excited? But we almost didn’t start Google because my co-founder Sergey and I were too worried about dropping out of our Ph.D. program. You are probably on the right track if you feel like a sidewalk worm during a rainstorm! That is about how we felt after we maxed out three credit cards buying hard disks off the back of a truck. That was the first hardware for Google. Parents and friends: more credit cards always help. What is the one sentence summary of how you change the world? Always work hard on something uncomfortably exciting!”
  • Archy – Wikipedia, the free encyclopedia
    • “Archy is a software system whose user interface poses a radically different approach for interacting with computers with respect to traditional graphical user interfaces. Designed by human-computer interface expert Jef Raskin, it embodies his ideas and established results about human-centered design described in his book The Humane Interface. These ideas include content persistence, modelessness, a nucleus with commands instead of applications, navigation using incremental text search, and a zooming user interface (ZUI). The system was being implemented at the Raskin Center for Humane Interfaces under Raskin’s leadership.”
  • What’s your open data idea? | David Crow
    • Coming on the heels of the City of Toronto’s announcement that it’ll be sharing a lot more data: “I have started to think about how we inspire and encourage the community to both build applications, but also businesses on top of the newly available data to help improve city services.”
  • SklogWiki: page of resources about the use of wikis in the sciences
  • Shtetl-Optimized » Wanted: Quantum GGM theorem
    • An anonymous commenter provides an insightful suggestion related to Scott Aaronson’s question about a quantum GCM theorem. The future of acknowledgements in scientific papers: “I’d like to thank Anonymous blog commenters for comments 4, 7 and 9 on my recent post.”
  • Milton Glaser: Ten Things I Have Learned
    • Glaser is a well-known graphic artist who came up with (among other things) the “I [heart] New York” design. It’s an interesting list.
  • Feynman at Google Scholar
    • I was looking up an old Feynman paper, and noticed something curious: his most-cited paper appears to be his paper on quantum computing, recently going past the paper where he introduces path integrals.
  • Backyard scientists use Web to catalog species, aid research –
  • Malcolm Gladwell: How David Beats Goliath: The New Yorker

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Biweekly links for 05/04/2009

  • Peter Suber appointed as a Berkman Fellow
    • Some excellent news: “Peter Suber will join the Center for a special joint fellowship with the Harvard Office for Scholarly Communication and the Harvard Law School Library. Professor Suber will be focusing on Open Access documentation efforts, as well as outreach around Open Access, across Harvard and beyond.”
  • I Want You To Want Me
    • Thoughtful essay about privacy, free speech, and online media.
  • Anthropology: The Art of Building a Successful Social Site
    • StackOverflow is by far the best and most useful Q&A site I’ve ever used. Here, co-founder Joel Spolsky talks about some of what makes StackOverflow successful. Interesting reading for people thinking about similar endeavours in other fields, e.g., science.
  • Merck Makes Phony Peer-Review Journal |
    • “The Scientist has reported that […] Merck cooked up a phony, but real sounding, peer reviewed journal and published favorably looking data for its products in them. Merck paid Elsevier to publish such a tome, which neither appears in MEDLINE or has a website, according to The Scientist.

      […] I’m sure many a primary care physician was given literature from Merck that said, “As published in Australasian Journal of Bone and Joint Medicine, Fosamax outperforms all other medications….” Said doctor, or even the average researcher wouldn’t know that the journal is bogus. In fact, knowing that the journal is published by Elsevier gives it credibility!”

  • Wikipedia:Peer review – Wikipedia, the free encyclopedia
    • “Wikipedia’s Peer review process exposes articles to closer scrutiny from a broader group of editors, and is intended for high-quality articles that have already undergone extensive work, often as a way of preparing a featured article candidate. It is not academic peer review by a group of experts in a particular subject, and articles that undergo this process should not be assumed to have greater authority than any other.”

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Biweekly links for 05/01/2009

  • …My heart’s in Accra » The importance of being a dork
    • “So here’s my pressing question: if the internet gives us new spaces in which to find common ground with very different people, what’s holding us back from becoming vastly more global and cosmopolitan than most of us are? Why, as I’ve argued elsewhere, do we seem to keep sorting ourselves into familiar groups?

      I’m starting to think that there’s something very special about the willingness to look like a dork. I don’t think it’s a coincidence that Matt Harding dances badly, but enthusiastically, and that this opens doors for him. Or that Dhani Jones finishes last in races, with a smile on his face. And I wonder whether we’d have more luck building bridges in online spaces if it were more socially acceptable to make fools of ourselves, laughing and being laughed at by our new peers.”

  • What If Scientists Didn’t Compete? – TierneyLab Blog –
    • “What if scientists, instead of rushing to publish or perish, chose to cooperate? Sean Cutler decided to do “a little experiment,” as he calls it, and you can see the results in the forthcoming issue of Science.

      The journal carries an article by Dr. Cutler and 20 other researchers in the United States, Canada and Spain reporting a long-sought technique for helping plants to grow with less water by activating the natural defenses that enable plants to survive during droughts. (Here’s the Science article; here’s a summary of the research.) Dr. Cutler, an assistant professor of plant cell biology at the University of California, Riverside, knew that the rush to be first in this area had previously led to some dubious publications (including papers that were subsequently retracted). So he took the unusual approach of identifying his rivals (by determining which researchers had ordered the same genetic strains from a public source) and then contacting them.”

  • Wikipedia:Deleted articles with freaky titles – Wikipedia, the free encyclopedia
    • “22.86 Centimetre Nails”: the metric version of “Nine Inch Nails”. (Honestly, this is all part of the research for my book…)
  • A million penguins
    • A fascinating experiment in wiki-novel writing from Penguin. The result is unusual: “For those of you who haven’t mastered its structure, the novel is broken down into seven discrete sections, plus one additional section that incorporates the more bizarre elements of this collaborative project (the ‘Banana version‘, the ‘Choose Your Own Adventure version‘, etc). Having said that, it seems unfair to single out one part of the book that’s weirder than the others. But you can see for yourself what I mean.

      The quote with which I’ve begun seems apposite because it captures two aspects of the book that have really stood out: a) the question of linearity b) the way that the wiki-novel seems so often to be about the wiki-novel. You could justifiably call much of it a meta-narrative.”

  • Paul David: The Historical Origins of ‘Open Science’
    • Likely to be well worth reading for people interested in the modern open science movement. (I haven’t read this version of the paper, but I did read a draft from 2007).
  • Turkey City Lexicon: A primer for SF workshops
    • “Roget’s Disease

      The ludicrous overuse of far-fetched adjectives, piled into a festering, fungal, tenebrous, troglodytic, ichorous, leprous, synonymic heap. (Attr. John W. Campbell) “

  • Image of the Week – Los Alamos’ “Map of Science”
    • “Scientists at Los Alamos National Laboratory (LANL) in New Mexico have produced what they call the world’s first “Map of Science” — a high-resolution graphic depiction of the virtual trails scientists leave behind whenever they retrieve information from online services.

      The research, led by Johan Bollen of LANL, and his colleagues at the Santa Fe Institute, collected usage-log data gathered from a variety of publishers, aggregators, and universities from 2006 to 2008. Their collection totaled nearly 1 billion requests for online information. Because scientists usually read articles in online form well before they can be cited in print, usage data reveal scientific activity nearly in real-time, the map’s creators say.

      “This research will be a crucial component of future efforts to study and predict scientific innovation, as well novel methods to determine the true impact of articles and journals,” Bollen said to the Public Library of Science.”

  • Facts and friction « Jon Udell
    • Computable knowledge: “But the more telling example, for me, was one that Stephen Wolfram showed in a post-demo discussion: “Suppose you want to know the distance to Pluto. We don’t just look it up. We answer the question: “What is the distance to Pluto right now?” And we compute the answer. ”
      I reckon that this notion of computable knowledge is going to take a while to sink in.”
  • Finding and connecting social capital « Jon Udell
  • What is the RSS of calendars? « Jon Udell
  • Open Source Software Apprentice –
  • The Secret to Happiness, According to Justice O’Connor
    • “I can tell you what I believe is the secret to a happy life,” she [Sandra Day O’Connor] said.

      “What’s that, Justice?” I asked… “What’s your secret?”

      “Work worth doing,” she answered firmly.

      “What about relationships?” I asked. From what I can tell, looking at modern science and ancient philosophy, if you had to pick a single factor as the one most likely to lead to a happy life, having strong relationships would be a strong candidate. Of course, most people form a lot of strong relationships at work.

      “No,” she said. “Work worth doing, that’s all you really need.””

  • Tobias J. Osborne’s research notes – non-linear notes on my research
    • Tobias’ tiddlywiki with his research notes.

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