MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Open Reading Frame' source. Mon, 17 Nov 2008 22:52:29 +0100 http://www.sennoma.net/main/archives/2008/11/veterans_day_2.php Today I put aside my troubles and remember the many dead of both World Wars -- indeed, of all wars -- for their sacrifice. Lest we forget. Suicide In The Trenches I knew a simple soldier boy Who grinned at life in empty joy, Slept soundly through the lonesome dark, And whistled early with the lark. In winter trenches, cowed and glum, With crumps and lice and lack of rum, He put a bullet through his brain. No one spoke of him again. You smug-faced crowds with kindling eye Who cheer when soldier lads march by, Sneak home and pray you'll never know The hell where youth and laughter go. -- Siegfried Sassoon 2006 2005 2004 (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1951805 Tue, 11 Nov 2008 16:45:01 +0100 1951805 http://www.sennoma.net/main/archives/2008/11/thieving_shitweasels.php As Nils and Paulo have pointed out, genetic testing company DNA Dynasty are thieves. On their front page, you can see this: and here on Flickr, uploaded in May of last year, is Ricardo's graphic for The DNA Network logo. The lazy bastards didn't even bother with a quick photoshop. Nils also points out that these lowlifes are peddling bullshit of the worst kind: "DNA tests for innate abilities" like intelligence and "emotional quotient" "Hair Analysis through Bio-sonic technology", including analysis of "emotions" and "chakra" "oxygenated water" "Negative Ion Detox Foot Spa" "Spine Corrector Insole" Ugh. (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1943327 Sat, 08 Nov 2008 06:49:17 +0100 1943327 http://www.sennoma.net/main/archives/2008/11/yes_we_did.php I would have liked to have cast my first vote as an American citizen for Obama, but I look forward to casting it instead to ensure his second term in office. Congratulations, Mr President. (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1938996 Wed, 05 Nov 2008 17:32:09 +0100 1938996 http://www.sennoma.net/main/archives/2008/10/least_i_can_do.php Abbas and the 3QuarksDaily team are looking for new columnists: Here's your chance to say what you want to the international audience of highly educated readers that 3QD has! Several of our regular columnists have had to cut back, or even completely quit, their columns for 3QD because of other personal and professional commitments, and so we are looking for three new voices for our Monday columns. We cannot pay, but it is a good chance to draw attention to subjects you are interested in, and to get feedback from us and from our readers. I feel terrible that I was not able to keep up as a regular Monday columnist; the least I can do is advertise this opportunity. And it is quite a remarkable opportunity. The quality of feedback is excellent, and the opportunities contained within the 3QD a... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1901387 Fri, 24 Oct 2008 06:45:56 +0100 1901387 http://www.sennoma.net/main/archives/2008/10/open_access_day_2008.php It's OA Day, and all the usual suspects are posting entries in the synchroblogging contest. I'm staying off the web except for 30 minutes or so mornings and evenings (because I desire and intend to finish the Project That Would Not Die by the end of the year), and that really only leaves me time to keep up with my feeds and friends. So, that's my excuse for not having a contest entry (well, that and I dislike contests and prizes... a rant for another time). But I can't let OA Day go unremarked, so check out the official blog and the FriendFeed room. Here is the blog feed (sorry it's Flash, but I don't have time to test other widgets -- and it is pretty): (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1875985 Tue, 14 Oct 2008 16:24:09 +0100 1875985 http://www.sennoma.net/main/archives/2008/10/no_one_goes_into_science_to_ge.php A while back, Heather posted an entry about salaries in France, and just came right out and said what she makes: The beginning junior professor (maitre de conférences, or MdC) fresh out of the Ph.D. (which never happens anymore) gets approximately 1700 euros in their pocket after benefits withholding each month, and this measure will bring it up to about 1800 euros. [...] A MdC with 15 years' seniority on the Le Monde comment thread earns 2600 euros a month; I earn 2300. (Unlike the French, I have an American indifference to revealing my salary to all; what with the fluctuating exchange rate it's approximately equivalent to that of a tight-belted American high school teacher.) I don't know that it's particularly American, but I've never minded telling everyone my income either. I un... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1870626 Mon, 13 Oct 2008 04:50:37 +0100 1870626 http://www.sennoma.net/main/archives/2008/10/what_she_said.php With one alteration (viz I have had no differences with Richard Poynder), what Dorothea said goes for me as well. (For more background see Matt at Journalology: 1, 2.) This is just a for-the-record, public statement that I fully support Richard Poynder's laudable and transparently conducted investigation of SJI and other publishers whose conduct threatens to bring Open Access into disrepute, and that if any such publishers take their legal bullying further than the bluff and bluster we are currently seeing from SJI, I will do what I can to help Richard fight back. Update 081006: Peter Suber and Stevan Harnad have issued a joint statement in support of the investigative work of Richard Poynder. I was hesitant to do so when it was just me following Dorothea's lead, but now I would like to ... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1855992 Mon, 06 Oct 2008 19:10:37 +0100 1855992 http://www.sennoma.net/main/archives/2008/09/history_in_the_making.php I have plenty to blog about and no time to do it in, but I can't turn down a request for a quick plug on such a cool topic: Aaron Rowe from Wired Science alerted me to the fact that Falcon 1 made it to space: the first privately developed liquid fueled launch vehicle to achieve earth orbit. Aaron's followup entry has some good background for those who haven't been following the SpaceX story. Our Star Trek future gets closer every day. (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1837107 Mon, 29 Sep 2008 01:23:22 +0100 1837107 http://www.sennoma.net/main/archives/2008/08/help_me_make_the_most_of_an_op.php Check me out: That means I've got about a week to put together a 30-40 minute talk. I won't have any trouble filling up the time, of course -- the real problem is what NOT to present. I aim to use the web instead of powerpoint, by creating a series of bookmarks that I can open in browser tabs (or from a History sidebar; haven't decided) and move through those like slides. I plan to follow the basic format of my old essays: we're all familiar with Free/Open Source software, the NIH just mandated a kind of Open Access so here's what that means and what that can do, and what else can be Open? leading into Open Data, Open Standards/semantic web, Open Licensing -- in short, Open Science. The Berglund Center is affiliated with Pacific University, a "a small, private university with a blend of... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1746050 Tue, 26 Aug 2008 19:48:28 +0100 1746050 http://www.sennoma.net/main/archives/2008/08/what_she_said.php With one alteration (viz I have had no differences with Richard Poynder), what Dorothea said goes for me as well. (For more background see Matt at Journalology: 1, 2.) This is just a for-the-record, public statement that I fully support Richard Poynder's laudable and transparently conducted investigation of SJI and other publishers whose conduct threatens to bring Open Access into disrepute, and that if any such publishers take their legal bullying further than the bluff and bluster we are currently seeing from SJI, I will do what I can to help Richard fight back. (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1729343 Sat, 23 Aug 2008 19:10:37 +0100 1729343 http://www.sennoma.net/main/archives/2008/07/an_open_access_partisans_view.php There's been a good deal of online chatter about this recent Science article that discusses the effects of online access on scholarship -- see, e.g., discussions here and here and blog entries noted therein.  The report is not available without paying a toll or subscription, but the abstract is freely visible: Online journals promise to serve more information to more dispersed audiences and are more efficiently searched and recalled. But because they are used differently than print -- scientists and scholars tend to search electronically and follow hyperlinks rather than browse or peruse -- electronically available journals may portend an ironic change for science. Using a database of 34 million articles, their citations (1945 to 2005), and online availability (1998 to 2005), I show t... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1639021 Sun, 20 Jul 2008 00:34:22 +0100 1639021 http://www.sennoma.net/main/archives/2008/07/lie_down_with_pit_bulls_wake_u.php Conclusions are presented in an appropriate fashionand supported by the text. Techniques used have been documented in sufficient detail to allow replication.Reports are presented in an intelligible fashion and written in standard English.Research meets all applicable standards, including the Helsinki Declaration, with regard to the ethics of human and animal experimentation, consent, and research integrity.Report adheres to the relevant community standards for research, reporting, and deposition of data. (Standards PLoS promotes across its journals).Which is to say that PLoS one holds authors to exactly the same scientific standards that every journal should follow. Which is to say that any methodological flaws, not "only... serious" ones, will see a paper revised, or rejected if the flaws... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1575389 Thu, 03 Jul 2008 09:40:46 +0100 1575389 http://www.sennoma.net/main/archives/2008/07/calling_all_bioinformaticians.php Mike of Bioinformatics Zen is looking for information; please help him out if you can, by taking the survey either here or at BZ. Take particular note of the following: The raw data entered into this questionnaire, along with any interpretation will be released into the public domain under a creative commons attribution license. If you are unhappy with answering any of the questions please leave them blank. By completing this questionnaire you consent to your answers being released. (Yes, I know it's repeated at the top of the survey: it's important.) Loading... (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1560778 Wed, 02 Jul 2008 01:08:05 +0100 1560778 http://www.sennoma.net/main/archives/2008/05/oa_and_licensing_new_kid_on_th.php This is an unpublished post that's so old (Aug '07) that I don't know why I didn't just post the damn thing; I've forgotten what I was intending to do with it. I'm posting it now because it contains pointers to useful thinking by David Wiley and others that is germane to the ongoing discussion of data licensing (see post below). I was reminded of this old draft of mine by Deepak's comment that copyleft may be harmful in the case of scientific data, a point David also makes in respect of his particular Open area, education. Much of what David says maps readily from his field to research, so without further ado: David Wiley of Iterating Toward Openness has been blogging up a storm about open content licensing: Noncommercial Isn't the Problem, ShareAlike Is ShareAlike, the Public Domai... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1434401 Mon, 12 May 2008 04:51:41 +0100 1434401 http://www.sennoma.net/main/archives/2008/05/data_are_difficult.php Scientific data are not only hard to come by, they're almost as hard to share, mainly because the scientific infrastructure is armpit-deep and sinking fast in the quicksand of patents, copyrights and ever-multiplying licenses. See Peter Murray-Rust, Antony Williams and Egon Willighagen for the latest dust-up over data licensing; I just want to point out this clear-eyed commentary by John Wilbanks: The public domain is not an "unlicensed commons". The public domain does not equal the BSD. It is not a licensing option. It is the natural legal state of data. It is a damn shame that we no longer think of the public domain as an option that is attractive. It's a sign of the victory of the content holders that the free licensing movements work against that something without a license -- someth... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1433717 Sat, 10 May 2008 21:35:06 +0100 1433717 http://www.sennoma.net/main/archives/2008/04/everyone_needs_a_hobby.php Mine, when I have time for it, is photography. I'll still post some photos, like the mouse below, to this blog; but now I have a separate blog for those images I would (if I weren't worried about sounding like a complete wanker) call "my art". The link is at the top of the new column at left, where I'll manually add thumbnails from that blog. It's at Expressions.com, because I haven't the time to make exactly what I want and of all the photoblogging services I tried, only Expressions gave me enough control over the format to make it (nearly) as simple as I wanted. So. Fwiw, there it is. Hat tip, again, to Andrew and Ralf. (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1385675 Sun, 20 Apr 2008 06:34:58 +0100 1385675 http://www.sennoma.net/main/archives/2008/04/in_which_gavin_baker_finds_one.php It really chafes my scrote when someone says something like this: A comment to bloggers. I do my best to credit blog posts by the author's real name. However, if you blog under a psuedonym [sic] and don't make it easy to find your actual name, I may not. Unless you want me to attribute your writings to your silly Internet handle, you should include your name somewhere prominent (if not on every page, on the "About" or "Contact" page). With all due respect, Mr Baker, it's not up to you where I should or shouldn't put my "real" name; plenty of people have damn good reasons for remaining anonymous online. Nor is it up to you to sneer at someone's "silly internet handle". Put the nick in quotes if you must, and move on. It's a name, it attaches to a person, and it matters -- at least it should... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1371908 Mon, 14 Apr 2008 23:33:08 +0100 1371908 http://www.sennoma.net/main/archives/2008/04/term_dilution_or_that_phrase_y.php As the terminology wars between "Free Software" and "Open Source Software" afficionados demonstrate, as soon as you stick a label on what you are doing, someone will come along and co-opt it. Sometimes, as with F/OSS, there are real disagreements to be had by reasonable people; at other times, well, not so much. This: "Open science" is liberated from methodological naturalism (MN), even though it begins with an MN position. That is, all scientists start their work in pursuit of natural explanations for events or natural solutions for problems. If evidence and logic point to an end of the road for natural explanations, on rare occasions a scientist using open science would be willing to consider an explanation which does not force him to a naturalistic conclusion. For instance, the genetic ... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1369656 Sun, 13 Apr 2008 23:33:52 +0100 1369656 http://www.sennoma.net/main/archives/2008/04/reminder.php Over at Free Genes, Jason Kelly has a nice reminder for those of us who tend to be disheartened by slow rates of progress in our chosen field, be it Open Science or, in Jason's case, synthetic biology. I liked it so much I'm stealing it. This: is a transistor, circa 1948. Now you can buy the equivalent of many millions of these for pocket change, in a device that will fit on your keychain. (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1369657 Sun, 13 Apr 2008 20:58:53 +0100 1369657 http://www.sennoma.net/main/archives/2008/04/good_question.php Egon has an interesting angle on Peter Murray-Rust's observation that you can't mine PubMed Central: I was wondering about this section in the CC license of much of the PMC content, such as our paper on userscripts (section 4a of the CC-BY 2.0):You may not distribute, publicly display, publicly perform, or publicly digitally perform the Work with any technological measures that control access or use of the Work in a manner inconsistent with the terms of this License Agreement.CC-BY 3.0 reads differently, but has similar aims. [...] Peter indicates that the NIH has put in place 'technological measures to control access' to the distribution of our work on userscripts (the PMC entry). That is in clear violation of the CC license. [...] What the PMC website should indicate, instead, is that te... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1368765 Sun, 13 Apr 2008 07:08:27 +0100 1368765 http://www.sennoma.net/main/archives/2008/04/removal_of_permissions_barrier.php Heather Morrison points to this excellent post by Glen Newton, wherein Glen proposes that Open Access should explicitly include machine readability: Open Access must include access by machines: * At minimum one must allow crawls of the site/content or (to reduce the impact of badly configured crawlers) create a compressed XML file containing all metadata and either content, or direct links to content and make it available for download (and if bandwidth is still an issue put it on a P2P network like BitTorrent). * Preferable is to offer some kind of API (OTMI) or protocol (OAI-PMH) to get at content and metadata and citations. * Better is to offer access to the XML of the articles in addition to the PDF and/or HTML; if the XML actually has some semantic content, then we are approachi... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1356047 Tue, 08 Apr 2008 06:40:54 +0100 1356047 http://www.sennoma.net/main/archives/2008/04/robs_right_or_you_say_deserter.php Rob is absolutely correct: anyone who lays down arms and refuses to kill on command is a hero. I don't give a rat's arse which "side" they're on. Rob's also right in that you won't hear much about this in the "mainstream" media, and whatever you do hear will be propaganda -- which is why I'm pointing to his entry. I know, I know -- politics is bad for me, not least because if I blog this there are quite literally a thousand other stories I should blog. But I'm not going to fall into that trap; I just wanted to say "Rob's right", because this particular story resonated with me. We now return to our usual semi-silence. (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1353930 Sun, 06 Apr 2008 19:25:35 +0100 1353930 http://www.sennoma.net/main/archives/2008/03/athymic_mouse.php (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1332447 Fri, 28 Mar 2008 04:20:56 +0100 1332447 http://www.sennoma.net/main/archives/2008/03/andy_michaels_is_a_filthy_spam.php Just got this bullshit trackback (on this totally unrelated entry): I\'m pleased to announce the introduction of two products, the latest is the Ice Cold New Marketer Seminar Series for internet marketers who are just starting out and looking for solid counseling on tools, resources, and services without all the techni... from this bullshit blog: http://andymichaelsblog.com/ (no Googlejuice for you, asshole). Andy, you're a disease with opposable thumbs. You're a plague, a pox, a parasite on all that is good and useful. Other people are making the internet into the greatest library that ever was, a scholarly resource, a tool for science, a home for the arts, a conversation, a force for social change -- but you, you're out there shilling. And you're not even selling anything real, you're s... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1320518 Sat, 22 Mar 2008 00:08:01 +0100 1320518 http://www.sennoma.net/main/archives/2008/03/hiatus_continues.php I'm still spending pretty much every waking moment in the lab -- it's OK Mum, I'm having fun and taking care of myself! -- because I have some really neat results and want to send them out into the world asap. (I will do my best to persuade the boss to submit to an OA journal and to put a preprint in Nature Precedings, but no guarantees there.) So, this entry is just to round up a couple of NUTs -- Nagging Unfinished Tasks. NUT the first: 2008 Science Blogging Conference -- I never did get around to posting about it, but I have left comments on other people's entries saying most of what I had to say. Mostly, it was a blast and I wish I could have that kind of experience more often, as it really recharges my enthusiasm. The one thing I meant to do, and didn't get around to, was point... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1289742 Mon, 10 Mar 2008 02:40:06 +0100 1289742 http://www.sennoma.net/main/archives/2008/02/open_science_conference_propos.php I'm probably too late with this to do any good, but Shirley Wu is putting together a proposal for an Open Science session at the Pacific Symposium on Biocomputing. You can read a draft of the proposal which already reads pretty well to me, and Shirley could do with letters of support: One thing that would really help outside of the proposal itself is to have actual letters of support. That way the organizers will know there is serious interest and commitment for a session on Open Science - it's a gamble for them, frankly, but much less of one if there is a good crowd on board.So if you would like to support this proposal and are willing to commit to participating should it get accepted, please send me an email to that effect (with as many details of your anticipated participation as you ca... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1213207 Thu, 07 Feb 2008 02:29:11 +0100 1213207 http://www.sennoma.net/main/archives/2008/01/wheeeeeeeeeeee.php I'm off to the 2008 North Carolina Science Blogging Conference! I have to travel all day Friday and Sunday for a one-day conference on Saturday -- and it's well worth every dull airport-infested minute! Last year's was tremendous fun; I'm looking forward to an unbroken attendance record down the years. You can still add ideas to the conference wiki, join in virtually via chat room, and watch at least one of the sessions online. Update: Bora has further details on how you can participate even if you're not there in meatspace. (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1159475 Fri, 18 Jan 2008 05:28:10 +0100 1159475 http://www.sennoma.net/main/archives/2008/01/mitch_waldrop_on_science_20.php I'm way behind on this, but anyway: a while back, writer Mitch Waldrop interviewed me and a whole bunch of other people interested in (what I usually call) Open Science, for an upcoming article in Scientific American.  A draft of the article is now available for reading, but even better -- in a wholly subject matter appropriate twist, it's also available for input from readers.  Quoth Mitch:Welcome to a Scientific American experiment in "networked journalism," in which readers -- you --get to collaborate with the author to give a story its final form. The article, below, is a particularly apt candidate for such an experiment: it's my feature story on "Science 2.0," which describes how researchers are beginning to harness wikis, blogs and other Web 2.0 technologies as a potentia... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1146231 Sun, 13 Jan 2008 03:28:50 +0100 1146231 http://www.sennoma.net/main/archives/2008/01/another_clarification.php Being careful with the language of the letter below made me see that, in earlier entries, I've fallen into one of the easy traps in which OA opponents would like to catch everyone: ...of these, 16 are listed as "grey" (won't allow archiving), 23 are "green" (allow refereed postprint archiving -- NIH mandate compliant) and 7 "pale green" (allow preprint archiving; many "pale green" publishers actually allow postprint archiving and are NIH compliant... ...at least 50% of PSP members are already complying with the NIH mandate, and a further 15% at least allow preprint archiving and may even be NIH-compliant. The majority of journals for which information is readily available are already compliant with the new NIH mandate... This phrasing is deeply misleading: it's not the journals or the pu... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1132135 Sun, 06 Jan 2008 09:41:11 +0100 1132135 http://www.sennoma.net/main/archives/2008/01/they_get_letters.php Peter Suber points out that no members of the AAP/PSP's ill-conceived PRISM "coalition" were ever identified, and that at least nine publishers publicly disavowed or distanced themselves from it; he then asks: Has AAP/PSP ever consulted its members about its position on the NIH policy? Are AAP/PSP members willing to see their dues spent on a lawsuit to delay it? I think it's worth finding that out. Listed at the bottom of this entry are the "green" and "pale green" EPrints/RoMEO publishers listed as members by the PSP (links and names taken directly from the PSP website). On closer inspection, it seems that RoMEO proper lists all of the "pale green" publishers as yellow, and (with one or two caveats concerning journals with long embargo periods) gives them all a "compliant" rating in re... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1131927 Sun, 06 Jan 2008 04:33:34 +0100 1131927 http://www.sennoma.net/main/archives/2008/01/quick_clarification.php The publisher list I've been using in the last few posts actually comes from EPrints.org, using information from SHERPA/RoMEO. I'll refer to the EPrints interface as EPrints/RoMEO from now on. This wouldn't cause any confusion and I wouldn't bother to point it out, except that RoMEO actually uses a four-colour scheme (green, blue, yellow, white) which EPrints has squished into three (green, pale green, grey). (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1131683 Sat, 05 Jan 2008 13:11:13 +0100 1131683 http://www.sennoma.net/main/archives/2008/01/does_the_aappsp_really_represe.php Via Peter Suber, Dorothea Salo and Heather Morrison, I see that the AAP/PSP has responded to the new NIH mandate in typical, PRISM-esque fashion. For anything I might have said in response, and much more, read the linked entries -- especially Peter Suber's. I have something else in mind. The PSP lists its members here ; it didn't take long to compare that list with the list of publishers indexed by SHERPA/RoMEO. Of the 355 publishers in the RoMEO database, 46 are members of PSP; of these, 16 are listed as "grey" (won't allow archiving), 23 are "green" (allow refereed postprint archiving -- NIH mandate compliant) and 7 "pale green" (allow preprint archiving; many "pale green" publishers actually allow postprint archiving and are NIH compliant, but are not listed as green because of various... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1130951 Fri, 04 Jan 2008 20:01:15 +0100 1130951 http://www.sennoma.net/main/archives/2008/01/changing_views_of_science.php I'm always a bit leery of edge.org, seeing as how it's first and foremost a promotional vehicle for John Brockman's stable of authors, but I do enjoy the Annual Question. This year's is no exception: When thinking changes your mind, that's philosophy. When God changes your mind, that's faith. When facts change your mind, that's science. WHAT HAVE YOU CHANGED YOUR MIND ABOUT? WHY? Science is based on evidence. What happens when the data change? How have scientific findings or arguments changed your mind?" What struck me about the answers was that a number of them point out, if indirectly, that the wording of the question is utter bollocks. Whoever wrote the question has drunk deep of the "impartial search for Truth" Kool-Aid and needs an infusion of Kuhn1 (or a week in an actual lab), st... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1129357 Fri, 04 Jan 2008 07:11:53 +0100 1129357 http://www.sennoma.net/main/archives/2008/01/public_domain_day.php Via Dorothea Salo and Peter Suber, John Mark Ockerbloom reminds me that New Year's Day is also Public Domain Day -- the day on which, each year, a new batch of works enters the public domain: In countries that use the "life plus 50 years" minimum standard of the Berne Convention, works by authors who died in 1957 enter the public domain today. That includes writers, artists, and composers like Nikos Kazantzakis, Diego Rivera, Dorothy L. Sayers, Jean Sibelius, and Laura Ingalls Wilder. In countries that use the "life plus 70 years" term, works by authors who died in 1937 enter the public domain, including works by J. M. Barrie, Jean de Brunhoff, H. P. Lovecraft, Maurice Ravel, and Edith Wharton. [...] In countries like the US and Australia, which are under 20-year freezes of all or most o... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1127316 Thu, 03 Jan 2008 05:54:50 +0100 1127316 http://www.sennoma.net/main/archives/2007/12/a_new_beginning_heres_why_1.php Rich Apodaca asks whether the new NIH OA mandate marks a new beginning, or more of the same. His argument hinges on the (admittedly unfortunate) phrase "in a manner consistent with copyright law", and he concludes that Neither HR 2764 nor any form of government intervention will bring widespread Open Access into being. Here's why I think Rich is wrong. Point the first: Rich claims that Most of the journals in question will be hostile to the idea of having their copyrighted material deposited into PubMed Central and so understandably won't allow it to be done by the authors of papers or anyone else. The available data do not support this. Of the 355 publishers indexed by SHERPA/RoMEO, 66% formally allow self-archiving; more importantly, 56% formally allow archiving after refereeing. (Ther... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1120704 Fri, 28 Dec 2007 07:07:19 +0100 1120704 http://www.sennoma.net/main/archives/2007/12/help_a_blogger_out.php (I post more on hiatus than when I'm supposed to be blogging, no?) Gary Farber is in all kinds of trouble. I'm going to do a little to help him out, and ask you, O my tens of readers, to consider doing likewise, because: 1. He asked. Ceteris paribus, what else does one need? 2. He doesn't seem to have anyone else. The thing here is, one of Gary's problems is intensely personal to me: I, too, have major depressive disorder. There -- in Gary's shoes -- but for the grace of a god I don't believe in, go I. I was lucky: all along, I had family and friends, and now especially I have my wife. These people stood in for me and stood up for me and picked me up and pushed me along, and I'd be dead without their selfless assistance. Really truly not-pining-for-the-fjords dead, and it really is j... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1068652 Tue, 04 Dec 2007 09:58:11 +0100 1068652 http://www.sennoma.net/main/archives/2007/12/if_it_wont_sink_in_maybe_we_ca.php Another brief un-hiatus, this one sparked by a question asked by Dave Munger at BPR3: If you know of a peer-reviewed, open-access journal that does not charge a publication fee, let us know about it in the comments. Practically every time I talk about OA, online or in meatspace, I hear "I'd like to support OA but I can't afford it, don't all those journals charge, like, $2500 per article?" No. They don't. Everyone seems to be thinking of PLoS, never mind that they waive their fees at the drop of a hat; the assumption that most OA journals charge (high) author-side fees is both widespread and completely wrong. In fact, more than 2/3 of the journals listed in the Directory of Open Access Journals (DOAJ) and more than 80% of OA journals published by scholarly societies charge no author-s... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1065793 Sun, 02 Dec 2007 22:36:50 +0100 1065793 http://www.sennoma.net/main/archives/2007/11/brief_hiatus_in_my_hiatus.php I'm not ending my blogging break, but I simply couldn't let this from Cameron Neylon pass by without comment: The UK Engineering and Physical Sciences Research Council currently has a call out for proposals to fund 'Network Activities' in e-science. This seems like an opportunity to both publicise and support the 'Open Science' agenda so I am proposing to write a proposal to ask for ~£150-200k to fund workshops, meetings, and visits between different people and groups. The money could fund people to come to meetings (including from outside the UK and Europe) but could not be used to directly support research activities. The rationale for the proposal would be as follows.'Open Science' has the potential to radically increase the efficiency and effectiveness of research world wide.The ... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1046651 Fri, 23 Nov 2007 02:44:30 +0100 1046651 http://www.sennoma.net/main/archives/2007/11/hiatus.php Astute readers will have noticed that there's not much going on here anyway. I've had immigration hassles (done with, I hope), health problems (fixed, I think) and I'm waaaaaaaaaayyyyy behind at work. I need a couple months' absolute tunnel vision: publish or perish, publish or perish, publish or perish. So, no blogging for me, and I won't be reading much except research papers either. I'll copy all my science/OA RSS feeds to Google Reader (which unlike Bloglines doesn't stop caching at 200) and try to catch up on the backlog over whatever Christmas break I get. [ahnuld] I'll be back... [/ahnuld] (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=1013312 Thu, 08 Nov 2007 03:43:45 +0100 1013312 http://www.sennoma.net/main/archives/2007/10/call_yer_congresscritters_righ.php The bill to make the NIH OA policy mandatory instead of voluntary is in trouble: from the ATA via Peter Suber (with some editing by yours truly): The Senate is currently considering the FY08 Labor-HHS Bill, which includes a provision (already approved by the House of Representatives and the full Senate Appropriations Committee), that directs the NIH to change its Public Access Policy so that participation is required (rather than requested) for researchers, and ensures free, timely public access to articles resulting from NIH-funded research. On Friday, Senator Inhofe (R-OK), filed two amendments (#3416 and #3417), which call for the language to either be stricken from the bill, or modified in a way that would gravely limit the policy's effectiveness. Amendment #3416 would eliminate the ... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=966888 Sun, 21 Oct 2007 19:54:57 +0100 966888 http://www.sennoma.net/main/archives/2007/10/a_big_step_in_the_right_direct.php This is excellent news: We are delighted to announce that a reviewer discount now exits for all those who review manuscripts for Chemistry Central Journal, and this is linked to the rest of the the BMC series journals. The review must have been received on time, and during the last 12 months. This means that if the submitting author has reviewed a manuscript for Chemistry Central Journal or any of the BMC series, they are entitled to a 20% discount off the article processing charge (APC) when submitting articles to any of these journals. We ask that qualifying authors request this discount at the time of submission. The number of articles submitted to these journals continues to grow significantly, and we are grateful those who agree to review for our journals. This is a terrific idea, a... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=950846 Mon, 15 Oct 2007 01:35:58 +0100 950846 http://www.sennoma.net/main/archives/2007/09/post.php The senate will vote during the week beginning October 15 on a bill that changes the NIH Open Access deposit policy from a request (which has generated about 5% compliance) to a mandate. This would be a leap forward for OA and science, not only in the US but throughout the world. If you're a US resident, please take a few minutes to write to your Senators in support of this bill. (Letters should arrive by close of business Oct 12.) The American Library Association has made it trivially easy to contact your congresscritters about this: go to their action alert, fill in your zip code, write a brief letter and hit send. For help in composing a letter, see Peter Suber's collection of talking points, background and other resources. Below is the letter I sent.Dear Congresscritter, I am a resea... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=928756 Thu, 27 Sep 2007 02:28:00 +0100 928756 http://www.sennoma.net/main/archives/2007/09/what_are_these_things.php Well, one answer is that they are MEFs -- mouse embryo fibroblasts -- since that's what I started with. Only the cells pictured are pretty clearly not regular fibroblasts; they look more like neurons or macrophages of some kind. MEFs are a mixed population, consisting of whatever grows out of a dissociated (minced) mouse embryo minus the head, so there are some early neural and immune cells in the mix. The cells pictured are what remains after selection with either G418 or puromycin -- I was making stably transfected cells, and this is one of the control plates. So what I'm wondering is, would a brief period of exposure to a selective agent like puro be a good way to isolate naturally resistant populations, and what would those populations contain? (Of course, whatever these things are, t... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=874914 Mon, 17 Sep 2007 04:35:58 +0100 874914 http://www.sennoma.net/main/archives/2007/09/repeat_satori.php I've noticed that whenever I come all over jackass, it's because there's something wrong with my position -- when I'm secure about something I seldom resort to snark. Outright venom, sure; snide formality and similar oily tricks, no. Case in point: I took an uncalled-for swipe at Maxine (again because I hadn't thought my own position through properly), and though I've apologized, I ought not be surprised or feel put-upon if people point to that incident as an example of bad online manners. But I feel bad about it, so mention of it gets me all defensive. This is doubly daft, since not only is such a response self-evidently counterproductive, I have no particular fear of being wrong. I'm a scientist: it's in my nature and my training to attach no value judgement to being right or wrong: w... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=863692 Tue, 11 Sep 2007 19:02:58 +0100 863692 http://www.sennoma.net/main/archives/2007/09/reply_to_timo_hannay.php Timo Hannay on Nascent, branching off from a discussion of intemperate responses to PRISM: A case in point is the criticism that my NPG colleague, Maxine Clarke, faced when talking about "open access" projects at NPG. Not everyone shared her definition of open access and she was accused by some bloggers of using the term as a marketing slogan. (Peter Murray-Rust, who made the original point, later recanted when he understood that Maxine was being genuine, so I don't take issue with him.) Mr Hannay does, presumably, take issue with me. I will apply Hanlon's Razor and assume Mr Hannay did not bother to read beyond the post he linked, since the very next is this one: In the entry below, I was not sufficiently careful to avoid Nature-bashing, or the implication that Maxine Clarke was morphing,... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=861734 Tue, 11 Sep 2007 05:57:30 +0100 861734 http://www.sennoma.net/main/archives/2007/09/nature_mission_statement_updat.php Since I spend a fair bit of time excoriating publishers, it's only fair that I take note of those who act in good faith. In response to the blogospheric reaction to the Nature mission statement, Maxine Clarke asked the appropriate persons to update the NPG web page (as you remember, Bob, the journal site already made clear the necessary distinction between the original and updated statements). Accordingly, the NPG page now reads: Nature's original mission statement was published for the first time on 11 November 1869. The journal's original mission statement was revised in 2000. The original mission statement is reproduced below: and there follows the same version of the original that was on the page last time I looked. It's nitpicking to note that I prefer the way the journal does it, w... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=843710 Wed, 05 Sep 2007 16:45:34 +0100 843710 http://www.sennoma.net/main/archives/2007/09/prism_and_pmr.php I'm swamped, but two quick points: 1. I'm not going to try to keep up with reactions to PRISM here, unless I think I have something potentially useful to add. If you want a news stream, read OAN or watch my PRISM tag on Simpy -- I'll grab everything I notice. 2. Peter Murray-Rust is blogging up a storm on publisher policies, copyright and Open Access: OUP wants me to pay for my own Open Access article - September 3rd, 2007 OUP: Thank you for the response - September 4th, 2007 Ingenta: It gets even worse; corrupt and resell - September 4th, 2007 (Source: Open Reading Frame) Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=843711 Wed, 05 Sep 2007 16:21:23 +0100 843711 http://www.sennoma.net/main/archives/2007/09/more_on_prism_lets_not_take_th_1.php Jonathan Eisen has got the right idea, listing the entire members' directory of the AAP and calling on academics to consider a boycott if those entities will not at least request dissociation from the PRISM program (as Rockefeller University Press has done) or its discontinuation. You can also read the members' list on the AAP site, and Peter Suber points out that we should pay particular attention to their Professional and Scholarly Publishing division: I suspect that AAP/PSP did not consult its members before launching PRISM. But in any case the members should know that the launch of PRISM tarnishes them, alienates authors, readers, and referees, and, if successful, will only harm science by entrenching rather than removing access barriers to the results of publicly-funded research.Peter... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=836406 Sat, 01 Sep 2007 19:30:42 +0100 836406 http://www.sennoma.net/main/archives/2007/08/a_bit_more_on_prism.php If you haven't already, go read Peter Suber's initial response -- it is, as always, clear, calm, comprehensive and compelling. (I hope to meet Peter one day; I imagine him as a kind of unflappable, scholarly James Bond...) This is your one-stop anti-PRISM shop for the time being: if you read nothing else, read this; and whenever PRISM rears its ugly head, make sure Peter's response gets an airing too. Peter has also responded to a Publisher's Weekly article that simply repeats the PRISM propaganda. The by-line is Rachel Deahl, a senior news editor at PW. I wrote to her, as follows:Dear Ms Deahl, I write in response to your recent brief article in Publishers Weekly ("AAP Tries to Keep Government Out of Science Publishing", August 23, 2007), in which you quote or repeat several egregious e... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=822993 Sun, 26 Aug 2007 22:29:24 +0100 822993 http://www.sennoma.net/main/archives/2007/08/prism_publishers_relying_on_in.php From Peter Suber: The AAP/PSP has launched PRISM (Partnership for Research Integrity in Science & Medicine).  I'm quoting today's press release in its entirety so that I can respond to it at length: A new initiative was announced today to bring together like minded scholarly societies, publishers, researchers and other professionals in an effort to safeguard the scientific and medical peer-review process and educate the public about the risks of proposed government interference with the scholarly communication process. [much egregious lying] Anyone who wishes to sign on to the PRISM Principles may do so on the site. Fortunately for us all, Peter has already responded; I won't excerpt his point-by-point rebuttal here, you should go read it all. This is disgusting. This ru... Open Reading Frame blogs http://www.medworm.com/rss/comments.php?id=818749 Thu, 23 Aug 2007 19:04:01 +0100 818749