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      <title>Open Reading Frame</title>
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      <description></description>
      <language>en</language>
      <copyright>Copyright 2010</copyright>
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      <docs>http://blogs.law.harvard.edu/tech/rss</docs> 

            <item>
         <title>turn, turn yadda yadda</title>
         <description><![CDATA[<p>Quite a difference <a href="http://www.sennoma.net/main/archives/2009/10/no_bad_for_a_cameraphone.php">two months</a> makes (no, I didn't photoshop the colours!):<br />
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<img alt="bvrtntcwinter.jpg" src="http://www.sennoma.net/main/archives/graphics/bvrtntcwinter.jpg" width="400" height="300" /><br />
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         <link>http://www.sennoma.net/main/archives/2010/01/turn_turn_yadda_yadda.php</link>
         <guid>http://www.sennoma.net/main/archives/2010/01/turn_turn_yadda_yadda.php</guid>
         <category>f/8 and be there</category>
         <pubDate>Sat, 02 Jan 2010 13:06:06 -0800</pubDate>
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            <item>
         <title>no&apos; bad for a cameraphone</title>
         <description><![CDATA[<p>From my flash new company phone:</p>

<p><br /></p>

<center>
<img alt="beavertontransitcenter.JPG" src="http://www.sennoma.net/main/archives/graphics/beavertontransitcenter.JPG" width="400" height="300" />

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<p><img alt="downtown.jpg" src="http://www.sennoma.net/main/archives/graphics/downtown.jpg" width="400" height="300" /><br />
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<p>The top image is from my commute to work in the morning, at Beaverton Transit Center where I missed my connection by (quite literally) seconds and had to wait half an hour for the next bus.  The bottom image is from my commute home in the evening, at SW 9th and Yamhill where I had ten minutes to wait for my train.  I took a neat little video too, soundtrack courtesy of a busker with a violin, but it's too big for snapfish and my phone is locked-in to Microsoft-related email services so I haven't figured out how to upload it yet.<br />
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         <link>http://www.sennoma.net/main/archives/2009/10/no_bad_for_a_cameraphone.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/10/no_bad_for_a_cameraphone.php</guid>
         <category>f/8 and be there</category>
         <pubDate>Mon, 19 Oct 2009 23:30:31 -0800</pubDate>
      </item>
            <item>
         <title>&quot;Guerrilla OA&quot; done right.</title>
         <description><![CDATA[<p>I was reminded recently (when Graham Steel uploaded <a href="http://www.flickr.com/photos/7914713@N05/3916005447/">this photo</a>) of <a href="http://mcblawg.blogspot.com/2007/09/here-is-report-in-relation-to-my.html">something I've been meaning to write about</a> for nearly two years.</p>

<p>For those who don't know him (which must surely exclude nearly everyone involved with Open Access!), Graham (<a href="http://mcblawg.blogspot.com/">blog</a>, <a href="http://friendfeed.com/mcdawg">FF</a>) is a patient advocate, which work has made him a staunch supporter of OA and all things Open.  (Those of us who promote OA from an academic or research perspective sometimes, I think, forget about the incalculable value that OA offers other professionals and the lay public.)</p>

<p>Graham's first foray into "guerrilla OA" (most emphatically not to be confused with <a href="http://contentliberation.com/">these well-meaning idiots</a>) was in September 2007, when he attended a conference and ran a one-man unofficial promotional campaign.  Do <a href="http://mcblawg.blogspot.com/2007/09/here-is-report-in-relation-to-my.html">read his own description</a>, but the basic strategy was to be a human signpost (wearing "Research Made Public" and "I'm Open" t-shirts) and distribute OA promotional materials in such a way as to give most of the delegates at least a brief exposure to the concept.</p>

<p>(Pause here to marvel at the dedication of the man whose belief in the possibilities of OA makes him willing, entirely at his own instigation, to arrange attendance, travel and accomodation, collect up the necessary materials and then physically go and do all this.)</p>

<p>Sadly, we can't yet clone Graham; but perhaps we can duplicate some of his efforts.  I wonder how much it would cost to make "guerrilla OA" kits like the one Graham made for himself, but aimed at conference delegates so that researchers could turn into "Steel lite" activists at every conference we attend.  Here are a few ideas:</p>

<ul><li>t-shirts to start conversations</li><li>a badge instead of a t-shirt ("free your research, ask me how") for those who prefer more formal attire</li><li>"OA in a nutshell" cards the size and shape of regular business cards, for handing out in conversation and leaving on appropriate tables</li><li>slides for your talk: start with Cameron's <a href="http://friendfeed.com/cameronneylon/3add0674/presentation-rights">"Presentation Rights"</a> and end with a "Basics of OA" slide</li><li>equivalent add-ons for your poster, such as a Copyright Notice and an OA Basics placard, about the size of a postcard so they should fit on most posters as an afterthought and would be easy to incorporate into the poster itself</li></ul>

<p>Here's another idea: it would only take half a dozen delegates to run an "OA stall", similar to the vendor stalls with which we are all only too familiar.  This would mean working with conference administration, so maybe they would even help with "recruiting"; alternatively, it should be simple to set up a website where one can advertise for help in running such a stall at a particular conference.  OA publishers could contribute materials (perhaps in return for help with costs), but I think transparent independence from any particular commercial effort would help tremendously in establishing credibility and producing a positive response.  A prominent "who are we and why are we doing this?" banner might be a good idea.  Flyers could include "OA:what's in it for you?", "Why the Impact Factor should be retired", and "Elsevier: just another greedy bottom-feeder, or SPAWN OF SATAN????".  (OK, maybe not that last one... though a single page with <a href="http://www.sennoma.net/main/archives/2009/04/scholarly_journals_vs_total_se.php">this graph</a> on it, or a reprint of <a href="http://www.sennoma.net/main/archives/2009/06/oa_vs_ta_costs_i_think_i_have.php">this</a> if I ever get around to publishing it, might be a good idea.)<br />
<br /></p>]]></description>
         <link>http://www.sennoma.net/main/archives/2009/10/guerrilla_oa_done_right.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/10/guerrilla_oa_done_right.php</guid>
         <category>open access/open science</category>
         <pubDate>Mon, 19 Oct 2009 16:01:59 -0800</pubDate>
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            <item>
         <title>coming up for air</title>
         <description><![CDATA[<p>Whew.  It's been a trip so far.  My new job is at a company that is starting up after a hiatus -- it's not what is usually meant by a start-up, but from what I can tell the atmosphere is pretty similar.  I'll link to it, and <em>maybe</em> talk about some of my work, when I have a better sense of where the boundaries are.  I don't want to be continually pestering the admin to vet my blog posts!  For now all I'll say is that we make HIV diagnostic tools, and it's good to be back in that fight.  I might post HIV-related content from time to time, but I'll add a disclaimer about my corporate connection.</p>

<p>I don't have a lot of free time, but I do want to keep talking and thinking about Open Science... now that I'm in biotech, it's harder to see how to do things openly, but that doesn't mean I shouldn't try.</p>

<p>For the moment, in lieu of any original content, here are two must-reads for anyone who reads me:  </p>

<p>Walt Crawford has devoted an entire issue of Cites&Insights to <a href="http://citesandinsights.info/v9i12a.htm">library access to scholarship</a>, and you should read it for a useful overview of the state of scholarly communication in general and not just because he says nice things about my efforts to put some numbers to the questions.  (At the risk of being ungrateful, I will add that I could have done with fewer swipes at Stevan Harnad, but then I must in fairness further add that I am under-informed about the library community perspective on the original archivangelist. Ymmv.)</p>

<p>Cameron Neylon has been <a href="http://blog.openwetware.org/scienceintheopen/2009/10/10/open-research-the-personal-the-social-and-the-political/">thinking about science and society</a> again.  Just do yourself a favour and read it, OK?  Here's a quote to whet your appetite:</p>

<blockquote>We need at core a much more sophisticated conversation with the wider community about the benefits that research brings; to the economy, to health, to the environment, to education. And we need a much more rational conversation within the research community as to how those different forms of impact are and should be tensioned against each other.  We need in short a complete overhaul if not a replacement of the post-war concensus on public funding of research. My fear is that without this the current funding squeeze will turn into a long term decline. And that without some serious self-examination the current self-indulgent bleating of the research community is unlikely to increase popular support for public research funding.</blockquote>
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         <link>http://www.sennoma.net/main/archives/2009/10/coming_up_for_air.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/10/coming_up_for_air.php</guid>
         <category>personal</category>
         <pubDate>Sat, 10 Oct 2009 18:46:14 -0800</pubDate>
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            <item>
         <title>Trick or treatment?</title>
         <description><![CDATA[<p><em>(Note: this is the infamous article on chiropractic that got Simon Singh sued. It is being reposted all over the web today by multiple blogs and online magazines.  Via <a href="http://bjoern.brembs.net/news.php?item.534.5">Bj&ouml;rn</a>.)<br />
</em><br />
<hr size="2"><br />
Some practitioners claim it is a cure-all, but the research suggests chiropractic therapy has mixed results - and can even be lethal, says Simon Singh.</p>

<p>You might be surprised to know that the founder of chiropractic therapy, Daniel David Palmer, wrote that "99% of all diseases are caused by displaced vertebrae". In the 1860s, Palmer began to develop his theory that the spine was involved in almost every illness because the spinal cord connects the brain to the rest of the body. Therefore any misalignment could cause a problem in distant parts of the body.</p>

<p>In fact, Palmer's first chiropractic intervention supposedly cured a man who had been profoundly deaf for 17 years. His second treatment was equally strange, because he claimed that he treated a patient with heart trouble by correcting a displaced vertebra.</p>

<p>You might think that modern chiropractors restrict themselves to treating back problems, but in fact some still possess quite wacky ideas. The fundamentalists argue that they can cure anything, including helping treat children with colic, sleeping and feeding problems, frequent ear infections, asthma and prolonged crying - even though there is not a jot of evidence.</p>

<p>I can confidently label these assertions as utter nonsense because I have co-authored a book about alternative medicine with the world's first professor of complementary medicine, Edzard Ernst. He learned chiropractic techniques himself and used them as a doctor. This is when he began to see the need for some critical evaluation. Among other projects, he examined the evidence from 70 trials exploring the benefits of chiropractic therapy in conditions unrelated to the back. He found no evidence to suggest that chiropractors could treat any such conditions.</p>

<p>But what about chiropractic in the context of treating back problems? Manipulating the spine can cure some problems, but results are mixed. To be fair, conventional approaches, such as physiotherapy, also struggle to treat back problems with any consistency. Nevertheless, conventional therapy is still preferable because of the serious dangers associated with chiropractic.</p>

<p>In 2001, a systematic review of five studies revealed that roughly half of all chiropractic patients experience temporary adverse effects, such as pain, numbness, stiffness, dizziness and headaches. These are relatively minor effects, but the frequency is very high, and this has to be weighed against the limited benefit offered by chiropractors.</p>

<p>More worryingly, the hallmark technique of the chiropractor, known as high-velocity, low-amplitude thrust, carries much more significant risks. This involves pushing joints beyond their natural range of motion by applying a short, sharp force. Although this is a safe procedure for most patients, others can suffer dislocations and fractures.</p>

<p>Worse still, manipulation of the neck can damage the vertebral arteries, which supply blood to the brain. So-called vertebral dissection can ultimately cut off the blood supply, which in turn can lead to a stroke and even death. Because there is usually a delay between the vertebral dissection and the blockage of blood to the brain, the link between chiropractic and strokes went unnoticed for many years. Recently, however, it has been possible to identify cases where spinal manipulation has certainly been the cause of vertebral dissection.</p>

<p>Laurie Mathiason was a 20-year-old Canadian waitress who visited a chiropractor 21 times between 1997 and 1998 to relieve her low-back pain. On her penultimate visit she complained of stiffness in her neck. That evening she began dropping plates at the restaurant, so she returned to the chiropractor. As the chiropractor manipulated her neck, Mathiason began to cry, her eyes started to roll, she foamed at the mouth and her body began to convulse. She was rushed to hospital, slipped into a coma and died three days later. At the inquest, the coroner declared: "Laurie died of a ruptured vertebral artery, which occurred in association with a chiropractic manipulation of the neck."</p>

<p>This case is not unique. In Canada alone there have been several other women who have died after receiving chiropractic therapy, and Edzard Ernst has identified about 700 cases of serious complications among the medical literature. This should be a major concern for health officials, particularly as under-reporting will mean that the actual number of cases is much higher.</p>

<p>If spinal manipulation were a drug with such serious adverse effects and so little demonstrable benefit, then it would almost certainly have been taken off the market.<br />
<hr size="2"><br />
<em>Simon Singh is a science writer in London and the co-author, with Edzard Ernst, of Trick or Treatment? Alternative Medicine on Trial. This is an edited version of an article published in The Guardian for which Singh is being personally sued for libel by the British Chiropractic Association. </em> <br />
<br /></p>]]></description>
         <link>http://www.sennoma.net/main/archives/2009/07/trick_or_treatment.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/07/trick_or_treatment.php</guid>
         <category>cheats, thieves, liars, degenerates, assholes</category>
         <pubDate>Thu, 30 Jul 2009 21:56:28 -0800</pubDate>
      </item>
            <item>
         <title>Yes!</title>
         <description><![CDATA[<p>I'm swamped (new job), but just had to point this out: if you are interested in scholarly communication, Open Science, bibliometrics or anything related (and if you're not, why the hell would you read me?), then you must read <a href="http://mndoci.com/blog/2009/07/23/a-step-in-the-right-direction/">this post from Deepak</a> and the <a href="http://www.plos.org/cms/node/478">related post from PLoS ONE</a>.   Bora <a href="http://scienceblogs.com/clock/2009/07/measuring_scientific_impact_wh.php">suggests</a> that we mark our calendars; I think he's right, and this will prove to be one of those milestones whose importance will be clear in hindsight.</p>

<p>So -- what they said, especially Neil.<br />
<br /></p>]]></description>
         <link>http://www.sennoma.net/main/archives/2009/07/yes.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/07/yes.php</guid>
         <category>open access/open science</category>
         <pubDate>Thu, 23 Jul 2009 22:12:27 -0800</pubDate>
      </item>
            <item>
         <title>Paying for toll access.</title>
         <description><![CDATA[<p>In response to the <a href="http://friendfeed.com/billhooker/bd2a2e97/oa-and-strategy">persuasive argument</a> that online and peer reviewed journal audiences have significantly less than 100% overlap, I'm going to start trying to re-publish some of my Open Access writing.  I'm considering submitting the draft below as a letter to the editor of Haematologica, in response to <a href="http://www.haematologica.org/cgi/content/full/94/6/764">this editorial</a>; comments, corrections and suggestions for where to send it are welcome.  </p>

<p>In particular, I'd like input on the following: the draft letter is basically an abbreviated version of <a href="http://www.sennoma.net/main/archives/2009/06/oa_vs_ta_costs_i_think_i_have.php">this post</a> -- should I, instead, work the full post (including <a href="http://www.sennoma.net/main/archives/2009/06/cost_to_libraries_oa_vs_ta.php">this</a> <a href="http://www.sennoma.net/main/archives/2009/06/update_and_correction_re_cost.php">revision</a> of Phil Davis' Cornell study) up into a paper/essay/article and submit that somewhere?  </p>

<p>If so, should I include only the self-reported figures for average TA journal author-side costs (see below), or should I pick a number of prominent journals and estimate their average author-side costs as I did in <a href="http://www.sennoma.net/main/archives/2009/06/authorside_fee_comparison_oa_v.php">this post</a>?</p>

<p>If the latter, obviously the methodology for the blog post is inadequate for a formal publication -- so how would one go about getting a reliable estimate -- that is, how many issues would one need to sample?  And which journals should I include?</p>

<p>(I'm inclined to think I should just send the letter, because to do the paper properly would be a lot of work.  The Davis update should be more than just plugging in new assumptions, it should really be repeated with the latest ARL numbers and new searches in Web of Science and/or Scopus.  On top of that, estimating average page number and number of color figures for a single journal, let alone a selection, is an enormous task.  So, frankly, it probably won't get done -- although I'm up for a collaboration if anyone out there is interested.)</p>

<p>Finally, one for the statisticians out there: if I do include the update to the Davis study, how would one go about a formal analysis of what is shown in Figure 3 of <a href="http://www.sennoma.net/main/archives/2009/06/update_and_correction_re_cost.php">this post</a>?  The question is this: to what extent is high ranking on the list of predicted expenses in an all-OA world predictive of high ranking on lists of serials expenditure, enrolment or articles published?  And is such an analysis (some kind of rank correlation, right?) really any better than the simple eyeball explanation I used in the linked post?</p>

<p><br />
----draft letter-----</p>

<p><br />
Dear Sir/Madam: </p>

<p>last month's issue of Haematologica featured an editorial entitled "Paying for open access" [1].  I write to point out that subscription-model ("toll access", TA) journals also impose author-side fees such as page and color figure charges.  In fact, in a 2005 survey, a greater proportion of TA journals than of Open Access (OA) journals charged such fees [2].  Recent financial and publishing estimates have made it possible to compare fees across the two models, as follows.<br />
 <br />
The NIH estimates that it spends $80 to $100 million/year [3] on the publication costs of some 80,000 papers [4], and approximately 5% of research publications worldwide are available through Gold OA with no embargo period [5].  On the overly conservative [6] assumption that the average author-side fee for Gold OA is triple the average author-side fee levied by toll access journals, the average publication charge paid by the NIH to toll access journals is between $909 and $1136 per paper.</p>

<p>Further, OA advocate Peter Suber has pointed out (pers. comm.) that this number is certainly an underestimate since some fraction of those 80,000 articles did not use NIH funds, either because they were published in no-fee journals or because the authors found other ways to pay.  Bearing this in mind, the NIH estimate is consistent with the handful of self-reported figures I have been able to find:<br />
<div style="margin-left: 10px;"><span style="font-family: Courier New;"><br />
<strong>journal</strong> ................................. <strong>avg. author-side fee</strong><br />
Molecular Biology of the Cell ................... $1829 [7]<br />
American Physiological Society (14 journals) .... $1000 [8]<br />
Molecular Biology and Evolution ................. $922&nbsp; [9]<br />
Molecular Plant-Microbe Interactions ............ $1275 [10]<br />
</span><br />
</div><br />
For comparison, the <strike>same issue</strike> last two issues of Haematologica <strike>in which the aforementioned editorial appeared also</strike> included 33 <strike>original</strike> research articles.  On the basis of current page and color figure charges (and including submission fees), I calculate that the authors of these papers paid an average of around &euro;<strike>600</strike> 560 ($<strike>840</strike> 790) per paper.  Though the sample is hardly representative, it seems likely that the average cost of a Haematologica paper is in this ballpark.  Such a figure is consistent with fees charged by other Gold OA publishers [6].</p>

<p>Authors considering the affordability of OA fees should bear in mind that they may well pay as much or more in page and color charges at a toll access journal, and should also ask what it is that they are paying for.  Readers of toll access journals must bear a further cost, either directly or through subscriptions, whereas OA articles are immediately and permanently free for anyone to read.</p>

<p><br />
Sincerely,</p>

<p>me.</p>

<p><br /><br /><br />
<strong>Update 090717:</strong> corrected the calculation; you can grab the data <a href="http://spreadsheets.google.com/pub?key=tJMflt0_s0uu0Sg33BZRAvw&output=html ">here</a> if you want to check my work or do something else with it.  This is another argument for re-publishing: it makes you check your work!  I got things wrong, and forgot to make the data available, the first time around.</p>

<p>I've submitted the letter; the full study I suggested is so much larger that I don't see it as salami publishing to submit that separately, if it ever gets done.  Following a suggestion from Heather Morrison in comments, I'm going to try putting it up as a research project on the <a href="http://oad.simmons.edu/oadwiki/Research_in_progress">OAD</a> and try to coordinate a team project.  I felt compelled to point out this blog entry, the CCZero license and the fact that, if they accept the letter, I intend to use a CC/SPARC Author Addendum to retain enough rights from their copyright transfer (why does an OA journal need that?!) to offer CC-BY-NC.  We'll see what happens.<br />
<br /><br /></p>

<p><strong>References</strong><br />
[1] Paying for open access. Haematologica, Vol 94, Issue 6, p. 764 doi:10.3324/haematol.11505</p>

<p>[2] The Facts About Open Access. Kaufman-Wills Group, LLC 2005 URL:http://www.alpsp.org/ngen_public/article.asp?id=200&did=47&aid=270&st=&oaid=-1. Accessed: 2009-07-17. (Accessed July 16 2009)</p>

<p>[3] US House of Representatives Subcommittee on Courts, the Internet, and Intellectual Property Hearing on H.R. 6845, the "Fair Copyright in Research Works Act". Thursday 09/11/2008 URL:http://judiciary.house.gov/hearings/hear_080911_1.html. (Archived by WebCite<sup>&reg;</sup> at http://www.webcitation.org/5iFx4iGru)</p>

<p>[4] US National Institutes of Health Public Access Frequently Asked Questions. URL:http://publicaccess.nih.gov/FAQ.htm#f4. (Archived by WebCite<sup>&reg;</sup> at http://www.webcitation.org/5iFxByIMV)</p>

<p>[5] Bj&ouml;rk B-C., Roosr A and Lauri M. Global annual volume of peer reviewed scholarly articles and the share available via different open access options. Proceedings of the 12th International Conference on Electronic Publishing ISBN 978-0-7727-6315-0, 2008, pp. 178-186 (http://elpub.scix.net/cgi-bin/works/Show?_id=178_elpub2008)</p>

<p>[6] Comparison of BioMed Central's Article Processing Charges with those of other publishers. URL:http://www.biomedcentral.com/info/authors/apccomparison/. (Archived by WebCite<sup>&reg;</sup> at http://www.webcitation.org/5iFxJ0Mex)</p>

<p>[7] American Society for Cell Biology Newsletter, April 2007: MBC and the Economics of Scientific Publishing. URL:http://www.ascb.org/files/mbc_cost_printing.pdf available from URL:http://www.ascb.org/index.php?option=com_content&view=article&id=64&Itemid=216. (Archived by WebCite<sup>&reg;</sup> at http://www.webcitation.org/5iFxptGx6)</p>

<p>[8] American Physiological Society AuthorChoice Frequently Asked Questions. URL:http://www.the-aps.org/authorchoice/faq.html. Accessed: 2009-07-14. (Archived by WebCite<sup>&reg;</sup> at http://www.webcitation.org/5iFy5XFnK)</p>

<p>[9] Society for Molecular Biology and Evolution: Editor's Annual Report 2008. URL:http://www.smbe.org/pdf/2008editreport.pdf available from URL:http://www.smbe.org/archive.php. (Archived by WebCite<sup>&reg;</sup> at http://www.webcitation.org/5iFxdKLqV)</p>

<p>[10] American Phytopathological Society Reports of Publications 2000. URL:http://www.apsnet.org/members/gov/2000/Reports%20of%20Publications.htm. (Archived by WebCite<sup>&reg;</sup> at http://www.webcitation.org/5iFwcmIBL)<br />
<br /></p>]]></description>
         <link>http://www.sennoma.net/main/archives/2009/07/paying_for_toll_access.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/07/paying_for_toll_access.php</guid>
         <category>open access/open science</category>
         <pubDate>Tue, 14 Jul 2009 01:52:40 -0800</pubDate>
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         <title>Please consider.</title>
         <description><![CDATA[<p>After seven years (for at least three of which I've been a fan), J&ouml;rg Colberg is <a href="http://jmcolberg.com/weblog/2009/07/conscientious_needs_your_support.html">asking for help</a> covering the costs of his photography blog, <a href="http://jmcolberg.com/weblog/">Conscientious.</a></p>

<p>I don't have time these days to follow photo blogs the way I follow, say, issues in scholarly publishing, but of all the photo blogs I used to read, Conscientious is the only one still on my regular reading list.  I like the way J&ouml;rg thinks and talks about photography, and he consistently points me to outstanding images and the artists who make them.  When he talks about not only maintaining but expanding the blog, I'm curious to know what he has in mind.</p>

<p>So I've sent him the price of a couple of beers, which is about all I can free up these days, and I'd like to invite my readers to do the same, if they have the means.  And whether or not you can spare a little cash, if you're at all interested in photography do check out <a href="http://jmcolberg.com/weblog/">Conscientious</a>.<br />
<br /></p>]]></description>
         <link>http://www.sennoma.net/main/archives/2009/07/please_consider_1.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/07/please_consider_1.php</guid>
         <category>helping hand</category>
         <pubDate>Wed, 08 Jul 2009 17:10:51 -0800</pubDate>
      </item>
            <item>
         <title>Perfect match?</title>
         <description><![CDATA[<p>Surely <a href="http://www.osti.gov/adoptAdoc/">this</a>:<br />
<br /><br />
<img alt="doe.jpg" src="http://www.sennoma.net/main/archives/graphics/doe.jpg" width="317" height="96" align="left" style="margin-right: 1em; margin-left: 1em; margin-bottom: 0.2em;" /><blockquote>You may find a technical report that you want to share with others or you think worthy of making broadly available on the Web to support the advancement of science. When you search for important science information in your area of interest, you can choose to sponsor the digitization of any adoptable technical report. The cost is $85 (approximately the same cost as ordering a hard copy). Discounts for multiples of 5 or more adoptions may be available. If you are interested in a larger scale project, please contact (865) 576-5699. </blockquote><br />
<br /><br />
is a job for <a href="http://en.wikipedia.org/wiki/Carl_Malamud">this guy</a>:<br />
<br /><br />
<img alt="malamud.jpg" src="http://www.sennoma.net/main/archives/graphics/malamud.jpg" width="200" height="243" align="right" style="margin-right: 1em; margin-left: 1em; margin-bottom: 0.2em;" /><blockquote>... Most recently, Malamud has set up the nonprofit public.resource.org, headquartered in Sebastopol, California, to work for the publication of public domain information from local, state, and federal government agencies. Among his victories have been digitizing 588 government films for the Internet Archive and YouTube, publishing a 5 million page crawl of the Government Printing Office, and persuading the state of Oregon to not assert copyright over its legislative statutes.</blockquote> <br clear="all" /></p>

<p>?<br />
<br /><br />
(CC-BY image of Carl Malamud from <a href="http://www.flickr.com/people/71753172@N00">Joe Hall</a> via <a href="http://commons.wikimedia.org/wiki/File:Carl_Malamud_at_Berkeley-2007-10-17-version.03.jpg">Wikimedia</a>)<br />
<br /></p>]]></description>
         <link>http://www.sennoma.net/main/archives/2009/06/perfect_match.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/06/perfect_match.php</guid>
         <category>open access/open science</category>
         <pubDate>Tue, 30 Jun 2009 10:56:16 -0800</pubDate>
      </item>
            <item>
         <title>ARTifacts II: everything is pretty if you look close enough</title>
         <description><![CDATA[<p>When you count cells, you often mix them with a dilute solution of a dye which is excluded by living cells but can cross the membrane of dead cells -- this allows you to count viable and dead cells separately.  Probably the most common dye for the purpose (at least, the only one I've ever used) is <a href="http://en.wikipedia.org/wiki/Trypan_blue">Trypan blue</a>, which is a very pretty blue color.  </p>

<p>Everyone has their own ways of adding the dye; I tend to recycle the lid of a discarded culture dish as a mixing surface, pipetting 10 &micro;l of 2X Trypan blue in buffered salt solution onto the lid and then mixing with 10 &micro;l of cell suspension.  Since the <a href="http://en.wikipedia.org/wiki/Hemocytometer">cell counter</a> only takes 10 &micro;l, that leaves half of each mixture drying in spots all over the lid as I count my way through my cultures.</p>

<p>One day I decided to take some photomicrographs of the resulting patterns.  The crystals are salts; I think the dye tends to dry into blobs rather than crystallizing.  The round things that look like alien eggs in images 2 and 3 are what was left behind by air bubbles.<br />
<br /><br />
<br /><br />
<center><img alt="DSC_1237.JPG" src="http://www.sennoma.net/main/archives/graphics/DSC_1237.JPG" width="600" height="399" /></center><br />
<br /><br />
<br /><br />
<center><img alt="DSC_1238.JPG" src="http://www.sennoma.net/main/archives/graphics/DSC_1238.JPG" width="600" height="399" /></center><br />
<br /><br />
<br /><br />
<center><img alt="DSC_1239.JPG" src="http://www.sennoma.net/main/archives/graphics/DSC_1239.JPG" width="600" height="399" /></center><br />
<br /><br />
<br /><br />
<center><img alt="DSC_1241.JPG" src="http://www.sennoma.net/main/archives/graphics/DSC_1241.JPG" width="600" height="399" /></center><br />
<br /><br />
<br /><br />
<center><img alt="DSC_1246.JPG" src="http://www.sennoma.net/main/archives/graphics/DSC_1246.JPG" width="399" height="600" /></center><br />
<br /></p>]]></description>
         <link>http://www.sennoma.net/main/archives/2009/06/artifacts_ii_everything_is_pre.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/06/artifacts_ii_everything_is_pre.php</guid>
         <category>visual &amp; various</category>
         <pubDate>Mon, 29 Jun 2009 18:49:10 -0800</pubDate>
      </item>
            <item>
         <title>ARTifacts I: lightning autoradiograph</title>
         <description><![CDATA[<p>I was reminded today, by Bj&ouml;rn's <a href="http://bjoern.brembs.net/news.php?item.529.5">post about modern art</a>, of something I've been meaning to post for a long time.  I'm hardly the first person to notice that the products and by-products of scientific experiments can be very pretty, and I find that often the story and the science behind the object or image gives it an extra dimension.  For instance this:<br />
<br /><br />
<center><img alt="zap2.jpg" src="http://www.sennoma.net/main/archives/graphics/zap2.jpg" width="514" height="798" /></center><br />
<br /><br />
is electrostatic discharge, captured on x-ray film -- static electricity that really is static.  </p>

<p>It's an artifact caused by wrapping developed chemiluminescent western blots in cling wrap prior to exposing them -- you have to wrap the blots so as not to wet the film, but it can create static discharges which fan out across your results when you peel the blots away from the film in order to develop it.  This is one that was well away from my data, so I scanned it just for itself.</p>

<p>I'm sure I could string together 500 words of postmodern bullshit about the fact that this picture was the accidental result of a real experiment, a (literal) spark thrown from the anvil on which knowledge was being forged...  all I need now is an agent with contacts in the art world and a bunch of people with more money than sense.<br />
<strong><br />
Update 090709:</strong> Ha!  I'm in good company, apart from my snotty remarks about the art world of course -- about half way through <a href="http://www.youtube.com/watch?v=sOBwF1jvw0k&feature=related">this story</a>, modern master Hiroshi Sugimoto talks about pictures he made in the darkroom without a camera, using static electricity.  And yes, they look a lot like my autorads!<br />
<br /></p>]]></description>
         <link>http://www.sennoma.net/main/archives/2009/06/artifacts_i_static_electricity.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/06/artifacts_i_static_electricity.php</guid>
         <category>visual &amp; various</category>
         <pubDate>Mon, 29 Jun 2009 17:46:37 -0800</pubDate>
      </item>
            <item>
         <title>...and now for something completely different.</title>
         <description><![CDATA[<p><br /><div style="margin-left:40px;"><strong>You Have Been Warned</strong><br /></p>

<p><em>Der Tod wird kommen, und deine Augen haben.<br />
&mdash;Cesar Pavese, selbstmord 1950</em></p>

<p><br />
You have been warned. It should be no surprise<br />
when blood and breath resign the long campaign.<br />
Death will come, and he will have your eyes.</p>

<p>All things must pass, and everybody dies.<br />
(Give thanks!&mdash;Were life less brief, all art were vain.)<br />
You have been warned, it should be no surprise</p>

<p>to grasp the brass ring, catch the final prize,<br />
and find that neither sleep nor dream obtain.<br />
Death will come, and he will have your eyes,</p>

<p>and after that&mdash;nothing. The poet lies<br />
for profit, and the priest looks to his gain,<br />
but you've been warned. It should be no surprise</p>

<p>when flesh the sovereignty of will denies:<br />
there is no will, all's chaos and chicane.<br />
Death will come, and he will have your eyes,</p>

<p>and that's an end to it. Say your goodbyes<br />
early&mdash;who knows what hours remain?<br />
You have been warned, it should be no surprise:<br />
Death will come, and he will have your eyes. </div></p>

<p><br /><br />
<br /></p>

<p>The quote comes from this poem (from <a href="http://turmsegler.net/20061202/der-tod-wird-kommen/">here</a>):</p>

<p><br />
<div style="margin-left:40px;"><strong>Der Tod wird kommen...</strong></p>

<p>Der Tod wird kommen und deine Augen haben,<br />
der Tod, der uns begleitet<br />
von morgens bis abends, schlaflos,<br />
dumpf, wie ein alter Gewissensbi&szlig;<br />
oder ein t&ouml;richtes Laster. Und deine Augen<br />
werden ein leeres Wort sein,<br />
ein verschwiegener Schrei, ein Schweigen.<br />
So siehst du sie jeden Morgen,<br />
wenn du dich &uuml;ber dich neigst, mit dir allein<br />
im Spiegel. O teuere Hoffnung,<br />
an jenem Tage werden auch wir es wissen,<br />
da&szlig; du das Leben bist und das Nichts.</p>

<p>F&uuml;r alle hat der Tod einen Blick.<br />
Der Tod wird kommen und deine Augen haben.<br />
Das wird sein wie das Ablegen eines Lasters,<br />
wie wenn man ein totes Gesicht<br />
wieder auftauchen sieht im Spiegel,<br />
oder auf eine verschlossene Lippe horcht.<br />
Wir werden stumm in den Strudel steigen.</div></p>

<div style="margin-left:200px;"><a href="http://de.wikipedia.org/wiki/Cesare_Pavese">Cesare Pavese</a>, geschrieben 1950,<br />
wenige Wochen vor seinem Freitod</div>
<br />
<br />
Here's a translation, as close as I could get to word-for word with no attempt at poetry (I know I have a few readers who speak German -- corrections/improvements are always welcome):
<br />
<br />
<strong>Update:</strong> already there are two comments improving my translation. :-)  Also, Ralf points to the <a href="http://www.stedo.it/poesie/pavese6.htm">Italian original</a>; I knew Pavese was Italian but had only ever seen the German version of this poem, without any translation credit, so I thought he wrote also in German.
<br />
<br />
<div style="margin-left:40px;"><strong>Death will come...</strong>

<p>Death will come and have your eyes,<br />
Death, who attends us<br />
from morning until night, sleepless,<br />
muffled, like an old conscience-prick<br />
or a foolish vice. And your eyes<br />
will be an empty word,<br />
a secret cry, a silence.<br />
So you see them every morning,<br />
as you lean over yourself, alone with you<br />
in the mirror. O expensive hope<br />
on that day we also will know<br />
that you are Life and Nothingness.</p>

<p>Death has a glance for everyone.<br />
Death will come and have your eyes.<br />
That will be like <strike>the unloading of a lorry</strike> letting go of a vice,<br />
as when one sees a dead face<br />
rising up again in the mirror,<br />
or listens to a fastened lip.<br />
<strike>We grow mute as the maelstrom rises</strike> We will step silently into the maelstrom. </div<br />
<br /></p>]]></description>
         <link>http://www.sennoma.net/main/archives/2009/06/and_now_for_something_complete.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/06/and_now_for_something_complete.php</guid>
         <category>handful of notes</category>
         <pubDate>Fri, 26 Jun 2009 08:44:17 -0800</pubDate>
      </item>
            <item>
         <title>OA vs TA costs: I think I have finally got this straight.</title>
         <description><![CDATA[<p>I made some errors in the last few posts, making the information somewhat scrambled -- my apologies.  Here is what I hope is a clear picture of what we know about the relative costs of OA and TA publishing.</p>

<p>1. The NIH estimates that it pays <a href="http://arstechnica.com/tech-policy/news/2008/09/open-access-science.ars">$100 million/year</a> in author-side charges, and supports the production of some <a href="http://publicaccess.nih.gov/FAQ.htm#f4">80,000 scholarly articles</a>; that's an average of $1250/article.</p>

<p><strong>Update:</strong> Peter Suber points out that some fraction of that 80,000 articles did not use NIH funds, either because they were published in no-fee journals or because the authors found other ways to pay.  I can't think of any way to estimate the actual number of articles the $100 million paid for in order to adjust the estimated fee/article, but it's worth remembering that it's an <em>under</em>estimate.</p>

<p>2. <a href="http://www.earlham.edu/~peters/fos/2008/04/what-is-oa-percentage-of-new-articles.html">Bj&ouml;rk <em>et al.</em></a> found that less than 5% of all articles worldwide are available through no-embargo Gold OA.  We don't know what proportion of the NIH's $100 million went to Gold OA fees, nor what the average such fee might be.  In order to be conservative, let's assume that the average Gold OA fee is triple the average TA fee (it almost certainly isn't <a href="http://www.biomedcentral.com/info/authors/apccomparison/">that high</a>).  Then (if that 5% is evenly distributed) the NIH paid for (0.95x80000=) 76,000 articles at $average and 4,000 articles at 3x$average, bringing the average author-side charge for a TA article to $1136.</p>

<p>3. Philip Davis' 2004 <a href="http://ecommons.library.cornell.edu/handle/1813/236">library costs spreadsheet</a> estimates the average subscription charge per scholarly article at between $970 and $1750, depending on what proportion of the library serials budget is allocated to scholarly publications.</p>

<center><img alt="subscriptionperarticle.jpg" src="http://www.sennoma.net/main/archives/graphics/subscriptionperarticle.jpg" width="383" height="262" /></center>

<p>Davis' original study estimated this proportion at 50% (on what basis I don't know), but I think the real value is closer to 90%.  My reasoning is based on <a href="http://www.sennoma.net/main/archives/2009/03/fawn_part_4_or_those_data_you.php">my observation</a> (see Table 2) that the average unit cost of a curated list of scholarly journals from <a href="http://osc.universityofcalifornia.edu/">UCOSC</a> is about ten times the average unit cost of "all serials" from <a href="http://www.ala.org/ala/mgrps/divs/acrl/index.cfm">ACRL</a>, <a href="http://www.arl.org/">ARL</a> and <a href="http://nces.ed.gov/">NCES</a> datasets. If that result is broadly representative it means that scholarly journals must contribute either a small fraction or the vast majority of the cost (see <a href="http://www.sennoma.net/main/archives/2009/06/cost_to_libraries_oa_vs_ta.php">here</a> for a brief explanation).</p>

<p>So that gives an estimated fee of between <strong>$2106 and $2886</strong> per toll-access article.  That money isn't all coming from the same place -- the NIH is paying author-side fees and libraries are paying subscriptions -- but it's all going to the same place, publisher coffers.</p>

<p>I've added a current (under)estimate of NIH costs for author-side fees, adjusted for a 2006 estimate of %OA by article, to a 2004 estimate of subscription fee/article, but I'm confident that the real cost (if I could get up-to-the-minute figures for all inputs) would be in the same ballpark.</p>

<p>Sure puts one-time, up-front Gold OA fees in a different perspective, doesn't it?  Here's a reminder (stupid Impact Factors in brackets just because I know a lot of people still think they mean something even though <a href="http://bjoern.brembs.net/news499.html.11">they don't</a>):<br />
<div style="margin-left:20px;"><span style="font-family: Courier New;"><br />
average revenue</span><strong><sup>1</sup></strong><span style="font-family: Courier New;"> per toll-access article .............. $2100 - $2900<br />
<span style="font-family: Courier New;"><br />
<a href="http://www.biomedcentral.com/info/authors/apcfaq/#howmuch"><strong>BioMed Central</strong></a><br />
Genome Biology (6.6) ..................................... $2250<br />
BMC Biology (5.1) ........................................ $1950<br />
Molecular Cancer (3.7) ................................... $1710<br />
Retrovirology (4.0) ...................................... $1390<br />
J. of Cardiovascular Magnetic Resonance (1.9) ............ $1195<br />
<span style="font-family: Courier New;"><br />
<a href="http://www.hindawi.com/apc.html"><strong>Hindawi</strong></a><br />
Comparative and Functional Genomics (1.6) ................ $850<br />
J. of Biomedicine and Biotechnology (1.9) ................ $975<br />
Mediators of Inflammation (1.2) .......................... $975<br />
Bioinorganic Chemistry and Applications (1.0) ............ $700<br />
<span style="font-family: Courier New;"><br />
<a href="http://www.plos.org/journals/pubfees.html"><strong>Public Library of Science</strong></a><br />
PLos Biology (13.5), PLoS Medicine (12.6) ................ $2850<br />
PLoS Pathogens (9.3), Neglected Tropical Diseases (n/a), <br />
Genetics (8.7) and Comp Biol (6.2) ....................... $2200<br />
PLoS ONE (n/a) ........................................... $1300<br />
<span style="font-family: Courier New;"><br />
<strong>Other</strong><br />
J. Medical Internet Research (3.6, <a href="http://gunther-eysenbach.blogspot.com/2009/06/open-access-journal-jmir-rises-to-top.html">best in field</a>) ........ $1590<br />
Biological Procedures Online (1.2) ....................... $1250<br />
J. of Clinical Investigation (16.9) ..................... ~$2500<br />
</span></div><br />
<br /><br />
<strong><sup>1</sup></strong> Update: since D0r0th34 has already pointed out one dumb thing I did, neglecting other revenue streams available to TA but not OA publishers, I think that rather than continually update this post I'll just go ahead and embed the FriendFeed discussion right here:<br />
<br /><br /><br />
<center><iframe src="http://friendfeed.com/billhooker/4159fc93/oa-vs-ta-costs-i-think-have-finally-got-this?embed=1" style="border: 1px solid rgb(170, 170, 170);" width="500" frameborder="0" height="400"></iframe></center><br />
<br /></p>]]></description>
         <link>http://www.sennoma.net/main/archives/2009/06/oa_vs_ta_costs_i_think_i_have.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/06/oa_vs_ta_costs_i_think_i_have.php</guid>
         <category>open access/open science</category>
         <pubDate>Sun, 21 Jun 2009 01:13:32 -0800</pubDate>
      </item>
            <item>
         <title>OA and strategy</title>
         <description><![CDATA[<p>Stuart Sheiber recently gave a <a href="http://oacaltech.blogspot.com/2009/04/dr-stuart-shieber-director-of-harvards.html">talk at Caltech</a>, which prompted the following blogospheric exchange with Stevan Harnad (which I recommend highly if you are interested in Green vs Gold OA and the intricacies of OA mandate politics): </p>

<blockquote><a href="http://openaccess.eprints.org/index.php?/archives/561-Harvards-Stuart-Shieber-on-Open-Access-at-CalTech-and-Berkeley.html">Harnad</a> --> <a href="http://blogs.law.harvard.edu/pamphlet/2009/06/11/the-argument-for-gold-oa-support/">Sheiber</a> --> <a href="http://openaccess.eprints.org/index.php?/archives/590-The-Argument-Against-Premature-Gold-OA-Support.html">Harnad</a></blockquote>

<p>followed by <a href="http://openaccess.eprints.org/index.php?/archives/591-On-Proportion-and-Strategy-OA,-non-OA,-Gold-OA,-Paid-OA.html">this related post</a> on "proportion and strategy" from Prof Harnad, the main points of which he also left as a comment on a couple of my posts:</p>

<blockquote>#1: The vast majority of current (peer-reviewed) journal articles are not OA (Open Access) (neither Green OA nor Gold OA ).<br />
#2: The vast majority of journals are not Gold OA.<br />
#3: The vast majority of journals are Green OA.<br />
#4: The vast majority of citations are to the top minority of articles (the Pareto/Seglen 90/10 rule).<br />
#5: The vast majority of journals (or journal articles) are not among the top minority of journals (or journal articles).<br />
#6: The vast majority of the top journals are not Gold OA.<br />
#7: The vast majority of the top journals are Green OA.<br />
#8: The vast majority of article authors would comply willingly with a Green OA mandate from their institutions and/or funders.<br />
#9: The vast majority of institutions and funders do not yet mandate Green OA.<br />
#10: The vast majority of Gold OA journals are not paid-publication journals.<br />
#11: The vast majority of the top Gold OA journals are paid-publication journals.<br />
#12: The vast majority of institutions do not have the funds to subscribe to all the journals their users need.<br />

<p>CONCLUSION I: The fact that the vast majority of Gold OA journals are not paid-publication journals is not relevant if we are concerned about providing OA to the articles in the top journals.</p>

<p>CONCLUSION II: Green OA, mandated by institutions and funders, is the vastly underutilized means of providing OA.</p>

<p>CONCLUSION III: It is vastly more productive (of OA) for universities and funders to mandate Green OA than to fund Gold OA.</blockquote></p>

<p>I think there is a considerable strategic error embedded in those premises and the conclusions which follow, the basis of which is the emphasis on "the top minority of journals (or journal articles)". The 90/10 rule is not relevant: the goal of OA is 100% OA, not 10% -- not even "the top" 10% in which is concentrated 90% of whatever your metrics are measuring.</p>

<p>Much of the potential of OA lies in the provision of a comprehensive corpus of information on which to build the <a href="http://www.sennoma.net/main/archives/2009/05/the_semantic_web_a_long_and_so.php">semantic web</a>.  Comprehensivity matters, because just as re-use beyond the scope of the original author's imagination is a primary impetus for information sharing between humans, it is folly to imagine that we can determine ahead of time what will matter to machines -- that is, which articles will be crucial to finding new and unexpected connections in text- and data-mining initiatives.  The more complete the corpus, the more likely we can refine from it insights that are currently unpredictable.</p>

<p>Also, in an odd bit of circularity, 100% OA is vital to the development of <a href="http://openaccess.eprints.org/index.php?/archives/552-The-Need-to-Cross-Validate-and-Initialize-Multiple-Metrics-Jointly-Against-Peer-Ratings.html">rich, fine-grained, multiply cross-validated metrics</a> that will likely be more reliable than <a href="http://bjoern.brembs.net/news499.html.11">existing metrics</a> in guiding management decisions and researcher information searches.  If we focus on "the top" journals and articles, we hamstring our best strategy for improving the methods with which we identify quality in the first place.  </p>

<p>It's also worth addressing claim #11 separately.  For the direct argument against the assertion that most of the "top" Gold OA journals charge fees, see <a href="http://www.earlham.edu/~peters/fos/2008/06/more-on-calgary-oa-author-fund.html">Peter Suber</a>:</p>

<blockquote>If this is a claim about quality, or about future submission patterns, as opposed to present submission patterns, then it's an assumption for which there is no evidence.&nbsp; Nobody has done the studies. [...] In the absence of studies, <a href="http://www.earlham.edu/%7Epeters/fos/newsletter/10-02-06.htm#quality">this is all we know</a>:       <blockquote>[T]here are strong and weak OA journals, just as there are strong and weak <acronym title="toll access">TA</acronym> journals. Hence, any analysis focusing on weak OA journals and strong <acronym title="toll access">TA</acronym> journals (as if to show the superiority of <acronym title="toll access">TA</acronym> journals) would be as arbitrary as one focusing on weak <acronym title="toll access">TA</acronym> journals and strong OA journals (as if to show the superiority of OA journals). Without some additional argument showing that the journals on which they focus are typical of their breeds, they would be guilty of cherry-picking and generalizing from an unrepresentative sample. </blockquote></blockquote>

<p>There is, however, a neglected and (in my opinion) important counter-argument: even if that assertion is true, it is surely equally or more the case that the vast majority of toll-access journals charge author-side fees <em>in addition to</em> subscription charges.  A <a href="http://www.alpsp.org/ngen_public/article.asp?id=200&did=47&aid=270&st=&oaid=-1">2005 Kaufman-Wills study</a> found that 75% of TA journals in their sample charged author-side fees.  There is at least as much reason to suppose that the top-ranked TA journals are to be found among the fee-charging cohort as there is to suppose the same of OA journals.</p>

<p>The NIH <a href="http://www.sennoma.net/main/archives/2009/06/authorside_fee_comparison_oa_v.php#comments">estimates</a> that it pays author-side fees to the tune of $100 million per year, and funds the publication of some 80,000 scholarly articles.  Assuming, in order to be conservative, <a href="http://www.earlham.edu/~peters/fos/2008/04/what-is-oa-percentage-of-new-articles.html">5% Gold OA</a> at fees that are triple the average TA fee, that averages out to $1136/article, but what's sauce for the TA goose is sauce for the OA gander: if the Kaufman-Wills figures are broadly representative then those TA journals that charge additional author-side fees are charging, on average, $1515 per article.  That's more than PLoS ONE, more than most BMC journals and more than any Hindawi journal.</p>

<p>It follows that, since we are not -- that is, I argue that we should not be -- "concerned about providing OA to the articles in the top journals", the fact that most Gold OA journals do not charge fees is in fact relevant to all strategies for increasing OA to the research literature.</p>

<p>I think I disagree with the second conclusion also -- in <a href="http://www.earlham.edu/~peters/fos/2008/04/what-is-oa-percentage-of-new-articles.html">the most comprehensive study so far</a>, about 8% of articles published in 2006 were available via Gold OA, whereas a further 11% was available as a self-archived copy.  I agree, of course, that both are vastly underutilized relative to the goal of 100% OA, but it doesn't seem to me that Green suffers more neglect than Gold.</p>

<p>Given the flaws in some premises and the first two conclusions, I don't believe that conclusion 3 stands up either.  I find Stuart Sheiber's <a href="http://blogs.law.harvard.edu/pamphlet/2009/06/11/the-argument-for-gold-oa-support/">argument</a> for the Harvard model compelling:</p>

<blockquote>In summary, a university that commits to the open access compact<sup><strong>1</strong></sup> will more easily be able to answer objections against green OA policies specifically because it has an approach to long-range support for gold OA publishing, not in spite of it. The two models are inextricably tied. I, like Professor Harnad, am interested in facilitating the adoption of green OA policies. I proposed the open access compact in large part because I expect that adoption of the compact will lead to more green OA policies. The open access compact is therefore contributory to the promotion of green OA, not a sidetrack to it. I of course encourage universities to adopt green OA policies before gold OA support, but given that dystopian fears of faculty are preventing adoption of such policies, an open access compact that might assuage these worries should not be delayed.</blockquote>

<p><sup><strong>1</strong></sup> The compact simply states that ""The university commits to underwrite reasonable article processing fees for open-access journals for which funds are not otherwise available".</p>

<p>Given all of the above, the optimal strategy seems to me to be the one adopted by Harvard: a Green OA mandate and careful (fiscally responsible) support for Gold OA.  <br />
<br /></p>]]></description>
         <link>http://www.sennoma.net/main/archives/2009/06/oa_and_strategy.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/06/oa_and_strategy.php</guid>
         <category>open access/open science</category>
         <pubDate>Fri, 19 Jun 2009 21:27:07 -0800</pubDate>
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         <title>Update and correction re: cost to libraries and author-side fees</title>
         <description><![CDATA[<p>In comments <a href="http://www.sennoma.net/main/archives/2009/06/authorside_fee_comparison_oa_v.php#comments">below</a>, Peter Suber points out that the NIH has amended its estimates to $100 million/yr spent on author-side charges and 80,000 manuscripts funded -- which brings the estimated average author-side fee to $1250, well in line with the individual journal estimates I made and the published figures I found.  This is an important number because it is derived from a very large sample of the scholarly literature and casts a very different light on OA author-side fees than the one that TA publishers are wont to shine on their competitors.  Compare, for instance, PLoS ONE at $1300, or the standard BMC charge of $1470 -- for a couple hundred dollars more than the average cost of a TA publication, you can make your work free for all users to access, immediately and permanently.  (<strike>It would be interesting to know what proportion of the $100 million is going to OA fees, though I doubt it would be large enough to make a significant dent in the average TA charge.</strike> Edit: according to <a href="http://www.earlham.edu/~peters/fos/2008/04/what-is-oa-percentage-of-new-articles.html">Bj&ouml;rk <em>et al.</em></a>, less than 5% of all articles are available via no-embargo Gold OA; taking this into account, and assuming that the average Gold OA fee is triple the average TA fee, gives an average of $1136/article.)</p>

<p>But!  However!  There is a flaw in my reasoning!</p>

<p>The problem is not with the estimate of author-side charges, but in my use of that estimate to <a href="http://www.sennoma.net/main/archives/2009/06/cost_to_libraries_oa_vs_ta.php">update Philip Davis' library costs study</a>.  The <em>point</em> of that study was to look at what libraries would pay in an all-OA model, which is why I used the fractional cost matrix<sup><strong>1</strong></sup> and graph in the first place.  See the problem?  Libraries don't pay the toll-access author-side charges, the NIH does!  This makes the model a little artificial, perhaps, since *someone* has to pay those charges regardless of which journal levies them; nonetheless, the idea was to estimate practical library costs, so the TA author-side fees should not be included.</p>

<p>Here's what the updated situation looks like with the subscription/article estimate NOT adjusted for TA author-side fees (see <a href="http://www.sennoma.net/main/archives/2009/06/cost_to_libraries_oa_vs_ta.php">my earlier post</a> for details of the calculations):</p>

<center><img alt="Davisupdatecorrected.png" src="http://www.sennoma.net/main/archives/graphics/Davisupdatecorrected.png" width="570" height="365" /></center>

<p>The fractional cost has to drop to 0.4 before there are <em>no</em> libraries predicted to pay more in the OA model -- as I pointed out in the original post, there are numerous realistic combinations that will result in a fractional cost of 0.4 or lower:</p>

<center><img alt="matrix2.png" src="http://www.sennoma.net/main/archives/graphics/matrix2.png" width="537" height="418" /></center>

<p>The new figures also show that the fractional cost has to drop below 0.2 before all 113 libraries are predicted to save money in an OA model.  That still seems to me to fall within a realistic range, given that <a href="http://www.sennoma.net/main/archives/2009/06/thats_the_way_you_do_it.php">70% of journals in the DOAJ</a> don't charge author-side fees and 45% of researchers in a <a href="http://www.earlham.edu/~peters/fos/2009/04/new-oa-report-from-rcuk.html">recent RCUK study</a> had their OA fees covered by their research funders, for a fractional cost of 0.135.</p>

<p>Nonetheless, it's worth taking a quick look at the libraries which are predicted to pay about the same in the OA and TA models.  At a fractional cost of 0.4, they are: UC Davis, LA and San Diego, Univ Colorado, Cornell, Harvard, Johns Hopkins, McGill, Univ Massachusetts, Univ Maryland, MIT, Univ Toronto, Univ Washington and Univ Wisconsin.  At a fractional cost of 0.3, only UC Davis, UCLA, Harvard, McGill, Maryland and Washington remain in the "pay about the same" category.</p>

<p>It's easy enough to guess what these universities have in common, and a simple analysis confirms it:</p>

<center><img alt="rank.png" src="http://www.sennoma.net/main/archives/graphics/rank.png" width="600" height="359" /></center>

<p>Shading the top six yellow and the next 8 blue for visibility and ranking the libraries according to FTE, serials expenditure and "estimated scholarly articles published" reveals that the 14 "pay-same" libraries have only a slight tendency to be among the larger schools, but cluster very strongly at the high end of the "scholarly articles published" ranking.  In other words, research-intensive schools that publish a lot may put more pressure on their libraries in the OA world (to the extent that libraries are likely to be asked to repurpose serials costs for OA charges).</p>

<p>Among other things, it was in order to examine this particular concern in detail that Davis carried out his original study, and for the same reason I have here updated it with more recent estimates and assumptions.  The newer numbers show that a realistic worst-case scenario is that the libraries in question (14 out of 113 total) don't <em>save</em> any money in the OA model. </p>

<p></p>

<p>-------------<br />
<sup><strong>1</strong></sup> I neglected to mention in earlier posts that I got the %fee x %funded matrix idea (of which the fractional cost graph is an obvious extension) <a href="http://www.earlham.edu/~peters/fos/newsletter/06-02-06.htm">from Peter Suber</a>.  My apologies to Peter; I'm usually more careful about crediting sources.<br />
<br /></p>]]></description>
         <link>http://www.sennoma.net/main/archives/2009/06/update_and_correction_re_cost.php</link>
         <guid>http://www.sennoma.net/main/archives/2009/06/update_and_correction_re_cost.php</guid>
         <category>open access/open science</category>
         <pubDate>Fri, 19 Jun 2009 17:30:50 -0800</pubDate>
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