Quite a difference two months makes (no, I didn't photoshop the colours!):

From my flash new company phone:

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.

I was reminded recently (when Graham Steel uploaded this photo) of something I've been meaning to write about for nearly two years.

For those who don't know him (which must surely exclude nearly everyone involved with Open Access!), Graham (blog, FF) 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.)

Graham's first foray into "guerrilla OA" (most emphatically not to be confused with these well-meaning idiots) was in September 2007, when he attended a conference and ran a one-man unofficial promotional campaign. Do read his own description, 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.

(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.)

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:

• t-shirts to start conversations
• a badge instead of a t-shirt ("free your research, ask me how") for those who prefer more formal attire
• "OA in a nutshell" cards the size and shape of regular business cards, for handing out in conversation and leaving on appropriate tables
• slides for your talk: start with Cameron's "Presentation Rights" and end with a "Basics of OA" slide
• 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

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 this graph on it, or a reprint of this if I ever get around to publishing it, might be a good idea.)

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 maybe 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.

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.

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

Walt Crawford has devoted an entire issue of Cites&Insights to library access to scholarship, 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.)

Cameron Neylon has been thinking about science and society again. Just do yourself a favour and read it, OK? Here's a quote to whet your appetite:

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.

(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 Björn.)

---

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.

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.

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.

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.

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.

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.

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.

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.

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.

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."

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.

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.

---

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.

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 this post from Deepak and the related post from PLoS ONE. Bora suggests 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.

So -- what they said, especially Neil.

In response to the persuasive argument 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 this editorial; comments, corrections and suggestions for where to send it are welcome.

In particular, I'd like input on the following: the draft letter is basically an abbreviated version of this post -- should I, instead, work the full post (including this revision of Phil Davis' Cornell study) up into a paper/essay/article and submit that somewhere?

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 this post?

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?

(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.)

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 this post? 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?

----draft letter-----

Dear Sir/Madam:

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.

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.

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:

For comparison, the same issue last two issues of Haematologica in which the aforementioned editorial appeared also included 33 original 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 €600 560 ($840 790) 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].

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.

Sincerely,

me.

Update 090717: corrected the calculation; you can grab the data here 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.

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 OAD 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.

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

[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)

[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^® at http://www.webcitation.org/5iFx4iGru)

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

[5] Björk 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)

[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^® at http://www.webcitation.org/5iFxJ0Mex)

[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^® at http://www.webcitation.org/5iFxptGx6)

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

[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^® at http://www.webcitation.org/5iFxdKLqV)

[10] American Phytopathological Society Reports of Publications 2000. URL:http://www.apsnet.org/members/gov/2000/Reports%20of%20Publications.htm. (Archived by WebCite^® at http://www.webcitation.org/5iFwcmIBL)

After seven years (for at least three of which I've been a fan), Jörg Colberg is asking for help covering the costs of his photography blog, Conscientious.

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 Jörg 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.

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 Conscientious.

Surely this:

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.

is a job for this guy:

... 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.

?


(CC-BY image of Carl Malamud from Joe Hall via Wikimedia)

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 Trypan blue, which is a very pretty blue color.

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 µl of 2X Trypan blue in buffered salt solution onto the lid and then mixing with 10 µl of cell suspension. Since the cell counter only takes 10 µl, that leaves half of each mixture drying in spots all over the lid as I count my way through my cultures.

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.