Everyone needs a hobby.

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.

In which Gavin Baker finds one of my pet peeves

stfu_noob.jpgIt 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 matter — a good deal less than the substance of whatever you’re quoting.
I realise that netonyms have been passé among the hipsterati for some time now, and my impression is that it’s a good thing, due mainly to being more comfortable online than crusty old luddites like me. Nonetheless, that you haven’t been online long enough to have a nick that half your friends use instead of your “real” name is no reason the rest of us should subscribe to your particular view of how the internets should work. You can quote me on that — you can even use my “real” name if you want.
Damn kids, get off my lawn, mutter grumble mutter mutter…

Term dilution; or, that phrase, you keep using it…

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 code stored in the DNA molecule has no precedent in naturalism, since all codes are the product of a mind. Open science would allow possible supernatural causation as a topic for further research. The scientist would not be restricted to naturalism as the only explanatory option. But alas! Professional scientists do not practice open science. They practice “closed science.”

has most emphatically nothing whatsoever to do with Open Science in the sense in which I — and my friends, colleagues and allies in the nascent movement, see e.g. blogroll to right — use the term.


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.

Good question.

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 text mining is allowed for the PMC OAI subset, but that they would highly prefer to use the PMC OAI or PMC FTP routes. This is the least they have to do.

No matter what, I still have the feeling that any technical obstacles are disallowed by the CC-license. Any legal expert here, that can explain me if the CC license allows controlling how people have access to my material?

In other words, can they do that? Like Egon, I await legal advice… how ’bout it, Creative Commons?

Removal of permission barriers is already part of the definition of OA

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 approaching the optimum.
The end goal is to support and encourage text mining and analysis of the full-text (preferably semantically rich XML), metadata and citations to allow literature-based exploration and discovery in support of the scientific research process.

Most importantly: hear, hear!
I do, however, have a nitpick to make. Heather makes no comment on Glenn’s idea that this is an addition to the definition of OA, but in fact I think it’s already built in to the accepted BBB definition. Peter Suber refers to the removal of price and permission barriers, to distinguish Open from “merely” free access, which removes only price barriers; I’ve quoted him on this before, so here he is again:

The best-known part of the BBB definition is that OA content must be free of charge for all users with an internet connection. However, the BBB definition doesn’t stop at free online access. It adds an extra dimension that isn’t as easy to describe, and consequently is often dropped or obscured. This extra dimension gives users permission for all legitimate scholarly uses. It removes what I’ve called permission barriers, as opposed to price barriers. The Budapest statement puts the extra dimension this way:

By “open access” to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.

The Bethesda and Berlin statements put it this way: For a work to be OA, the copyright holder must consent in advance to let users “copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorship”.

All three tributaries of the mainstream BBB definition agree that OA removes both price and permission barriers. Free online access isn’t enough. “Fair use” (“fair dealing” in the UK) isn’t enough.

Having said all that, though, I’ll add that an explicit description of machine readability requirements would be an addition to the accepted definition of OA — and one that I would welcome. Peter Murray-Rust recently noted that, according to the “price and permission barriers” view of Open Access, PubMed isn’t OA — even PubMed Central isn’t OA.
I’ll go even further: can anyone point me to a single Open Access repository? I don’t know of even one such site that removes both price and permission barriers. Surely there must be some, but the Big Names (PubMed Central, arXiv, Cogprints, CiteSeer, RePEc, etc — see ROAR) don’t seem to qualify, because digital objects in these repositories carry their own copyrights, rather than being covered by a blanket license provided by the repository.
Can this be true? Five years after the BBB definition came together, more than ten years since Stevan Harnad’s subversive proposal and on the first day of the NIH mandate — widely referred to as an OA mandate! — can it be that we really don’t have a single truly OA repository in all the world? And if it is true, would it help to make the official definition more explicitly machine-friendly?

Rob’s right; or, you say “deserter” like it’s a bad thing.

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.