Andrew Hessel in MungBeing Magazine, quoted (approvingly, to my astonishment) by Jonathan Eisen:

Twenty five years ago, kids flocked to computers, pushing the limits of what they could do. Similarly, the next generation of genetic engineers won't need laboratories or even PhD: they'll have laptops, cheap mail order DNA synthesis, and, thanks to Google and Wikipedia and open journals like PLOS Biology, access to mountains of free biological data. They'll work in basements, garages, and cafes, and they'll trade ideas and collaborate on genetic designs the same way open source programmers now write computer code. Keep in mind that it was only 30 years ago that a little company called Apple started out of a California garage.

Which reminds me of Freeman Dyson in the NYRB a while back:

Every orchid or rose or lizard or snake is the work of a dedicated and skilled breeder. There are thousands of people, amateurs and professionals, who devote their lives to this business. Now imagine what will happen when the tools of genetic engineering become accessible to these people. There will be do-it-yourself kits for gardeners who will use genetic engineering to breed new varieties of roses and orchids. Also kits for lovers of pigeons and parrots and lizards and snakes to breed new varieties of pets. Breeders of dogs and cats will have their kits too.

Most of that is, in my opinion, complete and utter bollocks.

Despite the attractive and often useful analogy, genomes are not really software, and bio-tinkering is nothing like coding. It takes a lot more time and equipment, for one thing. There's a reason you don't see many people building jet airplanes for fun. When is "cheap DNA synthesis" going to be available to the general public? Who is going to sell J. Random Teenager a PCR machine? Don't wave your hands and airily declaim that everything is possible and it's someone else's job to make it work (as Dyson did while he was flogging his book in the NYRB): describe for me the business model. Sure, in theory you can do those experiments in your kitchen -- but have you ever actually tried it? Take it from someone who does them for a living, you don't have the patience to make it work. No one does. It's one thing to hack away at a piece of code until it runs the way you want; it's quite another to "hack" something in which every change requires several weeks' worth of complex and time-consuming manipulations, to say nothing of a generation or ten.

And then there's regulatory oversight. We let people hack away at computers as much as they can stand, but a computer is not a living thing. It's not cruelty if you get mad at your linux box and pound it into flinders. Those pigeons and lizards and parrots and cats are not toys; they can suffer, and if you let Joe Public futz with their genomes they will -- horribly. (I happen to think a good percentage of pet breeders are scum, too. What kind of despicable arrogance is required to manipulate a living genome for nothing more than your own twisted aesthetic pleasure? You people with the dogs and cats whose faces are so squished they can barely breathe -- you're sick.)

Further to the question of oversight, let's think about consequences. You've seen computer viruses: think about a world in which Kevin Mitnick meets Dylan Klebold at a smallpox swap-meet. How do you like your brave new world of garage biology now? And that's just the potential for malicious success -- the dangers of stupidity and failure loom considerably greater. Get your syntax wrong or wire your motherboard the wrong way around and, well, nothing much happens. Fuck up a genome, though, and see how you like the result -- especially if it survives.

The Hessel/Dyson version of our biotech future is not going come into being. Not in a decade, not in a millennium, not ever. Quite apart from its being about as likely in practical terms as me learning to fly by flapping my arms, we -- as a society -- will not let it happen. Not if we have any bloody sense at all.

The Blogathon is today -- it's been running about six hours, with another 18 to go (on the A schedule; the B schedule starts in about 9 hours).

It's just amazing. Hundreds of people from all around the world take 24 hours out of their routine to make the world a little bit better, a little bit brighter -- because they can. It's an instant community of people who give a damn.

I can't do it justice -- go see for yourself. I'm posting highlights to the front page (though every blog is a highlight, and I wish I had time to feature them all!), and there's a surfing frame that makes it easy to make your way through all the blogs.

Do yourself a favor and have a look around -- maybe sponsor a couple of bloggers. Trust me, you'll like it.

Peter Suber commented on the last entry to clarify his position on the varying uses of the term "Open Access":

For me, OA in the strict sense removes both price barriers and permission barriers; all the major public definitions say so; and I'm only too glad to repeat this whenever it comes up. However, as a matter of word usage, the term now covers more territory than this and I've stopped fighting that fact. That is, the term is often used for content that is merely free-to-read.

Peter goes into more detail in a recent entry on his blog:

...many projects which remove price barriers alone, and not permission barriers, now call themselves OA. I often call them OA myself. This is only to say that the common use of the term has moved beyond than the strict definitions. But this is not always regrettable. For most users, removing price barriers alone solves the largest part of the problem with non-OA content, and projects that do so are significant successes worth celebrating. By going beyond [I would say "outside" -- BH] the BBB definition, the common use of the term has marked out a spectrum of free online content, ranging from that which removes no permission barriers (beyond those already removed by fair use) to that which removes all the permission barriers that might interfere with scholarship. This is useful, for we often want to refer to that whole category, not just to the upper end. When the context requires precision we can, and should, distinguish OA content from content which is merely free of charge. But we don't always need this extra precision.

In other words: Yes, most of us are now using the term "OA" in at least two ways, one strict and one loose, and yes, this can be confusing. But first, this is the case with most technical terms (compare "evolution" and "momentum"). Second, when it's confusing, there are ways to speak more precisely. Third, it would be at least as confusing to speak with this extra level of precision --distinguishing different ways of removing permission barriers from content that was already free of charge-- in every context. [...]

and in the Sept 2004 edition of the SPARC OA Newsletter:

One danger is the dilution of our term. That's why [this newsletter discusses] the BBB definition and its place in our history. But another danger is the false sharpening of our term. If we thought that the BBB definition settled matters that it doesn't settle, then we could prematurely close avenues of useful exploration, needlessly shrink the big tent of OA, and divisively instigate quarreling about who is providing "true OA" and who isn't.

The BBB definition functions as a usefully firm definition of "open access" even if it leaves room for variation. We should agree that OA removes some permission barriers (e.g. on copying, redistribution, and printing) even if it leaves different OA providers free to adopt different policies on others (e.g. on derivative works and commercial re-use). My personal preference, for example, is to permit derivative works and commercial re-use. But (as I wrote in FOSN for 1/30/02) I want to make this preference genial, or compatible with the opposite preference, so that we can recruit and retain authors on both sides of this question.

I've omitted a lot of good information to save space here; anyone interested in this issue should read all of the linked discussions. In particular, the SPARC newsletter goes into useful specifics about the OA-related activities of a number of publishers.

Peters Suber and Murray-Rust have both pointed out that one way to be specific about "levels" of openness is to be explicit about licensing -- PMR:

If the community wishes to continue to use "open access" to describe documents which do not comply with BOAI then I suggest the use of suffixes/qualifiers to clarify. For example:

• "open access (CC-BY)" - explicitly carries CC-BY license
• "open access (BOAI)" - author/site wishes to assert BOAI-nature of document(s) without specific license
• "open access (FUZZY)" - fuzzy licence (or more commonly absence of licence) for document or site without any guarantee of anything other than human visibility at current time. Note that "Green" open access falls into this category. It might even be that we replace the word FUZZY by GREEN, though the first is more descriptive.

I take Peter S to be saying that it's inevitable that "Open Access" will come to mean, in general use, more things to more people than strict BOAI, and we will not achieve anything by making arseholes of ourselves over it. (Even if that's not quite the way Peter S would put it, that's the way I've come to look at the situation.) There's no point in picking quarrels we don't have to have. It's enough to be more careful in our own usage, for which purposes suffixes a la Peter MR should prove very useful when we need extra precision. I don't think we need invent terms ("fuzzy") just yet -- "OA (specific licence, with hyperlink if writing online)" and "OA (free to read)" should cover most cases.

If we can get to the point where the average consumer -- basically, any researcher -- responds to an OA claim or label by asking "which licence?", we will have done an end-run around the problem of term dilution.

In the entry below, I was not sufficiently careful to avoid Nature-bashing, or the implication that Maxine Clarke was morphing, werewolf-like, into some kind of publisher pitbull. Thanks to Pedro, bdf and RPM for responses which made this clear.

Peter Suber provides a handy roundup of Nature's OA and free-to-read offerings:

[the Current Science partnership] won't be Nature's first OA journal.  Nature and EMBO publish Molecular Systems Biology, a full OA journal, along with a couple of hybrid OA journals.  Nature publishes another hybrid with the British Pharmacological Society.  It publishes a regular series of OA supplements to its flagship TA journal, and in January of this year began offering OA to the backfiles of its academic and society journals. 

In addition, Nature has a raft of non-journal OA projects, including a self-archiving policy, a data sharing policy, a neuroscience gateway, a signaling gateway, a networking site, mixed journalism and research sites on climate change and stem cells, blogs, podcasts, job listings, a news aggregator, and a preprint exchange. 

[Updated after talking to Timo Hannay to include] The Cell Migration Gateway, Dissect Medicine, The Functional Glycomics Gateway, GI Motility Online and The Pathway Interaction Database

It's worth noting that Peter uses the term OA for services and projects which I would describe as free-to-read (or free-to-use), but not OA. I would welcome clarification from Peter here, as I do not feel I am in a position to argue OA definitions with someone who helped draft its founding declarations! [update: see comments]

Even on my more restrictive reading, Nature does have a couple of full-OA journals and a handful of hybrids -- not "one barely-OA journal". Further, whether or not one considers them OA the free-to-read/use projects and services include some important and useful innovations. (The list above doesn't even include Connotea, a science-centric social bookmark manager which I use myself.) Nature is head and shoulders above any of its toll-access competitors in terms of web savvy and willingness to experiment, and I think it's important to recognize this whenever one (quite rightly!) criticizes them for not (yet) being Open Access.

What bothers me about calling Nature's free-to-read/use publications and doohickeys "OA" is the Low Fat/Greenwashing Problem, which Peter Murray-Rust describes thus:

Publishers blaze around "free" "choice", etc. which confuse rather than inform. For a publisher "open" and "free" are to be used like "low fat" "energy food" "healthy" as a way of legitimising current practice.

Everyone is familiar with companies which label their products "environmentally sound" or "healthy choice" when in fact they are paying only underhanded lip service to those concepts. It seems to me entirely possible that unscrupulous publishers may try the same tricks with "open access", and that the best defense is to insist on the BBB definitions. A number of commenters have wondered (can't find a link right now) whether we need another term for Open Access sensu stricto -- something like "BBB-OA", perhaps. (If you say that "be-three-oh-ay" it's not so bad.)

Let me finish, though, by pointing out that I do not wish to paint NPG as one of the unscrupulous publishers whose intentions worry me, nor Maxine Clarke as their sneaky shill. If NPG uses the term "open access" differently from me, I take that as a good-faith disagreement, and if Maxine uses the term in her employers' sense that is hardly "marketing". Specifically, I apologize for the phrase "if [Maxine] is going to start abusing [the term "OA"] as marketing for Nature", which contains an uncalled-for implication that I hope this entry will dispel.

You can get to like the taste of crow... you just have to eat enough of it...

Peter Murray-Rust recently pointed to Paul Wicks' (Nature Networks) blog article, "Is Publisher-Lead "open access" a swindle?", which refers to PMR's recent blog series on publisher licensing and permissions barriers in hybrid OA models. In comments on Paul's entry, Jennifer Rohn pointed out

The two dedicated open-access publishers (BioMed Central and Public Library of Science) don't have these problems. People who want to ensure their articles are truly going to be open access, published by companies who have put real thought into the publishing as well as business model, might want to look there.

PMR quoted that comment, to which Maxine Clarke replied (in a comment on PMR's entry) with what looks for all the world like classic publisher anti-OA FUD:

Hello, I declare conflict of interest as I am an editor at Nature, not in itself open access but our publisher has many open access projects and products.
In response to Jennifer's point: I agree that BMC has got an OA publishing/business model and indeed business, but the PLOS model is dependent on a large grant from a charitable foundation, so the jury is still out (in my opinion). As an editor I am concerned about the archiving and the preservation of the scientific record, for example.

I note the commendable upfront COI declaration and state for the record that I do not think Maxine was consciously engaging in FUD. It is nonetheless standard operating procedure for OA opponents to link PLoS to "charity" and cast vague aspersions on the ability of OA publishers to maintain the scientific record. PLoS was intended as a flagship-cum-icebreaker for OA; breaking even financially was always a secondary objective. Nay-sayers about the viability of OA in business are invited to explain the success of (at least) BioMed Central, Hindawi and Medknow. Persons who wish to claim that OA puts the record at risk are invited to explain how a proprietary archive in the hands of a for-profit publisher is safer than PubMed Central or the wide network of repositories linked by OAI-PMH. (Again, I don't think Maxine was making such anti-OA claims, but it bears pointing out that what she did say contains clear echoes of standard FUD.)

Peter MR's response to Maxine's comment was this entry, in which Peter sets out to find the "many open access projects and products" and gets no further than did Jonathan Eisen, who praised the establishment of Molecular and Systems Biology (NPG's only OA journal) only to find that in fact the MSB license is the same as CC-BY-NC-ND, which is far too restrictive to call itself OA. As Chris Surridge (of PLoS) puts it in comments on Jonathan's entry,

'Free Advertising' isn't 'Open Access' in my book.

Maxine had this to say:

Nature Precedings, several database publications, Nature Reports publications (3), Nature Network, Scintilla, online daily news service, gateways, blogs, many individual articles and collections of articles are freely available ("projects and products" as I mentioned in my comment to your earlier post. MSB is to my knowledge NPG's only formal open access journal.)

Peter responded with another post, giving the necessary background and pointing out that, excepting MSB,

...the rest of [Maxine's] list completely muddies the "open access" debate. If Nature believe that "open access" applies to any freely visible information on their site, most not peer-reviewed, many without licences and many with the publisher's copyright, then they are making my life much harder.

This is clear and unexceptionable in the context of Peter's ongoing quest for clarity in publisher OA-related policies. That context, or at least its existence and importance to the entry in question, was made clear by the entry itself, and I take ordinary netiquette to involve being familiar with an ongoing conversation before taking part. Nonetheless, Maxine again:

frankly I was not responding to anything you have written in the past few weeks, I was responding to your request to give examples of NPG's "open access" or "free" material.

This is weak at best. Peter asked for "pointers to [Nature's] open access products and the licences which they carry"; see also netiquette, ongoing conversations and. Claims of a limited response made in ignorance of context are either disingenuous or, if made in good faith, still no excuse.

Maxine continues:

It is your perogative to define terms however you like, but not your perogative to enforce other people to use the same definitions - I know what I mean by "open" or "free" content and I don't need to be told off by you for having a different definition to whatever your definition is

I don't know and I don't care what Maxine means by "open" or "free". I care what the BBB Declarations mean. Peter is not defining terms however he likes; he is working with published, widely accepted definitions. He is well within his rights to expect that other people will indeed use the same definitions: that is, after all, the point of having developed and published them. Nature does NOT have "many open access projects and products", it has one (barely) OA journal and the excellent Precedings, together with a number of commendable free-to-read initiatives (blogs, Nature Network, the various free-to-read web special collections, etc). "Open Access" is not a fuzzy buzzword that Maxine is free to define as she sees fit, and if she is going to start abusing it as marketing for Nature then she most certainly does need telling off.

Peter has apologized for being "over-brusque", which is a handsome gesture but in my opinion no such apology was called for.

[deleted widget -- it was slowing the page load waaayyyy down, not all the time but at least once a day. screw that.]

Hey, this one doesn't suck. The customization is not great, but the stuff you can't get to is set up in a way that suits me anyway. Plus, it's free.

[deleted widget]

I can't get rid of the unsightly space in the items with no description, because the "tagged by" is part of the %DESCRIPTION% variable. I won't be paying for this one if the customization doesn't improve. (It'll show up to 20 items, but I've set it to 5 because it's so clunky.)

Not going to use a commercial service when there's a free alternative (see FeedSweep, above) that seems OK.

Why is this so hard? Argh. This one's not free but I'll happily pay for something that works.

[deleted widget, see update]

Hoo boy, that's ugly. But it seems to work, and the tabs at the top are sorta nice -- you can separate feeds by category. (Not sure Simpy plays nice with that -- it's supposed to, but...) Oh, and there's a minimum width otherwise you get side-scrolling, don't like that.

Update: fails to refresh/show new content. Wonder if it's something Simpy is doing? This one's too damn ugly to bother, but I might test the others with different feeds.

Openness is spreading, one researcher at a time: Jeremiah Faith, a Boston U graduate student in bioinformatics, has put his lab notes online:

Open Notebook Science [...] is a term coined by Jean-Claude Bradley. The idea is simply that the heart of every person's research - their lab notebook - should be open to the world.

Since most of our scientific work is funded by tax payers who expect their money to be well-spent, it's interesting that openness isn't required. Science typically builds on the body of available knowledge - the more knowledge available the faster science goes. It's striking when you visit other labs in person; you see all of their unpublished work, and you know that most of their results and data won't be available to the bulk of the scientific community until a year after each particular scientific project is finished. By the time papers are in print, it's old news to the insiders. More striking is when you visit labs whose work you've thought about replicating and expanding on. It's not too uncommon to find that only one person in the entire lab is able to get the technique to work, and even for him the technique only works on Wednesdays. This type of information would be useful to know before you embark on a useless three months trying to adapt their method. But scientific publications are covered in a thick coat of high-gloss finish, making these unacknowledged difficulties hard to detect.

Lab notebooks on the other hand are flat black. As long as people keep them regularly updated, they contain the good, the bad, and the completely nonsensical results.

Today I test the waters of Open Notebook Science.

The latest version of my lab notebook is now automatically posted on J's Lab Notebook Page each night. I've been using an electronic lab notebook for two years now, so there's quite a bit of data in there - good and bad (300+ pages).

This is simply fantastic. One of the things that Open Science advocates most sorely lack is concrete examples. Doing research in public, instead of in secret, is a new and somewhat unnerving idea for most scientists; early adopters like Jeremiah are essential to take the edge off that unfamiliarity.

(It's also, to be honest, just plain fun to snoop around in someone else's lab notes! I was amused to note that Jeremiah talks to and about himself in his notebook, the same way I do -- "if I weren't so stupid I'd...", "next time load the control first, doofus", etc. I wonder if everyone does that?)

What do people think? Should I add this widget as a sidebar? I like it a lot; the only thing missing is a way to set all the items open as default. Meh, slow to load and fails to update. Might have been something I did but I'm too busy to figure it out right now.

Update: trying again: deleted widget, couldn't make it work (update). Might have been me but if it's going to be that much work I'll just write my own damn parser. How hard can that be? (Yeah yeah, famous last words.)

The 2007 Blogathon is underway!

Stay up late, make a difference: that's the Blogathon's slogan and raison d'être. It's a charity drive that started when, on a whim, founder Cat Connor¹ stayed up all night blogging. The next year, she decided to do some good with the idea by inviting others and drumming up some sponsors -- hence "blogathon", by analogy with "walkathon", "telethon" and so on.

That was 2001, and about a hundred bloggers raised more than $20,000 for 77 different charities. Those numbers roughly doubled in 2002 and again in 2003 (500 bloggers, $100K). Project Blog took over in 2004 while the 'thon was on hiatus, and long-time blogathon ally Sheana Director stepped up and ran the 2005 event; Cat and Sheana have been running the 'thon together since then (with the help of an army of volunteers). The 2006 event saw about 300 bloggers raise about $100K, and if the data I've been collecting are anything to go by, the 'thon will be bigger than ever this year:

The mechanics are simple: bloggers sign up to blog for their chosen charity, and sponsors pledge either a lump sum or an amount per hour blogged. The goal is to blog for 24 hours straight, with one post every 30 minutes. The money part is an honor system: sponsors donate directly to the charity. There's a FAQ file and a forum where noobs can go for further answers and advice. The big day is Saturday, July 28; regular kick-off is 6:00 am Pacific, but if you're observing Sabbath or have other commitments, you can start at 9:00 pm Pacific.

Signups are now open for bloggers and sponsors -- so what are you waiting for?

¹My wife. I cannot tell you how proud I am.

My latest offering just went up at 3QuarksDaily; the title is Competition in science: too much of a good thing.

As always, I don't want to dilute the conversation I hope to spark, so comments are off here.

Go read this. Seriously, go now, you can thank me later. It's the blog of an MSF doctor in the field and it's everything you might expect, with the added benefit that James can really write.

Dr Shellie has run the job search gauntlet and -- O frabjous day! Callooh! Callay! --- has multiple appealing offers from which to choose.  Reflecting on the process, and her years of anxiety leading to this point, she says:

... I think that if your goal is to get a tenure-track job at a research university in a place you want to live, it's hard to know your chance of success much in advance. Many smart people with excellent records do not get jobs. Which is too bad, since it can take 5-10 years just to get ready to apply -- counting the time you spend in a PhD and a postdoc. And how are you supposed to predict your chances then -- when you are starting grad school?

How indeed? I don't think the situation for postdocs has improved since this article appeared in 2002. In biomed research, I would guesstimate that about 10% of postdocs end up with "their own lab". Worse, this is not simply tough competition -- so many personal/political factors enter into the success equation that you might as well roll dice as try to forecast your future as a researcher by any rational method. It's my blog, so I'll go ahead and quote myself:

The system is broken: there are too many PhD graduates and not enough real jobs for them. A postdoc is not a real job; even a tenure-track position, one step up the foodchain from a postdoc, is not a real job. A real job will not be yanked out from under you every few years, unless you or your boss can continually win funding -- and when you get down to 20% funding levels, between politics and the sheer volume of work dumped on the granting committees, you might as well pick the names out of a hat. A real job does not leave you entirely at the mercy of your superiors, who can demand insane work hours from you, knowing that if you won't sacrifice your life on the altar of their lab/department/whatever, there are ten other PhDs clamoring for the chance to do so. I'm no fan of the dismal science, but the law of supply and demand does seem to be consistent with observed phenomena here.

Now, that gloomy beginning notwithstanding, this is not another postdoc complaint post. (That one is in the works; I'm saving up links for it here and here.) Right now I want to take a much more positive perspective, inspired by Dr Shellie, who asks:

How should I think about recruiting graduate students, when I am encouraging them to pursue an uncertain career path?

This is a very good question indeed, and the best thing about it is that a newly-minted research professor is asking it! Is it really ethical (anyone? anyone? BuellerFree-Ride?) to encourage students into grad school, given that the standard "career path" is long, tortuous and more than likely to land the weary traveler somewhere other than that fabled destination, the faculty slot?

Another way of looking at this is to ask: is the system so irreparably broken that we should dismantle it -- starting by turning away grad students -- or can we work with what we have, and fix it?  I'm a meliorist rather than a revolutionary myself.  Further, if you want to be a PI yourself you're going to have to take on grad students, and more generally if we want research to flourish we, as a community, are going to need grad students. 

So, since we're going to continue to lure bright-eyed, unsuspecting college kids into the postdoc trap via grad school, what can we do to reduce harm?  Herewith some thoughts:

1. Inform, inform, inform.  Let 'em know upfront what they're getting themselves into. 

1b. Repeat, repeat, repeat.  They're young, they'll think "it won't happen to me".  We're all bulletproof at eighteen.

2. Present alternatives, and treat those alternatives with respect.  Don't be another type-A asshole in a labcoat who thinks, and acts as though, any deviation from the One True And Shining Path To Glory (why, research of course) represents complete failure as a scientist and as a human being.  Scientists reading this are nodding their heads, the rest of you are probably thinking huh? surely he exaggerates -- but I assure you I don't.  Throughout the community of science, at least in academia where I've spent most of my time, there is a powerful and pervasive assumption that research is the pinnacle of human endeavour and that a person would only do something else because they couldn't make the grade in research.   This is not a conscious belief, it's a largely unexamined background of feeling, something absorbed by intellectual and emotional osmosis from a peer group of self-involved, highly-focused people who have, given their material situation, a deep investment in believing they are doing something that sets them apart and above.  It is also, of course, utter and unmitigated horseshit.  Don't perpetuate it.

3. Give a damn.  Your students are not fungible data-production units, they're people with lives outside the lab, hopes, dreams, and all that crap.  You don't have to get all touchy-feely if that's not your style -- just understand that some of your students will find that they don't want your job after all -- and that's OK.  Some will even start out with other destinations in mind -- and that's a good thing.  Wouldn't you like to see more people with solid research experience go into teaching, journalism, policy development, marketing, law, medicine and a dozen other vital professions?  Wouldn't you like to see an ecologist become US President right about now?  Don't take it as a personal affront if someone doesn't make emulating you their sole ambition; take the time to consider what might be best for them.

I'm sure there's more -- comments, please!  For one thing, I am clinging still to the last forlorn threads of hope that I might be taking on students myself one day, and those putative students will need all the help I can get.

Finally, to Dr Shellie, an answer of sorts: if you're asking yourself at this early stage whether it's ethical even to take on students, then you are probably just the sort of PI who should be taking on students, and who will provide them with solid lab experience with which they can do whatever they want -- even research.

Once more unto the breach, dear friends, once more: the dreaded Free Is Not Open argument rears its ugly head again. I've made my position (indeed free != Open, and the distinction matters) clear elsewhere, and was gratified recently to find PMR agreeing; now it seems that the Open Medicine editorial team takes the same position:

The Canadian Medical Association Journal (CMAJ) has just published:

•  Stanbrook et al. Congratulations to our colleagues at Open Medicine [commentary]. CMAJ July 3, 2007; 177.

Here is our response:

Although the endorsement by CMAJ's editors of open access medical publishing is welcome, we would like to take this opportunity to clarify several points raised in their commentary.1 First, there is an important distinction between open versus free-access publication. Open Medicine has not only adopted the principle of free access, that is, making content fully available online, but endorses the definition of open access publication drafted by the Bethesda Meeting on Open Access Publishing. This definition stipulates that the copyright holder grants to all users a free, irrevocable, worldwide, perpetual right of access to, and a license to copy, use, distribute, transmit and display the work publicly and to make and distribute works derived from the original work, in any digital medium for any responsible purpose, subject to proper attribution of authorship. Given that CMAJ holds copyright and charges reprint and permission fees, it is not in fact an open access journal.

In comparison, Open Medicine does not assume the copyright of our authors' work. We believe that it is only fair and just that authors retain the ownership of their work; as such, Open Medicine does not charge reprint or permission fees, and our work is available for reproduction for educational and teaching purposes without copyright limitations or charges.  We use a Creative Commons Copyright License that also ensures derivative works are available through an open access forum. It is through this creative and unlimited use of published material, with due attribution, that we believe scientific discourse can flourish. This truly open access forum also has a contribution to make to a journal's integrity, independence, and freedom.   [...]

Chris Surridge of PLoS also agrees, and supplies an excellent analogy:

Free Access to scientific research is great, and all publishers who make their content free to read should be praised for doing so. But this is not Open Access. It is like giving a child a Lego car and telling them that they can look at it, perhaps touch it, but certainly not take it apart and make an aeroplane from it. The full potential of the work cannot be realised.

Where the OM team refer to Bethesda, Chris links to Berlin and goes on to enumerate

...the four unmistakable marks by which you may know, wheresoever you go, the warranted genuine Open Access publication:

1. Content is made freely and immediately accessible to all.
This basically means that you can get it on the internet without paying anything in addition to what it costs you to access the internet.

2. Authors retain the rights of attribution.
So the work is the authors [' property]. The author doesn't sign over the copyright to the publisher or anyone else. Rather the author allows the publisher to publish the work under licence. A licence which also ensures that:

3. Content can be distributed and reused without restriction.
So I or anyone else can take Open Access content and use it, in whole or in part, for any purpose including purposes that have not yet been dreamt of as long as I don't infringe the Authors rights of attribution.

4. Papers are deposited in a public online archive such as PubMed Central.
This ensures, as best as anyone can, that the above three conditions continue to apply to the Open Access content in perpetuity.

It's been my contention that in the absence of explicit, conspicous and machine-readable Open licensing, condition 3 is violated because in this litigious age, the conscientious and the risk-averse will not download and derive without explicit permission. I got "explicit and conspicious" from Peter Suber:

The newer definitions [of OA] recognize one further element: an explicit and conspicuous label that an open-access work is open access. Readers should be told when a work is free of price and permission barriers. They might be reading a copy forwarded from a friend and not know whether the publisher would like to charge for access. They might want to forward a copy to a friend and not know whether this kind of redistribution is permitted. When an article has no label, then conscientious users will seek permission for any copying that exceeds fair use. But this kind of delay and detour, with non-use as the consequence of a non-answer, are just the kinds of obstacles that open access seeks to eliminate. A good label will save users time and grief, prevent conscientious users from erring on the side of non-use, and eliminate a frustration that might nudge conscientious users into becoming less conscientious.

and "machine-readable" from Peter Murray-Rust:

For me, if my robots cannot read the articles then as a human I have no interest at all in reading the "fulltext".

Peter MR is not saying that free access for humans is useless, but that to realize the full potential of text- and data-mining, OA materials need to be machine-readable, which includes letting the machines know what they are allowed to have.

I must confess that finding my thoughts echoed by such leading OA proponents makes me feel better about being, on this issue, at odds with Stevan Harnad. I simply cannot agree that Open "comes with" Free, and the distinction bothers me. It should be relatively easy to convert Free to Open -- simply add a Creative Commons or similar license -- but I think it would be better to do that proactively. If we gloss over the difference between Free and Open at this relatively early stage of OA, we risk creating a (potentially enormous) body of Free text that must be updated to include complete, useful permissions when at last we realize that Free Is Not Open. (The game's afoot: / Follow your robots, and upon this license / Cry "Free is not Open"!)