Nonsense, and pernicious nonsense at that.

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.

Restore your faith in humanity.

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.

OK, but I still don’t want to see “Open Access” become the new “Low Fat”.

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 which our hero takes his customary couple steps backwards…

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 journalsNature 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…

“Open Access” is not a marketing phrase and you are not free to use it as you see fit.

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.

testing FeedSweep widget

[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.

testing Feed Digest widget

[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.

testing feedfeeds widget

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.

Giving Open Notebook Science a Try

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?)

testing grazr feedwidget

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.)