Opening Minds about Closed Source

One of the most exciting experiences in blogging is when a post catches fire - metaphorically, of course. Often it happens when you least expect it, as is the case with my rant about Science Commons working with Microsoft, which was thrown off in a fit of pique, without any hope that anybody would pay much attention to it.

Fortunately, it *was* picked up by Bill Hooker, who somehow managed to agree and disagree with me in a long and thoughtful post. That formed a bridge for the idea into the scientific community, where Peter Murray-Rust begged to differ with its thesis.

Given all this healthy scepticism, I was delighted to find that Peter Sefton is not only on my side, but has strengthened my general point by fleshing it out with some details:

Looking at the example here and reading Pablo’s Blog I share Glyn Moody’s concern. They show a chunk of custom XML which gets embedded in a word document. This custom XML is an insidious trick in my opinion as it makes documents non-interoperable. As soon as you use custom XML via Word 2007 you are guaranteeing that information will be lost when you share documents with OpenOffice.org users and potentially users of earlier versions of Word.

He also makes some practical suggestions about how the open world can work with Microsoft:

In conclusion I offer this: I would consider getting our team working with Microsoft (actually I’m actively courting them as they are doing some good work in the eResearch space) but it would be on the basis that:

* The product (eg a document) of the code must be interoperable with open software. In our case this means Word must produce stuff that can be used in and round tripped with OpenOffice.org and with earlier versions, and Mac versions of Microsoft’s products. (This is not as simple as it could be when we have to deal with stuff like Sun refusing to implement import and preservation for data stored in Word fields as used by applications like EndNote.)

The NLM add-in is an odd one here, as on one level it does qualify in that it spits out XML, but the intent is to create Word-only authoring so that rules it out – not that we have been asked to work on that project other than to comment, I am merely using it as an example.

* The code must be open source and as portable as possible. Of course if it is interface code it will only work with Microsoft’s toll-access software but at least others can read the code and re-implement elsewhere. If it’s not interface code then it must be written in a portable language and/or framework.

Great stuff.

Update: Peter has written more on the subject.

Peer-Reviewed Open Journal of Science Online

One of the most eloquent proponents of the idea of open science is Cameron Neylon. Here's an interesting post about bringing peer review to online material:

many of the seminal works for the Open Science community are not peer reviewed papers. Bill Hooker’s three parter [1, 2, 3] at Three Quarks Daily comes to mind, as does Jean-Claude’s presentation on Nature Precedings on Open Notebook Science, Michael Nielsen’s essay The Future of Science, and Shirley Wu’s Envisioning the scientific community as One Big Lab (along with many others). It seems to me that these ought to have the status of peer reviewed papers which raises the question. We are a community of peers, we can referee, we can adopt some sort of standard of signficance and decide to apply that selectively to specific works online. So why can’t we make them peer reviewed?

Open Source Self-Governance

A little while back I wrote about the idea of using wikis for open government. Peter Suber - about whom Bill Hooker commented recently "not a sparrow falls in the OA world but PS knows about it!" - emailed me with some interesting news about an earlier project of his called Nomic:

Nomic is a game I invented in 1982. It's a game in which changing the rules is a move. The Initial Set of rules does little more than regulate the rule-changing process. While most of its initial rules are procedural in this sense, it does have one substantive rule (on how to earn points toward winning); but this rule is deliberately boring so that players will quickly amend it to please themselves. The Initial Set of rules, some commentary by me, and some reflections by Douglas Hofstadter, were published in Hofstadter's "Metamagical Themas" column in Scientific American in June of 1982. It was quickly translated into many European and Asian languages. Games were regularly played, and kicked off, the ARPANET, the Defense Department network which sired the Internet. Nomic has been used to stimulate artistic creativity, simulate the circulation of money, structure group therapy sessions, train managers, and to teach public speaking, legal reasoning, and legislative drafting. Nomic games have sent ambassadors to other Nomic games, formed federations, and played Meta-Nomic. Nomic games have experienced revolution, oppressive coups, and the restoration of popular sovereignty. Above all, Nomic has been fun for thousands of players around the world. For me, it was intended to illustrate and embody the thesis of my book, The Paradox of Self-Amendment, that a legal "rule of change" such as a constitutional amendment clause may apply to itself and authorize its own amendment. (Nomic is the third appendix of the book.)

The connection with open governance is clear. Peter passed on the news that people are trying to apply a Nomic-based approach to open source:

Just last week, by chance, a total stranger proposed a Nomic-variant as a serious system of "Open-Source Self-Governance" (his words).

Here's what that site has to say about the project, which is called Efficasync:

Efficasync is a method of open-source self-governance, where all the members of a group have the ability to examine, discuss and modify their group’s set of operational goals, reasonings, constraints, procedures and arrangements. In computer lingo, each member of such a group has both ‘read’ and ‘write(2)’ permissions to this set of governing statements. As demonstrated by the previous two lines, this document occasionally recasts a few traditional views of governance into a computer programmer’s frame of reference. The programmer’s paradigm holds a new, and potentially valuable, perspective for democratic governance. This document’s purpose is to describe a specific way, based on this new perspective, that a directly-democratic group’s governing infrastructure could be arranged. In doing this, the three main components which constitute Efficasync are explained: a Nomic, a particular graphical interface, and a starting set of ‘rules.’ This document was written with the intention of presenting a prototype for emulation and extension by groups wishing to operate as open-source selfgoverning entities.

Fascinating stuff.

More Parallel Universes

Some while back I wrote a piece called "Parallel Universes" looking at the surprising similarities between the world of open source and open access. So I was interested to see that there's trouble 't mill over the use and misuse of the term "open access":

I don't know and I don't care what [Nature editor] Maxine means by "open" or "free". I care what the BBB [Budapest-Bethesda-Berlin] 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.

Which is all rather similar to a discussion taking place in the computer world about who has the right to call themselves "open source".

This is GOOD SCIENCE!

"Open notebook science" is a great term devised by Jean-Claude Bradley - great, because it makes explicit exactly where you can find, read and hack the source code that underlies open science. One of the best observers of that world, Bill Hooker, has an interesting comment on a fellow researcher's adoption of the open notebook approach:

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?

Now, where have I heard this sort of thing before?

This is GOOD CODE!

Yeah, yeah, it's ugly, but I cannot find how to do this correctly, and this seems to work...Most of this was trial and error...Urghh

The programming comments of a very young Linus Torvalds as he hacked version 0.01 of a little program called Linux during the summer of 2001. Coincidence? I don't think so....

You'd Be Nuts Not To...

Bill Hooker points out that there is an important petition to establish a self-archiving open access mandate for Brazilian research circulating - and that anyone may sign it. So why not join in (Bill's post has a translation)?

Blooming Science Blogs

It is rather ironic that science, which is a paradigmatic example of openness in action, should be a relative laggard when it comes to getting formally behind open science. So it's good to see a couple of new blogs on the subject, as noted by Bill Hooker.

Better blooming late than never.