Yes! and no.

John Wilbanks is brilliant - let's just get that down first.  He makes some great points in his most recent posts (1,2), but I also disagree with a few of the things he has said.

In my abstract for the upcoming 4S conference, I echoed what Borgman and Bohlin both said, and one of his main points: the purpose of journals was, in Wilbanks' words, "registration, certification, dissemination, preservation." In today's world, dissemination is better done by other means besides journals, and maybe the other things are, too.

But, he says the hyperlink is more powerful than the citation because look what Google has done with them. See, I don't know about that. I think when publishers add in citations using CrossRef, Scopus, or Web of Science, that's a lot more meaningful than an aggregate of hyperlinks from disparate web sources. Page rank does take into account the authority of the source of the hyperlink, but in displaying these links in from web sources, there's no indication of that.  Clearly, locating an article in a web of citations from and to other journal articles would be more meaningful than just incoming web links - at least in the current system. I definitely think ResearchBlogging in-links are important and valuable, but whether they or any other web links could replace a citation network is dubious because of the authority (or even - eek - POWER - in the Bonaicich SNA sense).

I absolutely agree that it's incredibly easy to just make incremental changes in the existing system, while missing the forest for the trees. Cell's article of the future is really incremental and not revolutionary.  I get stuck in this, too. How can we make what's there better instead of asking the question if we should throw out and start fresh from requirements (current & future). On the other hand, I like the idea of videos of interviews of the author. That's the best part of the science podcasts I listen to - when the authors say why their work is cool and what they actually accomplished.

Wilbanks makes it seem that the journal article should be replaced with one massive jumble of all possible information and communication that's part of a science project. Mix together the protocol, the data, the data processing algorithms, the report of work completed and its context in previous work and importance to future work. Oh, and make this wiki-like and editable so if something needs to be corrected, it can be.

To be fair, later he says to click out to these things. That's where I am.  I think there is some value to taking a snapshot of the findings, placed in context of previous work, and with implications for future work, and preserving this - as is - indefinitely. This static thing should aggregate comments to it, and should link to the data and protocols and algorithms- as they were at the time of writing - and then as a moving target incorporating follow on work.  Maybe this isn't a journal article, but something new, but I do think there is some value for capturing and providing meta-information at a certain point (goodness knows I save a bunch of versions of all of the documents I work on).

I definitely agree that insightful and thoughtful work that forwards the cause of some area of science should be rewarded, regardless of venue. Right now, only peer reviewed journal articles are rewarded in many areas of academic science. It's not clear to me how contributions on the web can best be identified and used in this cause.

I think publishing means creating a static snapshot and sharing means an ongoing connection to work in progress. I don't think he makes that distinction. I do think that there's a need for both of these, and that they are different, and that they should be linked.

It's really up to the community to decide. No one came from above and dictated the current system - it evolved over time in response to certain problems and needs. At some point, parts of it stopped evolving and these might need a little revolution.