Awesome! - AJ Batac

You've got to love Improv Everywhere, they always have creative and fresh ideas for public performances. - cmiper

Fantastic ... that made me laugh. Improv Everywhere roolz. - M. Donaldson

That was very cool... I am sure people were going nuts... - Robert

Yeah Pedro, I would like to see the post-publication review on PLoS ONE, i.e. the comments on the papers, to be emphasized more. That's a killer feature that is under utilized. Similarly, I often link up PLoS ONE articles on my blog and never once have my trackbacks worked... strange, given that PLoS ONE is one of the only journals I know that allows commenting and trackbacks on articles, but the trackbacks don't work. - Kambiz Kamrani

There was also the little interesting remark (from an unidentifiable source) stating that BMC is already profitable and for sale. It will be interesting to see if this is really true, who ends up buying BMC and what will happen to BMC in the future regarding their publishing policies. - Pedro Beltrao

PLoS ONE serves a valuable function; it publishes "sound science". Not amazing or ground-breaking, but solid and worthy of attention. The kind of work that the majority of us do, I imagine. Disclaimer: my boss is an academic editor and I'm a reviewer. I don't think "not ground-breaking" equates to "lower review standards". Didn't Bora mention on his blog that 50% of submissions are rejected? - Neil Saunders

I really don't get the negative spin on the good financial results. NPG is also diversifying a lot with a growing list of Nature branded journals that include for example Nature Protocols (an experimental lower tier version of Nature Methods?) along with many other journals that do not carry the Nature name (http://www.nature.com/siteinde...). - Pedro Beltrao

PLoS ONE++ - j1m

I've just read the comment thread to the Nature news story. There is outrage about the "slurs" the commenters feel are cast upon PLOS but no factual responses to the facts presented in the article. I'd be more impressed if one of the commenters pointed to a factual problem with the article, rather than the usual "internet outrage" reaction because something is published that the commenter happens to disagree with but can't be bothered to support rationally. - Maxine

By the way, my disclaimer (comment above): I am an editor at Nature, the journal. - Maxine

A journalist writes: grass is green, sun is yellow, sky is blue. Declan writes: grass is green and that is BAD, sun is yellow and that is REALLY BAD, sky is blue and that is REALLY, REALLY BAD. He may have gotten all the facts right but he painted them in puking green in a way that suggests that good is bad, up is down and we are now in war with Eastasia. - Bora Zivkovic

Maxine, Paul Peters commented on the original, making a point that many have made (NPG has its own stable of "second-tier" journals). That's a fact, but you chose to obscure it in your response to Paul by focusing on the "Nature Whatever" group, which makes up about 1/3 of the ~60 journals published by NPG. It's not even (see Bora, above) a criticism of either publisher -- where did this idea come from that publishing solid science was bad? - Bill Hooker

Further, Butler seriously misrepresents the PLoS ONE review process, skirting the edge of disinformation in an attempt to paint it as somehow less rigorous than other journals. PO reviewers do not "only check for serious methodological flaws" as Butler claims. This is a petty smear, carefully worded to keep lawyers at bay but clear in its intent. - Bill Hooker

Sorriest (and most blatantly wrong) attempt I've seen by a for-profit publisher to debase the open-access movement. Incidentally, I do think there are reasons to have a different pricing structure for open-access than PLoS, but the attack on the review process at other PLoS journals while touting the lesser Nature journals rings hollow. Incidentally, it was a slanderous and misguided enough attempt to get me to join the commenting section of Nature and this website to talk about how bad it was. - Evans B

I've confused by your point about my reply to Paul Peters, Bill. I thought it was clear enough and it contained the URL (not a live link) to the numbers in question. I didn't "choose to obscure" anything, I am not that kind of person, I was correcting an error of fact that this commentator made. - Maxine

Bora, the news story didn't say green is green, etc, it had numbers in it. I haven't looked at the comments on the Nature site since this afternoon, but when I did, they were mostly of the "shock horror, Nature has run a news story about another publisher" variety. We often run news stories about scientific publishing/publishers. Do we need to write that we are one do you think? - Maxine

Sounds like it's all tits-up for toll access - Graham Steel

Yeah, no conflict of interest here. are Nature commentaries peer-reviewed research? - Timothy Driscoll via Alert Thingy

Maxine, thanks for the responses. Do the editors at Nature really miss the subtext of the following lines? "PLoS stays afloat with bulk publishing", "bulk, cheap publishing of lower quality papers", "PLoS One uses a system of 'light' peer-review to publish any article considered methodologically sound." The subtext is clear, that things are different in a bad way from how things are at Nature ... so where's that graph of Nature's financials? - Evans B

As a followup, are we really to believe that Nature recently added all the new NPG titles for any other reason than to capitalize on the very thing you condemn PLoS for doing? - Evans B

Yeah, sorry Maxine, didn't mean to say it quite like that. Mea culpa, I apologize. - Bill Hooker

My point, more carefully phrased, is that Paul's comment (though he made an error which I think effectively obscured the larger point) is just an example of a point that many have made: NPG has, indeed most publishers have, their Glamour Mags and their workhorses. Declan makes it sound somehow heinous to do this, but it's a standard business model. - Bill Hooker

What I'd like to see is a PLOS ONE with 0$ cost to the authors, where the light review puts it at a different level (counts for tenure points) from Nature Proceedings, but it still is free - community based - open access. The PLOS ONE reviewers don't get paid anyway right? So the only cost would be only for computing infrastructure, and a few people for organizing/moderating peer-review (infrastructure can be covered from donations, people can donate time). Imagine if this thing picked up like Wikipedia... - Ntino

factual points for maxine: a) the live link you (maxine) gave us only shows the impact factors of the "nature xxx" journals, not those of the >40 other lower impact factor journals that npg publishes. the PLOS accounts are public, and nature is entitled to publish the results of its sleuthing, but for the analysis to be convincing or useful, a comparison with the publishing models of other groups (or at least that of NPG) is essential. b) how exactly is evaluating a paper for methodological soundness "light" review ? and how does adding on a subjective assessment of potential impact somehow makes the review "heavy" (or "rigorous") ? more on all this in the original nature thread ... - mad -

Since not everyone has access to nature, I'll re-post my comment here: Why do we, with today's technology, still have about 20,000 different 19th century journals around? Nature Neuroscience editor Noah Gray points it out: "Nature Neuroscience aims to send 30-35% of papers out to review, so getting past that stage is the biggest hurdle." http://network.nature.com/foru... Why does this step come *before* peer-review? Shouldn't this come afterwards? Why is this considered "non-light"? : - Björn Brembs

Let scientists decide what is good science in their field and then have ex-scientists which usually are smart, knowledgeable, experienced and eloquent decide what is "hip" right now? Let's exaggerate our current system slightly: "non-light" peer-review is mainly a review by ex-professional scientists (either voluntary or involuntary ex-) for popularity. Publication in such journals usually decided who gets grants, tenure, a life. So basically, we have a system going in which ex-members (either members who left or didn't cut it) decide which members get promoted and which get fired. How many corpporate managers do you think would want to implement that in their company? Conflict of interest statement: I have published in Science and PLoS One; I volunteer as academic editor for PLoS One. - Björn Brembs

@Bjorn - Right now the different tiers of journals work reasonably well at sorting out the potential interest of an article. It is far from perfect but I don't feel I a missing important articles by not reading lower tier journals outside my field of research. Still I am interested in knowing the latest news on the very important discoveries in science. I agree that in principle this "sorting" could be done after peer-review and publishing but we don't have the tools to do this .. yet. - Pedro Beltrao

maxine wrote earlier: I'd be more impressed if one of the commenters pointed to a factual problem with the article, rather than the usual "internet outrage" reaction. ok.. now there are numerous pointed criticisms of the article, on the internet, much of which can be recapitulated by paraphrasing this thread. so now.. i'd be more impresssed if maxine/declan/one of the people at NPG actually responded to the most substantial of these comments in a factual manner, rather than merely cherry-picking the weakest links/arguments in rapidly posted comments and choosing to counter them. - mad -

In summary: should Nature journals write about the publishing business? I think the problem is that Nature see themselves as representing science; science publishing is a hot topic, articles about it in Nature journals are fair enough. Other people, however, see Nature as an arm of NPG with the business interests and conflicts of interest which that implies. It's always going to be controversial for them to discuss other publishers. - Neil Saunders

Timo Hannay at NPG has written a post at Nascent, one of the NPG blogs, about this news story on PLOS. It is being discussed by this FF group. - Maxine

Timo's article is even nastier than Butler's, if that is humanely possible. Where and when will Declan defend himself? All the damage control so far has been done by Maxine, Timo, Euan, Bob, etc. When will Nature give Declan a green light to defend his own words, his motivations, and his "information"? - Bora Zivkovic

Pedro has an excellent response to Timo's insinuation that PLoS is doing some kind of damage to OA: http://pbeltrao.blogspot.com/2... - Bill Hooker

Thanks. I just saw it and added it to the ever-growing linkfest. I had to go offline as we had another bad storm here so I wanted to unplug my computer. - Bora Zivkovic

Yeah, pretty naive stuff. - Neil Saunders

I'd like to see someone try to sell 'correlation is enough' to the FDA or equivalent - Cameron Neylon

Cameron: lol In journalistic terms the essay is good, but it's science where being only trend sensitive is not enough. And Anderson has not much clue on what's going on in biology, but he is probably right on what's going on in physics, which we don't really know. - Attila Csordas

Am reading the paper version of Wired at this very moment! The cover uses the headline "The End of Science." Now that caught my attention as I pulled it out of the mailbox! But yes, underwhelming. I don't think scientists are going to stop asking "why?" anytime soon, the way the article makes it sound. - Shirley Wu

like I said last time this came through - it's a tad grandiose. Did he just learn about data mining recently? - Mr. Gunn

Ah - plane travel tomorrow which is usually when I buy a copy- mind you probably be last months on this side of the pond anyway :) - Cameron Neylon

A good response: http://bactra.org/weblog/581.h... - Bill Hooker

I agree, Bill. Makes one think of the many propositions to replace wet lab experiments with in silico substitutions. You need both. - Heather

Chris still is onto something. In industry you can create value from correlations and "hunches" based on data. Even medical trials are just data and correlations. And in oder to save lives you don't really need to know why, just what. Science is a method, never forget that. Not a religion. And its limits are there, as well as its advantages. Other methods might be more efficient at doing something else, not? - dekay

Actually, that used to be the case. The focus these days is on the why, on the mechanisms. It's why VIOXX happens, cause you don't understand the why. Yes, you need statistical separation, you always have, even when you had limited data. More data only improves your statistics. - Deepak

For example, docking studies are increasingly trying to add more "physical" measures rather than rule based implicit, this is what the data tells us measures. Science is much too noisy, and the kinds of false positives you would get with Google are NOT acceptable. Is the scientific methods dogma. Can it change, yes, but not for the reasons that Chris is talking about - Deepak

Even Valleywag has an opinion on this, they are scientists too, and have a lab at the back: http://valleywag.com/5019748/w... "The problem here is that if we stop asking the question "why?" then we are basically making for the foundations of faith. You can always make statistics say nearly anything you want, it simply depends on the assumptions you make when you analyze and present them" - Attila Csordas

When Valleywag is right, it's a sad day - Deepak

Attila - no, Anderson is definitely not right about physics, either. It's a strange article. Data mining isn't replacing the old scientific method. It's augmenting it. - Michael Nielsen

Agree with Michael. The writer seems to think that somewhere in a big pile of data lies "everything", waiting to be extracted using algorithms. That's just not how science works. It's the questions that we ask and the interpretations that we devise that make it science, not the raw information. - Neil Saunders

I created a slide at my previous job, which had all the data sources (expression, proteomics, genotyping, histopath, name it) that exist related to a study on the edges, with the emphasis on there being a ton of heterogenous data, and in the middle a big "?". The point. It's all about the question, NOT the technology or data type - Deepak

Chris' piece is provacative ... but the Ars Tecnica piece touches on some key points - was /.-ed a bit ago, so my apologies if this is old news: http://arstechnica.com/news.ar... - Kaitlin Thaney

Kaitlin, that is a great article. Hopefully it will help the masses understand why Anderson is wrong. It also leads to a worry I have had about Google. They don't really understand science at a fundamental level. Maybe I am wrong, but I get that impression all too often. - Deepak

Although I admit I don't quite get the cloud part. It almost seems incidental - Deepak

I will be in Toronto Jul18-19 for 3Dsig - Adam Kraut

Not me - I'm going to every other conference between now and January (or so it seems anyway) - Cameron Neylon

Will be there for BOSC only and to see folks in Toronto but won't be at ISMB - Jason Stajich

ISMB only. Also still to book flights/accomodation. And create a web app for the poster... - Neil Saunders

I love the fact that the democrats allude that THEY are the ones who will respect the constitution. Neither major party has in the past, nor will they start any time soon. - Dave Roth

I'd be voting Republican (if I were a US citizen). - Robin Cannon via twhirl

I'm voting Republican, because, like, liberalz sukk! *pouts, folds arms and stamps foot* - Jason Menayan

I notice the postings kicking into simplistic bipolar mental models. If Republican stood for dog food and Democrat stood for cat food, which one would you be eating for breakfast tomorrow morning? - Kit Krash

this is the kind of patronizing democrat malaise that plagues the valley. - Kingsley Joseph via twhirl

yea but if your gung ho on either camp, I know a psychological strategy that will be having you eat either dog food or cat food by tomorrow morning. It's based on the principles of Aristotelian logic, consistency and memetic trojan horses. - Kit Krash