Today majority of people interested in protein evolution consider sequence space as overall empty space with just a large number of islands. Given combinatorial complexity, I agree on the empty space, but to me the space is organized into a small number of tree like structures, not separate islands. I suspect there will be discontinuities corresponding to differences between ancient peptides - something like different starting points. - Pawel Szczesny

I would not expect isolated islands since you need to be able to make the transitions. Even if they are rare we would see the transitions between the islands. I don't know the literature on this but maybe studying RNA sequence space and folding would probably give overall similar principles in what regards to this discussion of sequence space used. Given the lower complexity it would be easier (computationally). - Pedro Beltrao

not sure what similarity measure you're talking about - but, I really doubt that you'd find a mostly continuous space. If you're a creationist that's obvious, but if you're an evolutionist, it is quite obvious that the ancestral 'continuity' is long gone and not available to our sequencing machines... - General Kafka

OK, so the new discoveries will be where the transitions connect the islands, and in figuring out why some things are connected and some aren't(for evolutionary reasons), is that right? Doesn't this somewhat depend on what you start with as classifiers? - Mr. Gunn

Your result(s) of such an analysis depend(s) much on the way you want to do it. Do you intend to analyze the whole-length sequences or just domains? Or maybe just peptides? - Marcin

Mr. Gunn, Marcin - concerning the starting points (domains, peptides), this doesn't necessarily need to be decided up front, but rather can be a result of the clustering. I see the process as an analogy of BLAST, that for two sequences gives a number of HSPs. In the final space it should be possible to see what length is required to make a transition. If it's only few residues, two islands aren't really connected. Pedro, thanks for suggestion. - Pawel Szczesny

Good question. But what about quality of the report? - Maxine

I read this as "FriendFeed metric for reviewers" - which is an interesting but I now see, entirely off-topic idea. - Richard Akerman

Sure the quality of the reports is important and it is true that we internally rate the reports. But I am looking for something pragmatic and simple to give a sense of who has invested a lot of efforts in reviewing for a given journal. It is possible that a good reviewer reviewed only once (because of the exotic topic for ex.). But a bad reviewer will not be asked again and is selected out. So frequent and fast reviewers are usually good and work a lot for the journal, which is what I would like to reward. - Thomas Lemberger

(c) - I live in Waterloo, just outside Toronto. If some open-sciency people want to meet up, I'd be keen to meet. The Duke of York is a pretty good pub near the University of Toronto (http://york.thedukepubs.ca/). The Linux Caffe (http://linuxcaffe.ca/) is a slightly longer walk, but also good. - Michael Nielsen

I live in TO but I am not attending ISMB. - PauloNuin

I won't be there, but let's see what the back channel is like - Deepak

I'll be at ISMB only and will be in town July 16-24 - Neil Saunders

I'll be there for the conference and presenting a poster - Daniel Jurczak

would be interesting to know where everyone is staying so we can plan something (pub, restaurant, etc). The conference venue is really close to the entertainment district, but we can always arrange something close to UofT. - PauloNuin

I will be there for the main conference. Update - Actually I will be there from the 17th to the 23rd. - Pedro Beltrao

I will be at the 3Dsig satellite meeting on the 18th-19th but not the main event. - Adam Kraut

LinuxCaffe? How deliciously geeky and cool. Must go there. - Neil Saunders

yes, this is a much better article even if I don't agree with him. - Pedro Beltrao

The article is mostly just a statement of facts about what PLoS has achieved on the business side, versus what they set out to achieve. It looks to me like an exceptionally useful document to OA advocates - OA journals need sustainable business models, and Timo is dead right that the best way to achieve this is open discussion. - Michael Nielsen

Much better than the original. Still I think Timo misses the larger point -- see esp. comments by Bjoern Brembs -- it's time to do away entirely with the *whole concept* of "high-end" journals. Journal-level metrics (impact factor, rejection rates, perceived prestige) simply do not work as a way to rank and evaluate projects, ideas or scientists. Let peer review do what it can do -- weed out the obvious crap -- and let search and database software and the research community do the rest. - Bill Hooker

It also amuses me to see Nature folks with their lace hankies pressed to their horrified mouths over the "kneejerk backlash" and "internet outrage". The original piece was outrageous -- I think most of the responses have been quite calm and reasonable. I guess it all depends whose ox is being gored, no? - Bill Hooker

I'd like to see a publication discussing the economics of scientific publishing in detail. It's clear that there are ways to sustain open publishing. I'd like to get a better understanding of the cost structure, esp in a purely internet publishing environment. - Deepak

Deepak, I highly recommend Odlyzko's 1997 paper. It's dated, but full of insight: http://firstmonday.org/issues/... - Michael Nielsen

Michael, will check it out, thanks - Deepak

@Bill - agree, some of the Nature people don't seem to get internet debate. Sure, it happens rapidly, is occasionally hasty and not fully thought through, brash or even a little rude at times, but we're hardly descending to, say, YouTube comment level here. In general I see commentary by interested parties, rather than a mob waving torches. - Neil Saunders

Hey - I missed this discussion but just posted to Timos blog saying basically what Bill H said --- the original piece was outrageous - Jonathan Eisen

I also commented on the post (of course with my usual plug on getting rid of journals). But I also had another idea: with editors choosing after peer-review, each editor would get the chance to establish a track record: how many of the chosen papers really were high-end? Measuring editor performance objectively... - Björn Brembs

I'm not seeing any comments showing up on the Nascent piece... - Bill Hooker

Also, would Nature make a profit on its own, or is it being subsidized by the NPG "second tier" the way PLoS ONE looks set to start propping up PLoS Biol? We'll never know, of course, because NPG won't put their finances in the spotlight. - Bill Hooker

Still no comments on the post itself - I wonder when they'll show up? They must be scathing.... - Bora Zivkovic

I have posted some comments but nothing there yet. Kind of annoying to be honest but Timo might not check/approve comments on weekends. - Jonathan Eisen

Yes, I am assuming that everyone is away for the weekend and that the comments will show up on Monday - not everyone is 24/7 like we are. - Bora Zivkovic

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