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    NATURE Takes On PLoS
    By Hank Campbell | July 2nd 2008 11:31 PM | 59 comments | Print | E-mail | Track Comments
    Let's be honest; Nature and AAAS, non-profit or not, have employees and those employees would like to remain so. That requires money and a lot of it. Non-profit has never meant 'free', it just means they can't give money to shareholders - it certainly does not mean charity.

    So it goes with PLoS. I am not the fan of all of PLoS One most here are (and that is not any kind of official position of this site - I am in the minority and not a researcher) because I think that it is difficult separating the wheat from the chaff.   Some PLoS publications do not really do that well. I have seen any number of editorials that are no more than political or ideological diatribes yet they get to call themselves 'peer reviewed' and I am not sure that doesn't impact the reputation of the quality material produced there.

    Declan Butler at Nature is critical as well. Now, automatically there will be knee-jerk speculation that a guy working at Nature has a hidden agenda - Nature is a business and has to protect its revenue.  We are in the top 20 science sites worldwide and have never so much as merited a mention from Nature. Is that because they have blogging and feature articles and we do also? Not likely, because Nature owns Postgenomic and they should practically be co-branded with Seed Media's Scienceblogs - Postgenomic appears on the front page of their site and I imagine all 70 Scienceblogs writers are in it and the young man who runs Postgenomic has never responded to a dozen requests by writers here to have their blogs listed (and that's not a knock on Scienceblogs - they have the craftiest, most aggresive marketing out there and more power to them for it) so if Nature were worried about a competitor they would not endorse Scienceblogs and thus its parent magazine, Seed.

    (Disclosure: we have a partnership with Imaginova, which owns Livescience, and their content appears on our site and our content appears on theirs)

    But Scienceblogs also has a paid writer that works for PLoS One and they have gotten free advertising from PLoS so they clearly have friends on both sides of this discussion.

    (Disclosure: Jonathan Eisen occasionally blogs here and is Academic Editor in Chief of PLoS Biology and brother to the PLoS co-founder, so we have friends on one side of the discussion)

    GrrlScientist is even on a panel at the London science blogging conference being hosted by ... Nature ... so her criticism of a Nature employee for criticizing PLoS can be confusing.

    Except it isn't confusing at all. It's a beautiful endorsement of science and blogging and independence.

    She is an independent thinking person with an opinion about an isolated matter. So is Declan Butler at Nature. He may not personally dislike the PLoS open access concept at all (I certainly love it, only I would want more than open access and instead endorse free publishing as well) but if he believes 'peer review lite' articles are getting published in PLoS One just so they can collect $1,250 he has every right to say so - he even has a duty to say so.

    And it's specifically PLoS One he has an issue with, not PLoS Biology or Medicine;
    Since it launched, PLoS One has published 2,526 articles — more than PLoS Biology has published in its five years of existence, and that growth shows no signs of abating. PLoS One has published 1,158 papers since the beginning of this year, which is almost as many as it published during the whole of 2007. Another factor is that it costs authors only $1,250 to publish in PLoS One.
    Can there be all that much quality with 200 articles per month being shoved out the door? It's not for me to say. We publish over 200 articles a month here and they're all good - but we do not call them peer reviewed.

    The great thing about our science community ( us, Scienceblogs, Livescience blogs,Nature blogs, Discover blogs, everyone out there too) is that, in matters like this, we can tweak each other a little as needed - and people will get wound up because they are passionate (I have no doubt my equal criticisms of all three groups in question could come back to haunt me) but at the end of the day we are all a community and we have integrity and no problem with speaking our opinions.

    Should Nature writers with integrity be a fan of all open access publications? Well, no, not if it is a free-for-all just to make money. Nor should we. Declan Butler taking what he knew what would be an un-popular stand, especially given his employer and the claims of bias it would engender, is to be applauded. Not saying anything would have been the easier, diplomatic road. And completely wrong.

    It shouldn't be inferred that Butler is some kind of paid shill attacking PLoS just because he works for a competitor any more than it could be said that GrrlScientist is a shill for PLoS because of marketing arrangements PLoS has with Scienceblogs.

    Should she have said Nature employs 'paid toadies' and then specifially mentioned Butler? No, but Scienceblogs is always going to be on the dramatic fringe of science discourse and I think that will be water under the bridge in a month or two. I'm not a zoologist so I have no idea if Butler is a toadie - plus, he has a blog of his own, so he can defend himself.

    At the Nature Science Blogging conference in London they will likely be the best of friends, regardless of their differing opinions on this one issue. If being able to fight it out on issues and get along smashingly as people is the future of science writing, I am all for it.

    Comments

    jeisen
    I do not object in any way to either people criticizing the PLoS One approach or people criticizing PLoS or open access in any way. And Butler is welcome to make such criticisms. What I object to is that Butler's story to me seems poorly worded, illogical, and somewhat inane. For example, one part that I find illogical is the attempt to make the success of PLoS One a negative for PLoS in general. I think it is fair to ask is PLoS One publishing good or bad articles and also to ask if PLoS's other journals are doing the same. But he provides no examples at all of bad articles in any of the journals. Another problem I have with the article is that it hints at some mysterious fixed business model for PLoS and (1) does not cite anything and (2) implies that PLoS should stick to a single fixed business model and if it does not this is proof that PLoS is doing poorly. I could go on and on. But again, what I did not like about the article is the lack of logical flow and poor arguments. I do not object to criticisms of open access or PLoS or PLoS One and think such commentaries are frequently useful and a good part of the discussion of scientific publishing. I note I have a direct role in PLoS journals and agree with you that there is nothing wrong with Nature writing about PLoS just as I frequently write about things in Nature. For more on my views on this see my blogger blog . I have not yet put a version or form of it over on my ScientificBlogging Blog < /a> yet ... Jonathan Eisen, UC Davis, Tree of Life Blog
    Jonathan Eisen, UC Davis, Tree of Life Blog NOTE - THIS IS A CROSS POSTING FROM MY "TREE OF LIFE" BLOG .
    adaptivecomplexity
    As you and Jonathan have pointed out, PLoS ONE is a different beast, and that's important to keep in mind. The other PLoS journals are excellent, with largely traditional peer-review systems (although they obviously operate on a different business model).

    PLoS One is an experiment, a new peer-review model. That experiment may succeed or fail, but it's status does not diminish the quality of the other PLoS journals - and other publishers shouldn't use PLoS One's different peer-review model to trash PLoS's alternative business model.

    I didn't realize that the Nature Publishing Group was considered non-profit. It's not making money for MacMillan?

    In any journal, I don't think 'peer-review' means much for opinion or commentary pieces - I'd bet many researchers agree with you that opinion pieces published in peer-review journals do not have some sort of extra stamp of approval.

    Reviews and research papers are where peer-review really counts.

    Mike

    Mike
    Hank
    Mike - As you and Jonathan have pointed out, PLoS ONE is a different beast, and that's important to keep in mind. The other PLoS journals are excellent, with largely traditional peer-review systems

    I assume I see a lot more of the schlock than you two do, since you mostly look at the Biology part.

    We have hundreds of members and 30,000 articles here - if we publish 'science' pieces advocating intelligent design or wormholes or perpetual motion, would you feel that any publication in even a remote section reflects badly on the entire site, or would you tell people to not let some low quality stuff detract from what the good scientists do?

    Jonathan - I could go on and on. But again, what I did not like about the article is the lack of logical flow and poor arguments.

    I was objecting primarily to the guy being called a 'toadie' for stating something unpopular - ironically, the person doing the name calling is also a paid writer for a large media company yet is saying another large media company is telling its writers what to publish as part of their corporate agenda - and would object to that apellation being attached to her motivations. I'll never understand that logic.

    adaptivecomplexity
    if we publish 'science' pieces advocating intelligent design or wormholes or perpetual motion, would you feel that any publication in even a remote section reflects badly on the entire site, or would you tell people to not let some low quality stuff detract from what the good scientists do?

    I think there are two answers to this: each journal should be judged independently, and you could say the same thing of science web sites - if you had a separate section, or sister web site specifically for pieces out on the fringe, an unmoderated free-for-all section, separate from the main, higher-quality science stuff, this argument is fine, but if they're all mixed together, that's another matter.

    Another point to consider is that when a new publication venture is just starting up, before they've established a reputation, they have to guard that reputation more carefully - later on they can take more risks and even make mistakes without too much of a negative effect.

    Mike

    Mike

    Mike
    Hank
    Fair enough. And I forgot to reply to ...

    I didn't realize that the Nature Publishing Group was considered non-profit. It's not making money for MacMillan?

    If they are actually making a profit I bet we will have a competitor in two years. I tweak PLoS a little in this, and Nature too, because as an outsider in this industry I think they are both making some pretty big mistakes.

    Interesting analysis of the linkage between different entities. I had no idea that I was linked to either Nature or PLoS.

    The truth is, I'm not. I am very much in support of PLoS as an enterprise, and Open Access as a model, but not because one of the 71 or so bloggers on Scienceblogs.com works for them. In fact, there are bloggers on sciencblogs.com that really don't like at all and hope to never have to have a thing to do with, while others I consider colleagues. With Corurnix (A Blog Around the Clock) who works for PLoS, the nature of our relationship is the opposite of what your analysis might suggest. He is a genuinely nice guy so it is hard to dislike him, but one of the things I like about him and the MAIN reason I read his blog is because of the PLoS connection and the Open Access discussion. In other words, your analysis, while interesting, has the causal arrow going backwards in this case.

    Hank
    Hi Greg,

    Well, lots of us read each other for lots of reasons, you have always been on my blogroll, for example, but in what I wrote there should either be causal arrows everywhere or, in a perfect world of translation between intent and word, none at all.

    I am defending Declan for taking a stance he knew was going to be a tough one against ad hominem attacks he then received about it. At the same time I wrote of grlscientist going after him in a positive light when I wrote her attack

    isn't confusing at all. It's a beautiful endorsement of science and blogging and independence.

    She is an independent thinking person with an opinion about an isolated matter.

    The tangled relationships between Nature, PLoS and Seed have to be mentioned precisely because it shows that there can't be a corporate agenda - though if Butler can be tainted with a corporate agenda simply because of his employer then so can you or grlscientist every time you have a pro- or con- opinion about virtually anything. Hardly fair.

    Either we extend the same ethical courtesy to everyone until proven otherwise or we have to accept that people are going to do the same to us because we are in the blogging community. I am certainly in the camp of assuming people are ethical first. By the nature of her diatribe against Butler, she is on the side of assuming he is an evil, for-sale writer yet she thinks we all should ignore the fact that she also gets paid by a media company with corporate offices and a profit motive.

    So I laid out the topology of the corporate relationships more so everyone could eliminate the agenda issue (and I disclosed that we have corporate friends, Nature not one of them so no reason for me to defend them, and people here who work for PLoS as well, so no reason to attack them) and stick to the subject and not so anyone could spend more than 3 seconds wondering about anyone's personal motivation.

    In other words, to you I accomplished exactly the opposite of what I intended. :)

    P.S. If she had read more than one article of Butler's she would know he has been a big fan of open access. Letting anything called 'open access' get a free pass does more harm to open access than good.

    No, I get your point and I totally appreciate it. My pointing out of the causal arrow was meant to confuse the point further, totally apropos.

    However, I'm guessing that there is a big difference between me wiring a blog post, you (or Grrl) writing a blog post, and Butler's piece. No editor looks at my stuff (or Grrl's). Well, they might look at it, but post hoc. There is no corporate, editorial or whatever decision being made, and in fact Sblings have been known to aggressively attack our keepers (as in the James Watson fiasco). I'm assuming it is the same for you ... that you all are independent bloggers, independent of each other and the cooperate overlords and any affiliations they may have.

    I honestly do not think this is the same as Butler, staff writer and columnist for Nature. In other words, I would be very surprised if the editors of Nature are shocked and amazed at his piece.

    Now, are they collaborating? Are the Nature Publishing Group people and Butler collaborating on this? Here is an unavoidable truth:

    It looks like they are collaborating. This is a hacked-up mashed-up attack. Not Butler's usual work. So, they either are collaborating or they are not, but either way, it looks like they are. This is why I've stated that I expect to see a clarification and even a bit of back pedaling. That might be as simple as Butler saying "Hey, this is all me, folks, sorry if it looked otherwise." Then so be it.

    Hank
    It looks like they are collaborating. This is a hacked-up mashed-up attack. Not Butler's usual work. So, they either are collaborating or they are not, but either way, it looks like they are. This is why I've stated that I expect to see a clarification and even a bit of back pedaling. That might be as simple as Butler saying "Hey, this is all me, folks, sorry if it looked otherwise." Then so be it.

    I guess there is always the chance of corporate mucking about but it remains perception. Like I mentioned in my blog, the relationship between Nature's postgenomic.com and scienceblogs is very strong. The young man who runs postgenomic has never added a single columnist from this site despite numerous requests from writers (unless 'Postgenomic collects posts from hundreds of science blogs and then does useful and interesting things with that data' means, quite literally, just 'scienceblogs' ha ha) and we have some darn well-known people in science here writing stuff that has been syndicated all over the world, so the quality is high. His site appearing on the front page of yours and refusing to include anyone here looks like collaboration between your groups yet it could hardly be pushed off on you personally. And it is probably just looks from a corporate point of view, not reality.

    So it goes with Nature and Declan's piece. Looks don't mean much. I do not seriously regard PLoS as a competitor to Nature so I see no reason, other than journalistic desire, for anyone there to write that piece much less mandate it. An editor may have approved it but it is not like they made Butler into a corporate attack dog - a 'toadie' was the term used - and he went along with it.

    Had you written the response to Butler's article it would likely have been a balanced examination, much like your comments here. But grrlscientist was on an ad hominem diatribe. Her work does not make it look like all of scienceblogs is engaged in personal attacks any more than Butler's article can implicate all of Nature.

    I basically intended to defend the guy's ethics from an unwarranted personal attack and to mention anecdotally that I agree that PLoS One occasionally puts out stuff that is suspect. This does not make me an enemy of open access or open science either. I am the one person among the varied groups and people mentioned here that I know makes $0 in this industry so obviously I am a fan of open science and open science communities.

    Until today I have never herd of Postgenomics. In what form does it appear on the front page of Sb?

    But Decian is an employee of NPG and a regular writer for Nature. THis strrange postgenomics thing you are talking about ... which I'm pretty sure is not real, or is a matter of some kind of spam bot activity or something, is a very far sight different from the responsibilities of being employed and/or under contract, and there is a huge difference between a blog (like this one, like mine, and like the nature network blogs) and space within a journal.

    Oh, I wrote a response, and it was not balanced ... it was cynical. I see Butler's piece as a goof, a gaff, and a giggle. So I'm primarily making fun of it. But yea, if I took him seriously, I'd write a seriously balanced piece, of course.

    But this Postgnomic thing ... that's crazytalk. I don't know what that is. Where on the front page is this thing?

    Hank
    We're getting tangential. I am not picking on postgenomic, I was demonstrating that we are not defending Nature because we have a relationship with them (if anything, they must dislike us) and your writers are willing to go after Nature despite the strong relationship you have with them.

    It's not crazy talk unless I were actually alleging that it is corporate positioning, or if it were untrue.

    This is your home page 1 minute ago. It is clearly not crazy talk. :)


    So if they are a bot leeching you they are doing it with Seed's endorsement.

    The hot topic on postgenomic is this PLos versus Nature thing. They have lots of blogs on there talking about it, small ones and large ones. If you didn't ask to be on there and you are there anyway they added you automatically but have not added numerous writers from here who eventually started asking just to be ignored and get a chuckle out of it. NY Times bestsellers and guys who have written well known books and textbooks and had numerous TV appearances have a good sense of humor about being blocked out on some website that claims to be about science blogging.

    But if I were as conspiratorial as the writer on scienceblogs calling Butler a 'toadie' for their employer, I would allege that entirely blocking out a science community with 500,000+ uniques and 3,000,000 page views a month is intentional to protect their being on your front page. This blog, for example, is not on the list among all bloggers on postgenomic yet I am willing to bet it is in the top 3 most read on this subject.



    Hi,

    The screen shot is a piece of paid ad space, so I wouldn't take that as an endorsement.

    I've never heard of PG, and checking them out, they look like most of the spam mirrors I see. I'd be curious to see if they are real.

    As we talk I'm learning more about this. Postgenomic is a blog aggregator I, for one, am not on it, even though my blog is ranked highly on a number of services ... what that means, I don't know.

    This box on the seed home page is interesting. I dont know what that is.

    I asked our editor about postgenomics and it's link to seed, and she said, and I quote: "Huh???"

    (That was a private conversation, but I think it's OK).

    So, Postgenomic is owned by Nature, and then Scienceblogs.com is linked to Postgenomic in some way, and postgenomics shuns scientificblogging blogs because of that relationship???? HOW DARE THEY!!!!

    If anything like this is going on, I'm going to blog it, buy jove!1! Seriously!

    (Which is pretty much the extent of my powers)

    That thing on the home page you have a picture of: How do you now that is not a paid ad? Probably not, does not say "ad" on it. Who knows, maybe we have some deal going? But I don't think there is any kind of co-branding between this blog aggregator widgit thingie and Scienceblogs.com. Or Seed.

    No, we are not talking about the same thing at all.

    Hank
    PalMD - If this postgenomic tool, which generates no money, was created by one guy at Nature and is touted as just a community service by Nature, is paying $20,000 a month to be on your site, I'd say Nature has far too much money on their hands. It is an ad, but probably not a paid one.

    Greg - I assume you do have a deal that involves no money. :)

    Again, it was just anecdotal, not an indictment, to demonstrate that there is no favorable relationship between Nature and us that would cause me to defend Butler - and girlscientist's independence was applauded in my article for going after them even though Nature clearly has a relationship with you.

    We go after people too - no one here is selling out for anything. We appear on the front page of Livescience but our writers have poked fun of Livescience articles on plenty of occasions.

    Scienceblogs.com does not have an arrangement of any kind with Nature that I'm aware of. None. Bloggers have only the looses relationship with Scienceblogs.com. Simple contract.

    As for advertising - that was a one-time thing, a tit-for-tat cross-advertising between scienceblogs.com and PLoS ONE when, for a couple of days, each has banner ads promoting the other. That was the extent of it. I work for PLoS and blog for Sb and my job is this kind of stuff, so I would be aware if there was anything more happening between the two organizations. Both are happy with my blog being what it is and where it is as far as I am aware. There is a mutual liking, I guess, but there is no business connection between the two.

    Hank
    Well, if that kind of promotion is your kind of stuff for them, by all means arrange it here - it eliminates the favoritism, old boys network appearance that way. We have 500-600,000 uniques a month now of hardcore science readers across the political and ideological spectrum and we go up every month. I think it would be great advertising for PLoS to appear here and we could do the same thing there.

    Eisen blogs here along with his own site and everyone here likes PLoS so I assume there is mutual liking as well.

    I'll suggest that to the Marketing folks.

    Postgenomic is, if I remember correctly, one of the many Web2.0 tools developed by Euan Edie and other folks at Nature over the past couple of years (others are: Scintilla, Connotea, Nature Blog Network, etc.). I think it is very useful as an aggregator of science-related blogging. Being specifically oriented towards science blogs, it is in many ways more useful than Technorati or Google Blogsearch which do essentially the same thing - aggregate.

    The development of these tools by Nature suggests strongly to me that Nature is readying itself to go OA. They invested in development of these tools which work ONLY if Nature content is OA. PLoS developed OA journals first and is building Web2.0 styled applications a little later. Nature is doing the reverse. Perhaps the two may even collaborate on this in the future, who knows.

    Unlike 'Science', which is oblivious of the changes in the publishing world, or 'Cell', which is actively opposing OA, my feeling was always that 'Nature' is the most attuned of the Big Three - watching, studying, exploring and getting ready to adapt to the changing world and thus gain an upper hand over Science and Cell.

    Thus, I am really surprised by the extremely ugly and insidious articles by Butler and Hannay targeting PLoS. Do they really fear PLoS so much? I have heard already many times that "CNS disease" has become "CNSP disease", i.e., the need for people in some areas of science to publish in Cell, Nature, Science.... or PLoS-Biology, in order to get jobs, promotions, tenure, grants, etc. Is this a salvo at the fourth competitor, the one seen as the most dangerous competitor in the future as Science and Cell inevitably sink due to their own inertia?

    Hank
    Postgenomic is, if I remember correctly, one of the many Web2.0 tools developed by Euan Edie and other folks at Nature over the past couple of years (others are: Scintilla, Connotea, Nature Blog Network, etc.). I think it is very useful as an aggregator of science-related blogging. Being specifically oriented towards science blogs, it is in many ways more useful than Technorati or Google Blogsearch which do essentially the same thing - aggregate.

    I keep saying postgenomic was just an anecdotal talking point but it never seems to resonate. :)

    I don't care who has marketing agreements with whom - my reason for laying it all out was to show that relationships are interconnected and complex. You have friendly relationships with Nature and they with you and friendly relationships with PLoS and they with you. So girlscientist went after Butler based on her gut (with too much hyperbole? Absolutely) and was right for doing it - but I didn't think he deserved the personal attacks. Attack the issue, not the individual. The relationship between Scienceblogs and Nature was irrelevant and rightfully so.

    Your perspective on the OA thing adds a new dimension. AAAS is not as oblivious as they seem to many but NPG is by far the most aggressive/progressive in this segment. If they are targeting PLoS as a competitor despite my (current) belief that PLoS is only a threat to smaller groups and not Nature, there may be corporate position to that effect. But would an individual writer be complicit in that? I may be naive (okay, I am naive) in believing that everyone is honest until proven otherwise but I don't think Nature can give those kinds of marching orders to writers any more than Seed could give them to you.

    They could try, but it would be a disaster.

    "to show that relationships are interconnected and complex. You have friendly relationships with Nature and they with you and friendly relationships with PLoS and they with you"

    Scienceblogs does not have a relationship with PLoS or Nature.

    Hank
    If postgenomic is on your front page (and they have not paid tens of thousands of dollars every month for the last year to be there) and 8 out of 10 of the blogs on the main blog page of postgenomic is scienceblogs, scienceblogs does have a relationship - you just may not know about it. Obviously 8 out of 10 scienceblogs may well be the most popular on postgenomic and as long as other sites are excluded there is no way to know if that is fair to the entire community. Nature owns it. They are responsible for it. So your relationship is with Nature. If Nature is this big corporate overlord micro-managing everyone they are not suddenly letting one employee have free rein when it comes to marketing terms with you.

    I don't know of any other site besides yours that has advertised for free on PLoS. So having a community manager for PLoS writing for you may not mean a formal relationship but it has certainly resulted in a positive one. Obviously if PLoS starts giving free advertising to us and Discover and Livescience that evens the field a little. Until then you are in the camp of denying any motivation for Seed/scienceblogs and assuming the worst about Nature.

    Postgenomic is a tool. You can get a widget, just like the one Sb, and put it on your sidebar. No need to pay.

    The advertising was not free - it was reciprocal. Pageview for pageview. And there are always ad banners on top of ONE pages, if you have not noticed. I have no idea what is paid, what is free - not part of my job description to know.

    Yes, Sb and PLoS are happy that I exist on Sb - nice for both, nothing wrong with it. Does not mean there is a "relationship", nor exclusivity, nor business connections.

    Hank
    Postgenomic is a tool. You can get a widget, just like the one Sb, and put it on your sidebar. No need to pay.

    I didn't think you paid him - I am certain without you that site would have no traffic at all so the benefit is one way. I am just surprised Scienceblogs took up real estate on its front page worth $10-20,000 a month to a real advertiser and gave it for free to a Nature tool to which Seed/Scienceblogs apparently has no relationship or attachment at all and can't possible generate any traffic for you.

    It doesn't make much sense. But it ain't my company. :)

    I do not know the details (these things are not told to us and if they were I woudl probably forget the details) but I think there is a lot of real estate that is not used on those screens, or sold at all. In other words, there is no meaning to the presence of a particular little square thing ... it does not imply a liability of 10 or 20K or anything else.

    YOu could do an experiment, Hank. Contact Seed and ask to buy that spot. Offer them a hundred dollars a month, r five hundred, or whatever. I bet they'll take it.

    Hank
    YOu could do an experiment, Hank. Contact Seed and ask to buy that spot. Offer them a hundred dollars a month, r five hundred, or whatever. I bet they'll take it.

    Oh, I bet they won't. :)

    While you and I and the rest of us can all slap each other around as individuals on topics like this and then get a beer and laugh afterward I am pretty confident Seed as a corporate entity is not terribly interested in giving us discount advertising on scienceblogs.

    It's worth a try, though. I owe you a beer if they take $500 for anything => 250,000 impressions.

    Hank, ol' buddy. Shell Oil is on our front page. Phoenix University is on our front page. Euroscience is on our front page. Hell, Movable type is on our front page.

    There is some polling widget that is used on 3.14.

    Yes, in a sense, everything, everyone is connected in the great chronosynclasticinfindibulum. But no, there is no relationship.

    You have lauded Grrrl for not letting her relationship with Nature (which arises from the connection with the blog aggregator) stand in the way of her slapping down Butler. You are telling me that I have relationships ... which implies all sorts of things even if you moments later try to play down the relationship with PLoS and Nature.

    These relationships don't exist, Hank. He was acting alone, fired from the upper floor of the book depository. No one else was involved!

    I will leave you now to your conspiracies. But if any of them grow feet beyond your little corner of the blogosphere, a team of guys with black suits and dark glasses is gonna come lookin' for you.

    In the mean time, a little advice from me to you: If, every time an opportunity you would like for your blog or for scientificblogging is manifest somewhere else, you bellyache about it, but as soon as the prospect of YOU having the same thing comes near your grasp you reach for it gleefully, you will start to give people a poor impression. This is not how to build relationships.

    Not that there are any relationships. None. Honest.

    Friendly advice. I like your blog. Keep your nose clean.

    Woooshh... (that's me going back to my blog....)

    There is an essential difference here:

    Declan Butler WORKS for Nature.
    Sciencebloggers are HOSTED by Seed.

    Ergo.

    Butler writes what his Bosses tell him to.
    Sciencebloggers write whatever the heck they want.

    Even myself - I write on the PLoS Blog what my bosses say is OK, I write on my Sb blog whatever the heck I want (I can even be critical of PLoS or Seed if I want to).

    Hank
    There is an essential difference here:

    Declan Butler WORKS for Nature.
    Sciencebloggers are HOSTED by Seed.

    That is basically saying that NY Times writers are told what to write (and it is Democrats doing the telling) and that all paid journalists have sold their souls for a paycheck to a corporate overlord. Again, I may be naive, but I don't think that is the case.

    I think they have meetings and pitch stories, just like in news rooms all across the world, and if they feel strongly and an editor is convinced they get to run with it. 'PLoS is a threat and we need an attack dog' just does not sound plausible to me but you guys have a different culture than we do. You, girlscientist and likely others there all feel that same way (that he was doing a hit piece on PLoS by corporate mandate) while I think he did research, felt like he had a story and was given a green light.

    I think I am supposed to be the evil cynical Republican businessman and you are supposed to be the optimistic believer in community effort. How is it that I am the one thinking he feels like he has facts on his side and was doing an investigation of the numbers and you think it is a big corporate conspiracy??? :)

    I would be incorrect to assume that Nature does not maintain control over what their staff writes in their journal. Seriously.

    1) Because he did it before

    2) Because Nature would not have published it if they did not agree with it and like it and thought it was good for them - in other words, even if he did it all by himself, the Nature bosses gave him the approval. He did not publish that on his blog, it was published in Nature. It does not matter if Nature asked him to write it or if he wrote it first and then they decide to publish it - they approve.

    Either they are so blinded by their own internal in-house thinking that they really cannot see how insulting the article (both article, actually) is, or they did it on purpose.

    They hosted themselves on their own petard, or hoisted themselves on their own sword. Perhaps they were naive. By now they probably realize their mistake and are trying to do damage control with various Nature people commenting on various blog about this. With one notable exception - Declan Butler is nowehere to be seen. Where is he? Why is he not defending his article and explaining his motivations and why/how that piece ended up getting published by Nature?

    Hank
    By now they probably realize their mistake and are trying to do damage control with various Nature people commenting on various blog about this. With one notable exception - Declan Butler is nowehere to be seen. Where is he? Why is he not defending his article and explaining his motivations and why/how that piece ended up getting published by Nature?

    I just don't think they are that organized - but I think that about science writers in general. I would have no idea if someone here started getting attacked and I could certainly not mobilize any support. Granted, we only have a few people in the actual blogging community and most are feature writers instead but I think people would feel slightly intruded upon if a 'circle the wagons' request were introduced by me.

    If Butler wants a big audience for a rebuttal, he can do it here. It will have more exposure than Nature blogs or his own site (though I assume an article on Nature would have higher readership than an article here so he may be saving it up for that.) You spend time reading the good stuff on scienceblogs and probably not much here but we make no secret that we will let anyone have their say as long as it's science and people stick to issues. We can be pro- and con- on just about everything except evolution, where the con- violates the 'it has to be science' rule.

    If he is game, we could even do it in a debate format; Butler getting a statement and then rebuttals and someone like J Eisen (or you, if your scienceblogs agreement doesn't prohibit you being published on another blogging site) doing the same. We're pretty neutral culturally and I am certain I am the only person here who defended him so it isn't like we could be labelled as having an agenda for either side.

    "I just don't think they are that organized"? Are you kidding? It's Nature! A business organization - a Big One, too. Nothing goes under their banner without approval from the higher-ups after a committee meeting. They are organized as hell. They are nothing like "science writers" or "science bloggers" who are independent individuals - they are a corporation and they do everything according to marching orders.

    As for Butler, once Nature gives him a green light, I am looking forward to seeing his defense, here or anywhere.

    Hank
    "I just don't think they are that organized"? Are you kidding? It's Nature! A business organization - a Big One, too. Nothing goes under their banner without approval from the higher-ups after a committee meeting.

    Well, to us, you are ALL big business organizations - we are the little independent guy in the big 20 science sites that are otherwise either government or funded by media companies. You have a print magazine and NY offices and a sales force selling ads for you and venture capitalists who expect a return on their investment - and they pay you money to write and expect you to generate an audience - just like Nature.

    If I believe Butler is for sale because he gets a check with a MacMillan (or NPG? I have no idea) name on it, I don't see why I wouldn't think the same thing about your group and you taking money from Seed. Yet you say that is not the case and I believe it, just like I believe he is not a paid hitman being told to go after PLoS and I don't believe the NY Times is full of paid shills going after Republicans.

    Butler is not for sale.

    Butler does, however, work for Nature Publishing Group. They are the publisher, he is the writer.

    He is not for sale because they own him. Own. Him.

    Which is generally a pretty good deal for a writer, and he probably gets some leeway, but he does not write a piece and put it in the journal for the editor to read the next day!!!!!! He writes for the editors. The editors take the copy at some point in the process and he never sees it again until it is printed. Honest, that is how it works!!

    I used to run a monthly. My writers were my cattle. My word slaves. And I was a good editor. (As in nice)

    Hank
    Well, I have to defer to you on the 'word slave' thing. :)

    As I have said a few times, my naivete in these matters of corporate skullduggery is confessed up front even though I assume I have more corporate experience than 99% of the people in the science blog community - I have never had this kind of thing come up in 17 years of meetings about competition and business. So even now I am happy to live in a peaceful volunteer wonderland (here) where we are quite popular and no one tells us what to do or talks about what 'sells' to the audience and I can believe everyone else does the same.

    I'm going to defend Butler's right to say what he believes and to not be accused without proof of being a corporate toadie. I generally think it's immature verbage and tone even as I applauded grrlscientist for speaking out on the issue. Like I said in my blog post, I bet they will get along fine at the conference.

    Seed Magazine and scienceblogs.com are somewhat separate entities, as I understand, both ran by Seed Media Group, but even occupying separate offices (as in 'physical space') in NYC.

    All Seed gives us is hosting and tech support - we have complete 100% freedom to do whatever we want with our blogs, i.e., we are entirely independent actors. Nobody at Seed can tell us what to write and what not to write - that is explicitly stated in our contracts.

    Do we feel loyalty? Sure, why not - nothing wrong with being proud of being on Sb: it is a hand-picked collection of 70 best science blogs written in English language, so of course we are proud of it.

    But when SMG dragged their feet in ditching Watson off the advisory board or whatever, a bunch of us blogged angrily about it. In other words, we are individuals.

    People working for Nature are not - they are employees. They get salaries to do what they are told to do. We get pocket money based on our traffic - enough for a couple of beers for most of us.

    We are there because we like the prominent soapbox, the tech support, and the sense of community we have developed on there (I know, not everyone likes each other, but we meet in meatspace, we communicate, many of us became personal friends, etc.).

    Thus it is really surprising to me that you would in any way equate Nature employees with sciencebloggers. After all, I believe you have no editorial control over blogs on your site - why do you suspect that it is any different on Sb?

    Hank
    Thus it is really surprising to me that you would in any way equate Nature employees with sciencebloggers. After all, I believe you have no editorial control over blogs on your site - why do you suspect that it is any different on Sb?

    I don't, as I said. But I also do not think any reputable publication in this industry dictates personal positions to its writers. There would be too many disgruntled former employees spilling the beans if that were true.

    As I said, I think Butler pitched a story, convinced an editor and ran with it - like any writer in thousands of places do every day. You seem to think a corporate committee came up with a story and told him to match the data to a strategic corporate topology they created. Employee does not mean corporate hitman.

    Saying that there is a special case for the relationship between Seed's corporate need to make money and scienceblogs independent contractors generating it (no corporate mandate for positions) but that Nature cannot possibly have respect for its writers means you are using specific knowledge about Seed's positive corporate culture and then assuming the worst about Nature's, which you know little about.

    I just don't assume the worst about Butler or Nature. As I have said, they are not friends of ours and you and others at scienceblogs have had plenty of bad things to say about us, but I never said it was part of a corporate strategy dictated to you in order to smear us. So I have no reason to think that is the case with Butler and Nature going after PLoS.

    There can be anecdotal evidence - like us mysteriously not appearing on any Nature-owned supposedly community-oriented sites like scintilla or postgenomic - but that doesn't make me think Nature has it in for us.

    In this instance, we disagree, but only on Butler's motivation - something neither of us can truly know. We both agree that we like open access. I think he likes open access. But if peer reviewed is going to continue to mean something, there should be a minimum standard and, if everything in PLoS One meets that standard, it's far too low.

    I think the degree of loyalty is variable. Proud? Easily, of each other, for the most part. Do we all agree and get along? HA!

    On the beer thing: That is a bit of an exaggeration. Honestly, my home computer gear is used mainly for writing my blog. I don't think the bits of dough I get from Sb by itself is going to keep me in current gear. For most of us, this is a loosing proposition.

    And for someone like PZ who gets piles of traffic, he also travels to events on his own dime quite a bit. I estiamte that he spends quite a bit on travel expenses related to the blogging thing. I think he paid his own way and put himself up for the framing slapdown, for instance.

    But right, as the man says, there is a big difference between a contract blogger and an employee.

    Think of it this way. If I call Rupert Murdock a poopy face, and it turns out that he sues the owner of Seed, he (murdock) will not have standing because of our contract. If Butler calls Rupert Murdock a poopy face and Murdock sues, Nature Publishing Group will be named in the suit and will be potentially liable.

    NPG owns Butler.

    Skipping over much of the debate here I do not get one thing. What is the evidence that the minimum standard of PLoS One is too low? There are a variety of other journals that say, for their field, that they aim to publish a large volume of papers also without asking if a paper is the most strikingly novel thing in the world. As I will be blogging about soon, my first and only PLoS One paper that came out 7/2 was put through the ringer. The reviews were fair but quite extensive and required us to do new analyses, revise the paper enormously, and even then our paper was not accepted until the revised version was re-reviewed. Hank and Declan make arguments about their gut feeling that PLoS One papers have to be bad because PLoS One publishes a lot. Well, show some evidence. Nature was an entire unit must publish more than PLoS One. So must ASM and ACS. If you are convinced that PLoS One has so corrupted the scientific publishing enterprise, start presenting some evidence. And not single examples but some data on the % of papers that are bad there versus other journals.

    Hank
    Since you missed most of the comments and maybe didn't read my blog, let me be clear on something again; there is no 'Hank and Declan make arguments about their gut feeling' ...

    I don't think he deserves to be called a corporate toadie for writing an article he thinks has merit. I generally think there is too much name calling and histrionics in the science blogging community and you don't see it here because we are serious people who tackle issues and not people. This is my favorite site, and the favorite of hundreds of thousands of others, for that reason. All of us commenting here have a sizable audience, but they are different audiences.

    If I read 5 articles and 2 of them are not not very good, it is not a statistically valid sample, yet we have had people in the blogging community disregard us because they did not like one article - out of 30,000 here. So I am not unsympathetic to the idea that an entire publication cannot be disregarded because of a few articles. I have lived it.

    There can be no statistically acceptable metric of a 'bad' paper much less a % of them, other than the press release PLoS One stamped a peer review on and published, to their regret. I think we all agree (and they do too) that was bad. But if it's 2 out of 2500, and you are certain all the rest are as good as anything out there, I am okay with it. You read more of them than me and certainly know more about how PLoS works.

    "But if peer reviewed is going to continue to mean something, there should be a minimum standard and, if everything in PLoS One meets that standard, it's far too low."

    PLoS ONE has, in many ways, higher standards of peer-review than most other journals:

    First, it has to be, because of continuous stream of nasty insinuations that it is "not peer-reviewed" or "lightly reviewed" or some such mythological crap.

    Second, freed of the burden of deciding if a manuscript is Earth-shaking, paradigm-shifting, IF-raising, mind-boggling, media-worthy or money-raising, the peer reviewers at PLoS ONE can devote their full attention to the quality of the work. As a result, many manuscripts go through 2-3 rounds of revisions. 30-40% get rejected (compare that with most other smaller journals which reject 1-2% - what's the point of review if everything gets published in the end?). I have linked to all the posts on this hullabaloo - go check the comments including statements by ONE authors testifying how thorough the peer-review of their manuscripts was.

    What is the evidence that the minimum standard of PLoS One is too low?

    No credible evidence. Supposition and innuendo. I actually read a LOT of that journal and in my opinion it is not of lower quality than, say, PNAS or any of my own field's main journals, or Current Biology. Higher than these, probably.

    Hank
    Gentlemen, it is a losing proposition for any of us to go through 200 articles a month and argue about what is good or bad - it's a subjective measure. My intent was to extol grrlscientist for taking a stand on this even though she is going to be at a Nature-sponsored conference this summer while arguing that calling someone a 'toadie' for writing an article she did not like was just plain wrong.

    I respect that Butler saw a correlation between money and a lower standard of peer review (real or imagined) and called it out. If anything, the debate it created either reaffirms that PLoS One is doing a great job or it shows them they need to tighten up the quality a little - both of those are good things. Open access still wins.

    Gentlemen, it is a losing proposition for any of us to go through 200 articles a month and argue about what is good or bad

    Proceedings of the National Academy of Sciences is a weekly. The current (1 July) issue has, by my rough count, 58 research articles (I did not count commentaries or corrections).

    I don't recall hearing suggestions that this publication volume means that PNAS must be second-tier, or poorly reviewed.

    Hank
    So you are saying that 200 peer reviewed articles per month is achievable and no one criticizes the quality of PLoS in Medicine or Biology so there should be no reason PLoS One does not have the same quality. I think we all agree with that.

    If you feel like PLoS One never prints anything that isn't equivalent to PNAS then indeed there is no argument to be made. I just wonder why, if Nature was out to slur PLoS, they didn't go after Biology or Medicine, since no one seems to believe outside of Nature that PLoS One has that 'light peer review' stigma. If they want to instill doubt and have no basis for it, they could just as easily do it for something more of a threat, like Biology, right?

    jeisen
    Hank -- I never called your nor Declan a corporate toadie. My problem is with his logic and evidence and the presentation of what he wrote as News. It was an opinion and one without much evidence presented behind it. I wads questioning one aspect of this argument - the notion that PLoS One is bad because it publishes a lot of papers. I think this is a lame argument and as others have pointed out lots of quality journals publish a lot of papers. Whether PLoS One will be considered a high Q journal in the long run or a low Q journal or a medium one is to be determined. But without evidence for PLoS One publishing lots of crap, his piece should have been written in a blog or presented as a thought piece and NOT as news. Jonathan Eisen, UC Davis, Tree of Life Blog
    Jonathan Eisen, UC Davis, Tree of Life Blog NOTE - THIS IS A CROSS POSTING FROM MY "TREE OF LIFE" BLOG .
    It's easy to go after PLoS ONE because PLoS one is trying to do something different with their reviewing process - they've limited pre-publication review to an examination of how good the the research is, in terms of techniques, data analysis, and that sort of thing. (In other words, their criteria is basically "were good practices used, and used appropriately."

    Instead of focusing on questions like "is this groundbreaking" or "scientifically important" or "a novel finding" during pre-publication review, they've put into place tools to make it possible for readers to conduct that sort of review post-publication.

    Doing review differently, even just a little bit, makes them an easy target for accusations that they're doing things worse.

    I think - and I said as much in my response to Butler - that it's a real shame that he decided to go with the "it's different, so it can't be as good" spin instead of actually looking at the question of how well it actually works.

    Hank
    I think - and I said as much in my response to Butler - that it's a real shame that he decided to go with the "it's different, so it can't be as good" spin instead of actually looking at the question of how well it actually works.

    That's a terrific point. We can hope he shows up somewhere to talk about this. To my (limited) knowledge the only other time he took on PLoS One was http://www.nature.com/nature/journal/v447/n7148/full/4471040a.html

    "The paper is total drivel, it should have been picked up in the review process," claims Tim Farley, an official in the World Health Organization's HIV-prevention team in Geneva. "And coming from PLoS One gives [the views in the press release] a public perception of validity. In public health there are severe dangers in such stuff getting through."

    "There are lessons to be learned from all papers that we publish; we are a young journal," says Chris Surridge, PLoS One's managing editor, adding that its peer-review model is constantly under refinement. "We are feeling our way."

    So he had a valid case then. If he sees this as a recurring problem he should say something. Would not Scienceblogs writers say something if they thought bad papers were getting legitimized by having a peer review stamp?

    Butler may not want to walk into the scienceblogs lions den and discussing it on Nature may miss the audience concerned about his work but postgenomic showed 3 or 4 non-Scienceblogs sites discussing this ... and there is also us, though since Nature is apparently part of the evil empire (which would explain why we are not on those Nature community sites they own) he may not be allowed to comment here by those corporate overlords some of you think control his every word.

    Actually, I think the PLoS ONE system is a step or three closer to real peer view than the Nature system, which is generally thought of as a few steps away from peer review.

    Wow - thanks to Greg for sending me the link to this article and the comment thread. I feel like I have been given keys to a whole world, so I apologize if my post comes off like the scribblings of a kindergartner among grad students.

    In my opimion, Mike D. and Bora have hit the tender spot when it comes to publishing in a journal which depends on subscriptions and sales for its decisions to publish or reject a paper.

    I am not a scientist nor an academic, and so I have no experience when it comes to publishing papers. None. But with their comments, both Mike and Bora have illustrated the key to PLoS. Work is published more based on its quality than its sale-ability at PLoS One and this illustrates its value. The work is available for future research and simply adds to the database for its own sake and not necessarily because of its "sexiness." That is both the beauty and the necessity of OA, its there to build the base of knowledge if for no other reason that it there.

    Is that why Butler is threatened by PLoS One?

    Would not Scienceblogs writers say something if they thought bad papers were getting legitimized by having a peer review stamp?

    Depends on the writer. I can't think of a single issue that's motivated 100% of us to write a post.

    Seriously, though, speaking for myself, it would depend on the size of the problem. Peer review is one of those systems that's really easy to compare to the Churchillian definition of democracy - it's the worst there is, except for everything else that's been tried. Every journal, sooner or later, is going to have a peer review problem of some kind.

    I'm not likely to jump on a journal if a couple of sub-par papers get through now and then. But if a journal is routinely publishing seriously flawed papers, I very well might.

    those corporate overlords some of you think control his every word.

    That's a bit of a strawman. I don't think that any of us have claimed that Nature has complete control over every single thing Declan says.

    What has been claimed - and I think it's probably right - is that a news commentary article written by a full-time Nature staff writer like Butler, appearing as it did in the print version of the journal, is probably also a reflection of the views of the editorial staff.

    Hank
    I certainly agree with what you say here about giving a publication a break if bad things slip through (and discussed it above, having had the same experience of being judged for one article out of thousands) but in regards to my saying

    those corporate overlords some of you think control his every word.

    I said that because one of your brethren wrote ...

    NPG owns Butler

    and reaffirmed that belief in a few places here, so it wasn't a strawman. It seems to be commonplace in this field of journalism, or at least a belief of people here about Nature employees.

    This is a straw man and it is being brought up in relation to my comments on this. Hank, you 've got to try to get the subtleties right here. Let me suggest the following:

    1) Nature editorial staff does not approve every word Butler writes.

    2) Nature editorial staff is never unhappy with the words butler writes.

    3) Butler's writing is somewhat narrowly defined for many issues, very narrowly defined for select few issues (this PLoS thing being one of them).

    Do these seem contradictory? Do I seem to be saying that the editors control yet do not control what Butler is writing? That is because these arrangements are indeed complex and involve negotiations sometimes very overt sometimes not so overt.

    The exact way in which this plays out at Nature is something I do not know. But I promise you that a successful leader in the field like NPG is not employing loose cannons, nor are they making their writers feel like they have rings in their noses to be led around with.

    Butler is not doing whatever he wants to do. But I am and you are. He is a staff writer, you and I are bloggers.

    The minute Nature hires me as a staff writer, my blog goes down to one on-controversial posts week and I fall into line. If I feel that I can't do that, I don't take the job. Not that I'm getting any offers or anything.

    Hank
    This is a straw man and it is being brought up in relation to my comments on this. Hank, you 've got to try to get the subtleties right here.

    :)
    But it's not a strawman if I am actually basing it on things you just admitted you said!

    However, your points farther down clarify it nicely. They are contradictory and complex, like my outlining the convoluted relationships in the science blogging(individual) and science (corporate) world.

    Hank
    Just as an aside, since threads get confusing, if you click on the big blue NEW next to a comment, it will take you in sequence to each new comment.

    If you take 15 seconds and get an account, a traffic counter in the upper left will also track comments for you and make it a little easier. You can even create a bio and stick a link to your blog in there for a lovely backlink. We are such givers.

    i haven't read every comment. but hank, there is no ideological/political litmus test on scienceblogs. there's a lot of liberal politics, but scientists & science lovers are on average a very liberal bunch. i know, since i'm one of the "token conservatives" at scienceblogs. i don't post on politics much, and i'm certainly out of place, but i was one of the original sciencebloggers and you can use google to see that i have published print pieces in *the american conservative* and on the web in *frontpage magazine* before i got on board with scienceblogs. i generally come out as a moderate libertarian though i have some socially conservative views.

    best
    razib of gene expression

    Butler did a hatchet job on the World Innovation Foundation and made assumptions that looked as though the Foundation was something that was not in the public interest. He appears to have an aversion not to do a balanced job and where this is a clear sign of ulterior motives. Indeed, he gives one good comment for every ten bad comments. Another sign that he has other things on his mind. Most probably financial for himself and his publication. He is a very obnoxious person who comes over in basically a threatening manner if you ever have the horrible experience of being interviewed by him (sorry did I mean interogated). Really not a nice person inside I would say.

    We are now taking Nature to task about the highly misleading article that Butler published in January 2008. Indeed we have started at the top with giving submissions to the holding company where Nature are a division. It is hoped that Butler eventually learns his lesson the hard way from this growing rebuff by the Foundation and when all this comes out in the international press and most probably the US and European Courts. His side kick Oliver Morton supports him in whatever Butler does and therefore is no better in giving support to a balanced article. That is of course when the knives are out for you and where PLoS has also suffered from this experience. In many ways therefore through this baptism of fire, we could say that we are now really like brothers with PLoS in many ways. Conscientious objectors at least.

    Therefore good luck for the future of PLoS in their endeavours, but please PLoS do not upset Butler again. He does not like anything that is against his personal and company interests. You have been told so don't do it again or you will be very unpopular in certain previously stated circles. Nature thinks that it is big, but not that big when the world eventually fully learns about their unsavoury tactics and hidden agendas.

    Dr David Hill
    World Innovation Foundation Charity
    Bern, Switzerland
    www.thewif.org.uk

    Hank
    Sure, Nature is no friend to new media - they sure as heck are not friends to us (1 million readers a month and 2 years in existence and too many prominent researchers to count writing here and no Nature article or subsidiary site supposedly about science has ever included or mentioned us ... ever) - but I  objected to him being called a 'toadie' for criticizing one part of PLoS.    The comments here were not representative of the basically nutso people who went after him.  They really were nuts.  Here people were pretty tame, comparatively.   

    But even here there were people here acting like I was a shill for Nature because I defended him - us, the lone independent science blogging site of any real size in a sea of well-funded media companies claiming to care about independent science - which is the best irony of all.

    Butler is not perfect - a journalist who has no detractors is a PR person - but he's pretty darn good.