Gut microbes in Panaque

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Gut microbes in Panaque

Post by racoll » Sat Oct 27, 2012 1:14 pm

McDonald et al. (2012). Phylogenetic Analysis of Microbial Communities in Different Regions of the Gastrointestinal Tract in Panaque nigrolineatus, a Wood-Eating Fish. PLoS ONE 10.1371/journal.pone.0048018.

This is open-access paper (click the link above). If you don't know what means, please take the time to watch this excellent video on how the money YOU pay in taxes is being wasted.


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Re: Gut microbes in Panaque

Post by naturalart » Sat Oct 27, 2012 2:47 pm

Thanks Racoll, I now, personally, dub you a true 'free-thinker'. :-BD

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Re: Gut microbes in Panaque

Post by Mike_Noren » Sat Oct 27, 2012 4:17 pm

Good video.

The public should know how ridiculous and offensive the publishing situation is in science. Here's an article on the subject of how the publishing houses are raking in cash from scientists and libraries, with a 60% profit margin: http://jrsm.rsmjournals.com/content/99/9/452.full
It's from 2006, but it's not gotten any better since then.
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Re: Gut microbes in Panaque

Post by TwoTankAmin » Sat Oct 27, 2012 5:34 pm

It would be nice if it was this simple. However, there is always more than meets the eye in these discussions, and everybody has their own axe to grind. The conflict I see is how do readers know what in open access is quality information and what in open access is bad science.

I am a bit of a nut regarding nitrifying bacteria and have been reading scientific literature on it for a couple of years now. One of the more interesting studies in this area has to do with ammonia oxidizing archaea. The first study on this in terms of aquariums is an article on Plos One. Without going into details, I wanted to know how reliable this outfit was so I began to research it. What I discovered was it is a part of a bigger organization which publishes all sorts of research. In fact, the parent org. has a couple of leading well respected peer reviewed journals as well as the Plos One open access. My investigation left a very bad taste in my mouth regarding Plos One, especially regarding their peer review policy. Rather than go into details I will offer the following links and folks can read and decide for themselves.

This is quite a long article http://richardpoynder.co.uk/PLoS_ONE.pdfand very interesting.
http://scholarlykitchen.sspnet.org/2011 ... wing-down/
This one deals with the Plos One peer review process http://journalology.blogspot.com/2007/0 ... s-one.htmland finally http://scholarlykitchen.sspnet.org/2012 ... er-review/

Basically as far as I can tell Plos One is a money factory for Plos.org which gets directed into financing the other more stringently peer reviewed Journals it publishes. But you can decide for yourself.

By way of full circle- The lead name on the Archaea study I mention above which made the bold statement that it Archaea and not bacteria that oxidize ammonia in tanks later published another related piece which appeared in a more traditional peer reviewed journal. The conclusions there were a bit different. But, in my opinion, was some of this was due to the differing standards regarding peer review. I also wondered why the initial study was in Plos One but the subsequent one was not. I wonder why?

And this highlights the issues involved. Is speed of publishing now more important than the quality of the information? What effect does the reduction in the stringency of the the peer review process for Plos One, and similar open access publication platforms, have on the quality of information published. What effect does the fact that these sort of platforms publish studies rejected by journals with much more stringent control/peer review processes have on the quality of what is published.

One of the things I have done relative to my hobby or researching the nitrifying bacteria is to decide for myself how substantial the peer review process is for some publications. I have actually gone to the publishers site and read their peer review and author submission policies to satisfy my curiosity.

Like I said, these issues are never quite as simple nor cut and dried as they first appear.
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Re: Gut microbes in Panaque

Post by racoll » Sat Oct 27, 2012 6:17 pm

TwoTankAmin wrote:What effect does the fact that these sort of platforms publish studies rejected by journals with much more stringent control/peer review processes have on the quality of what is published.
Absolutely none. Have a read of this.

As someone who has published two papers in PLoS ONE, and been a peer reviewer for them also, my experience has been that this journal was absolutely no less rigorous or in fact faster, than any other "proper" journal I have published in. In fact, the harshest review I've had was in PLoS ONE.

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Re: Gut microbes in Panaque

Post by Jools » Sat Oct 27, 2012 7:06 pm

When I was young, I actually thought that the reason papers were expensive (to me then) was OK because all the profit went into more research and I was only really looking at pictures and maps without much understanding of what else was going on. Later, and as the husband of an writer and academic who did her post-grad on aspects of the history of the printing press in Europe, I was soon educated on this mess. As a technologist it appears to me as a theatre of absurdity indeed; something that would benefit from open global access and aggregated indexing is kept protected. I think evolution will (sadly, slowly) kill off the publishers who do not embrace digital publishing if not fully open access then at least a more equitable financial model.

Don't get me wrong, I do not think they should necessarily be free - tax dollars might pay for severs and so on, but £1 a PDF or whatever seems just fine to me - and I think would actually make more money. Someone creating a pay per paper service on the basis of making .1p a download and maybe, just maybe, even more people would actually read their work!

PS This is a good discussion, but if it goes much further one of us mods/admins will split it off. But, meantime, have at it!

Jools

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Re: Gut microbes in Panaque

Post by TwoTankAmin » Sat Oct 27, 2012 11:51 pm

I had a quick read of the link. I did not give it the sort of read it would take to do a reasonable critique. However, I quicly saw a few things I found hard to accept. If another researcher did the same study, I wonder how closely the list of papers selected would match between he two selecters. My feeling was the author had a conclusion he sought to support from the outset. I could be wrong.

racoll- I am curious what your reaction was to some of the links I posted regarding Plos One? One interesting note, I have corresponded with two Ph.D. microbiologists over the past couple of years regarding nitrifying bacteria. One considers Plos One peer review to be worthless and the other thinks Plos one is great. However, the one who likes it has some connection to the the founders and/or the NIH.

While I do not feel that anything published in Plos One is necessarily "bad science", I prefer to trust what I read from the more traditional peer reviewed journals over what I find on Plos One.
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Re: Gut microbes in Panaque

Post by Mike_Noren » Sun Oct 28, 2012 10:12 am

TwoTankAmin wrote:The conflict I see is how do readers know what in open access is quality information and what in open access is bad science.
That is the same in also in the pay-walled journals: all journals, including the highest impact ones like Nature, Science and Lancet are brimming with bad science (ESPECIALLY the highest impact journals - I see Nature etc as sensationalist "science tabloids"). The reader himself has to judge if a study is good or junk; I guesstimate that in my own field of molecular systematics about 20-30% of studies are so flawed they should not have been published.

I can not comment on the specific case you mention, because I do not know the subject.

The scientific quality control of an article is the review, and some junk articles do get through. PLoS ONE is no different from Nature in that regard.

(There are also journals with extremely low standards, which will print anything, which subvert or corrupt the review process, which are fraudulent money-making machines for the publisher and/or are vanity vehicles for a self-publicist, but this is not tied to them being open access or not.)
Is speed of publishing now more important than the quality of the information? What effect does the reduction in the stringency of the the peer review process for Plos One, and similar open access publication platforms, have on the quality of information published. What effect does the fact that these sort of platforms publish studies rejected by journals with much more stringent control/peer review processes have on the quality of what is published.
The fundamental thing here is that the big publishing houses do not have more stringent quality controls than open access journals. The editor winnows out studies which are not formatted correctly or are obviously flawed/plagiarisms/crackpottery or have subjects unsuitable for the journal, but the scientific quality control is done by the reviewers, and I see no reason to think that the stringency of review is higher in pay-walled journals than open-access journals.
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Re: Gut microbes in Panaque

Post by racoll » Sun Oct 28, 2012 12:12 pm

TwoTankAmin wrote:I prefer to trust what I read from the more traditional peer reviewed journals over what I find on Plos One.
I have to reiterate that the PLoS ONE review process is there to make sure that the conclusions are supported by the data and analyses (methodologically sound), but not judge the perceived importance or novelty. Flawed studies should be filtered out by this process. Despite the high acceptance rate, PLoS ONE has a reasonable impact factor (4.1).

In this regard I agree entirely with all Mike Noren's comments above. It's all down to the reviewers. Dodgy papers get into all journals. I've reviewed papers for high-tier quality journals, and seen reviews along the lines of "yup, that's fine", when even me, as a grad student then, could see serious problems. In contrast, a review I had from PLoS ONE was something like 10 pages long (and that's good, as it improved the paper)!
TwoTankAmin wrote:racoll- I am curious what your reaction was to some of the links I posted regarding Plos One? One interesting note, I have corresponded with two Ph.D. microbiologists over the past couple of years regarding nitrifying bacteria. One considers Plos One peer review to be worthless and the other thinks Plos one is great
Yes, opinions can be quite polarised. I note that I have met far more scientists who are positive rather than negative about PLoS ONE. Unsurprisingly, the people who dislike it, have not published in the journal.

The staggering success of PLoS ONE is bound to attract negative comments. However, this success (look at the stats below) of the journal speaks louder than that, to me. Numerous PLoS ONE-clone journals have also been launched by most of the big publishing groups now.
http://en.wikipedia.org/wiki/PLOS_ONE wrote:In 2006, the journal published 138 articles; in 2007, it published just over 1,200 articles; and in 2008, it published almost 2,800 articles, making it the largest open access journal in the world. In 2009, 4,406 articles were published, making PLOS ONE the third largest scientific journal in the world (by volume) and in 2010, 6,749 articles were published, making the journal the largest in the world (by volume).[6] In 2011, the journal published 13,798 articles

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Re: Gut microbes in Panaque

Post by dw1305 » Sun Oct 28, 2012 2:06 pm

Hi all,
For what it is worth as a failed academic who still works for a University, I would definitely agree with Racoll and Mike's comments on PLOS ONE. Again it isn't my subject area (all though my research career both started, and terminated shortly afterwards, with work on Spent Mushroom Compost), but it looks a very interesting paper, which definitely suggests that Panaque nigrolineatus should be regarded, at least partially, as a true xylophagous organism.

I'll need some time to look through them all, but along with Donovan German's more recent (2011) Loricariid publications <http://german.bio.uci.edu/pubs_1.html>, it should definitely get us a bit further in understanding Panaque digestion, and the implications for feeding them in the aquarium.

cheers Darrel

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Re: Gut microbes in Panaque

Post by TwoTankAmin » Sun Oct 28, 2012 2:29 pm

I have two big prolems with Plos one in terms of their review policies. First, Plos one is not in favor of reviewer anonimity. I find that a big problem. Second, they allow authors to exclude specific reviewers. These are the policies, as stated on the Plos one site which lead me to have formed my opinins.
7. Confidentiality

The review process is strictly confidential and should be treated as such by reviewers. As the author may have chosen to exclude some people from this process, no one who is not directly involved with the manuscript (including colleagues and other experts in the field) should be consulted by the reviewer unless such consultations have first been discussed with the Academic Editor.
9. Anonymity

Although reviewers may remain anonymous during the review process, we strongly urge them to relinquish this anonymity to promote open and transparent decision-making.
11. Competing Interests

As far as possible, we respect requests by authors to exclude reviewers whom they consider to be unsuitable.
My personal feeling is all of the above works to compromise the integrity of the review process and to make it less trustworthy and valid. Compare it to the review policies of other peer reviewed journals.

One final comment, and please don't take it the wrong way. But the people I read/talk to who most support the Plos One model are researchers who want to be published and who dislike a more stringent review process as it excludes a lot of things from publication. Since most researchers must publish or die, they are under extreme pressures to get their work into print someplace. Again, this doesn't mean their work is all and always unworthy, but that it may just not cut the mustard, so to speak. The issue is what is more harmful in the long run, willingly publishing potentially inferior work or unfairly excluding worthy wor?

But as I have been told before, we will just have to agree to disagree on this subject.
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Re: Gut microbes in Panaque

Post by Mike_Noren » Sun Oct 28, 2012 4:15 pm

TwoTankAmin wrote:I have two big prolems with Plos one in terms of their review policies. First, Plos one is not in favor of reviewer anonimity. I find that a big problem. Second, they allow authors to exclude specific reviewers.
* These are not issues with open access, but specifically with editorial decisions of Plos one.
* I find it odd that Plos One want reviewers to not be anonymous. I don't understand the rationale; it seems obvious that non-anonymity will have a chilling effect on the reviewers, and that is not a good thing.
* The big publishing houses also request that you suggest reviewers for your paper, and to name who you do NOT want to review your paper. That you get to suggest your own reviewers seems like a bigger problem than that you can say who you DON'T want as reviewer.
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Re: Gut microbes in Panaque

Post by racoll » Sun Oct 28, 2012 4:33 pm

TwoTankAmin wrote:Plos one is not in favor of reviewer anonimity. I find that a big problem
Really, why? It allows to reviewers to, basically, be a******s. You are forgetting that as well as sifting out the bad stuff, peer review is also for helping people improve their manuscripts in a constructive and positive way (that's how I see it, anyway). When you sign your name on the review, it does make you write it in a different way. Besides, it is only a suggestion; you can remain anonymous at PLoS ONE if you choose. Sometimes there are good reasons to be anonymous, however, especially if you have to reject a paper (you don't want to make too many enemies!).
TwoTankAmin wrote:Second, they allow authors to exclude specific reviewers.
Well, this is standard practice at many journals, and by no means specific to PLoS ONE. There are egos and much competition at play in science, and not all reviewers will be completely objective.
TwoTankAmin wrote:researchers who want to be published and who dislike a more stringent review process as it excludes a lot of things from publication
Most manuscripts will get published somewhere, eventually, so I don't agree that a "stringent review process" excludes work from the scientific record. It just excludes it from that journal, in order to maintain that journal's importance and relevance. The manuscripts will just be submitted elsewhere.

Now, in the PLoS ONE model, impact is measured by altmetrics at the article rather than journal level, and that's the beauty of the internet.

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Re: Gut microbes in Panaque

Post by TwoTankAmin » Sun Oct 28, 2012 6:10 pm

racoll- I have read the review policies at several sites for different journals as well as those for Plos One. I do not see any similarity in the orientation of the other journals and Plos One. Plos one says it respects a reviewer's right to be anonymous but strongly urges them to suggests they relinquish that anonymity. Here is an example of the review policy at The Nature Journals:

Anonymity We do not release reviewers ... r policy.
from http://www.nature.com/authors/policies/peer_review.html

Here is another from Guidelines for Reviewers of ASM Journals- I read research published in their Applied and Environmental Microbiology relative to the nitrifying bacteria (and Archaea).

Do not discuss the paper with its autho ... directly.

Plos One review policy in no way resembles the above two and more I have looked into as well. While it is common to ask authors to suggest experts qualified to review, this is done in cases where the material is so esoteric if can be difficult to find qualified reviewers. This does not mean such suggestions will be taken, And nowhere else have I seen a policy which permits the authors to reject reviewers. Only Plos One does this as far as i can tell, and that is a big red flag to me.

Yes anonymity does allow idiots to hide, but it does also encourage frank criticism and the reverse is far more insidious. Intimidation of reviewers is much more detrimental and, imo, much more likely at Plos One than getting an arse of a reviewer with an axe to grind is in general.

As I said above, I guess we are just going to have to agree to disagree on this subject.
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Re: Gut microbes in Panaque

Post by racoll » Sun Oct 28, 2012 6:43 pm

TwoTankAmin wrote:I have read the review policies at several sites for different journals as well as those for Plos One. I do not see any similarity in the orientation of the other journals and Plos One
Despite their preferences, the policies are in effect identical: the choice is up to the reviewer. Regarding contacting authors during the review process, that's a separate matter, and although it may not say so specifically on the PLoS ONE Web site, this would be unacceptable at any reputable journal.
TwoTankAmin wrote:anonymity does allow idiots to hide, but it does also encourage frank criticism
It is possible to have frank criticism in an open and constructive fashion. It all depends on how skilful the reviewer is in getting their point across. I agree that anonymity should be an option, however.
TwoTankAmin wrote:While it is common to ask authors to suggest experts qualified to review, this is done in cases where the material is so esoteric if can be difficult to find qualified reviewers
No, this is done routinely by most journals.
TwoTankAmin wrote:nowhere else have I seen a policy which permits the authors to reject reviewers. Only Plos One does this as far as i can tell, and that is a big red flag to me
Again, this is very common policy at many journals. The names given are only recommendations (as are the suggested reviewers). The editor can send the manuscript to the opposed reviewers if they choose (and sometimes they do!).

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Re: Gut microbes in Panaque

Post by racoll » Sun Oct 28, 2012 6:56 pm

If you don't believe me, here are the excerpts from the Web pages from three "proper" journals I have submitted manuscripts to:
Authors must submit, with their manuscripts, names and e-mail addresses of 4 unbiased, expert potential referees who have not previously read the manuscript. Authors may submit names of potential referees that they request not be used and may also request a particular handling editor.
At submission, authors are asked to provide the names and contact details of at least four preferred referees. These should be scientists qualified to provide an independent assessment of the work.
Authors should also use the cover letter to explain their choice of preferred or non-preferred reviewers and editors

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