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Author Topic:   Evolving the Musculoskeletal System
Wounded King
Member (Idle past 142 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 290 of 527 (581759)
09-17-2010 11:52 AM
Reply to: Message 284 by Percy
09-17-2010 8:51 AM


Peer review
I know Koonin's website calls them peer reviews, but those are just reviews. Peer reviews are conducted prior to publication and play a significant role in whether a paper is published, the reviewers are anonymous, and their comments are not made public. Plus Koonin is editor-in-chief of Biology Direct.
What is your problem that you see no shenanigans? Has anyone else here ever cited a paper whose author was also editor-in-chief of the journal that published it? Just you so far, right?
I don't really see any reason to cast aspersions on Biology Direct and its review process. I certainly don't see why you think the review wasn't done before publication or why you consider it not to consititute peer review. It also seems a bit misleading to call it Koonin's website if you mean the Biology Direct site hosted by Biomed Central.
Biology Direct has an open review process because anonymous reviews have their own associated issues and many of the new online open access journals are trying alternative approaches.
How it works is the article's author suggests members of the editorial board that they think would be suitable to review their work. In the interests of openness the reviewer's comments and the author's responses are also published.
One thing I think might have improved this is some comment from the editor who gave the article's publication the go ahead as to how they reached that decision since some of the reviews are pretty critical and Koonin's responses seem more argumentative than anything else. I've drafted arsey responses to reviewer's myself but I get the feeling that when he was writing them Koonin was very aware that these were going to be part of the public record rather than just an internal discussion between himself, the reviewers and the editor. It would also go some way towards obviating concerns, like yours, that one of the joint editors in chief might have been giving an easy ride on a pretty flakey article.
I don't see any problem in general with people publishing in Journals on which they are a senior member of the editorial board, provided they don't handle their own submissions. It seems a bit unfair if someone with an international reputation couldn't publish in Nature because they were also an editor.
TTFN,
WK
P.S. Having opened up this can of worms I may not be able to contribute anything further for a while as I am going to be on holiday for the next 2 weeks.
Edited by Wounded King, : No reason given.

This message is a reply to:
 Message 284 by Percy, posted 09-17-2010 8:51 AM Percy has replied

Replies to this message:
 Message 292 by Omnivorous, posted 09-17-2010 1:01 PM Wounded King has replied
 Message 293 by Percy, posted 09-17-2010 1:11 PM Wounded King has replied

  
Wounded King
Member (Idle past 142 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 309 of 527 (584128)
09-30-2010 2:25 PM
Reply to: Message 292 by Omnivorous
09-17-2010 1:01 PM


Re: Peer review
Do you really think that a review process that entails the author/editor picking his reviewers, knowing that their comments will be made public, will result in as vigorous a review process as anonymous reviews?
Well many review processes ask you to suggest someone people you think would be a suitable reviewers already so as far as 'picking' reviewers goes I think there is already an established element of this.
As to comments being made public, I don't see why it should necessarily change what they say, in some ways this is a reflection of the way the system is organised. Because the reviewers need to be on the editorial board many of them are not in a position to be cowed. These aren't necessarily people just starting out on their research careers who need to avoid treading on the toes of big guns. When Nature and others did some experimental testing of open peer review in the 90's they found that a lot more people refused to review papers when asked, but the editorial board of Biology Direct already know the score and have signed up for it.
I'm not sure why the opportunities for abuse of anonymous review are only occasional and those for reviewer timidity in open review are ever-present. I would have thought that the opportunities are ever present in both cases, but similarly often not pertinent. But the opportunity existing seems to be all you are going on, and I have to say that the reviews for the Koonin paper don't seem all that timid to me.
I certainly think there is room for a diversity of different approaches to editorial review and it certainly doesn't hurt the vigour of scientific research if we don't just limit ourselves to one review model.
TTFN,
WK

This message is a reply to:
 Message 292 by Omnivorous, posted 09-17-2010 1:01 PM Omnivorous has replied

Replies to this message:
 Message 311 by Omnivorous, posted 09-30-2010 4:28 PM Wounded King has not replied

  
Wounded King
Member (Idle past 142 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
Message 310 of 527 (584130)
09-30-2010 2:43 PM
Reply to: Message 293 by Percy
09-17-2010 1:11 PM


Re: Peer review
The key point is that a read of that paper indicates that Koonin thinks "spontaneous formation" of something extremely complex is a necessary prerequisite for life, and he does what creationists do here all the time, make up an incredibly tiny probability out of thin air. My bullshit alarm bells are going off like crazy, and I'm wondering why yours aren't, too.
I'm with Bluegenes on this one, Koonin is grossly overstating the improbability with his 'no-RNA world' scenario and doing so for a specific point. I really doubt for an instant that Koonin considers this any sort of definitive probability calculation for a naturalistic origin of life.
As for the paper, as far as biology goes there is basically nothing there to discuss, I'm not qualified to comment on the physics aspects.
I of course don't know when the paper and reviews were put up at the website, and I made no comment about it, but since the author's comments appear on the reviews, and *not* the other way around with the reviewers comments on the paper, obviously Biology Direct's process is backwards.
I don't see how that follows at all, it would certainly be very confusing to have the main manuscript broken up by 4 different sets of reviewers' comments. The usual process is that a manuscript is submitted, sent out to review, the reviewers send in their comments and then the author responds to those comments and makes any appropriate changes to the manuscript that they and/or the editor considers suitable before publication.
To me the order of manuscript, reviews, responses, seems prefectly natural and when responding to reviewers comments it is quite common to do it on a point by point basis as Koonin does for the more lengthy reviews.
TTFN,
WK

This message is a reply to:
 Message 293 by Percy, posted 09-17-2010 1:11 PM Percy has replied

Replies to this message:
 Message 312 by Percy, posted 09-30-2010 9:13 PM Wounded King has replied

  
Wounded King
Member (Idle past 142 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
Message 314 of 527 (584317)
10-01-2010 10:19 AM
Reply to: Message 312 by Percy
09-30-2010 9:13 PM


Re: Peer review
The reviewers weren't actual peer reviewers making sure that Koonin's paper satisfied scientific criteria prior to publication.
In what way? Because you don't agree with the final editorial decision? The reviewers comments are the basis for an editor to decide if they should publish or not, and if they think it doesn't satisfy the requisite criteria they can say so.
The reviewers were writing reviews that had nothing to do with whether Koonin's paper would be published.
This is an arguable point, Biology Direct's system, does mean that the published comments won't neccessarily directly affect publication, but the reviewers need to have agreed to review the paper in the first place after a first look and have the option of reccommending it not be published.
Their comments had no influence on Koonin's paper.
Koonin does note some changes he made in response to the reviewers comments, including adding extra explanatory material. Even in blind reviews author's can choose to ignore or rebutt some reviewers points
The reviewers were not anonymous.
So?
If this is how things now work in your neck of the scientific woods then you sound like an apologist for a system that has gone badly awry.
Well if you love blind peer review so much why don't you marry it ? But seriously, I don't know why you are so against a bit of heterogeneity in review processes. There are plenty of journals with traditional anonymous peer review, is there really no space in your worldview for any alternative approaches? If the science is bad then it won't be followed up productively and it won't be cited, consequently the journal's impact factor will drop. Biology Direct's current impact factor is 3.3 which isn't bad at all, especially for a journal that is only 4 years old.
Peer review in science doesn't begin and end with getting your work published, it is an ongoing process of re-evalution by an entire community of related researchers. I expect to have to explain this to creationists who seem to think that the fact their favourite apologist got something published in a peer reviewed journal once upon a time confers upon them some sort of infallibility, but I'm a bit surprised you seem to see the journal's review process as the be all and end all.
TTFN,
WK

This message is a reply to:
 Message 312 by Percy, posted 09-30-2010 9:13 PM Percy has replied

Replies to this message:
 Message 316 by Percy, posted 10-01-2010 12:06 PM Wounded King has replied

  
Wounded King
Member (Idle past 142 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
(1)
Message 317 of 527 (585156)
10-06-2010 8:13 AM
Reply to: Message 316 by Percy
10-01-2010 12:06 PM


Re: Peer review / topic drift
Hi Percy,
You just make a whole lot of assertion's here without anything to back them up.
What you're really asking is why I'm pointing out the flaws in an inferior process
Well I would like to know what evidence you have that it is an inferior process.
Koonin's paper would have been very unlikely to receive any serious consideration by a reputable journal
Well I would contest your assertion that Biology Direct is not a reputable journal, but that aside how do you know this? Are you saying flakey or sub-par articles don't get published with blind peer review? You should come to one of our lab meetings for a journal club some time, half the time is spent with the PIs saying what a load of shit the research is and how it wasn't worth publishing.
I've often thought the whole Penrose-Hammeroff quantum microtubule model for consciousness was an unneccessary load of tosh, but I don't neccessarily think the journals that published their papers were promoting inferior science.
and that appendix in particular would likely have received considerable critical attention.
You still seem to think that those calculations in the appendix are something Koonin is putting forward as a genuine scenario, did you miss where he said ...
Koonin writes:
The model considered here is not supposed to be realistic by any account. It only serves to illustrate the difference in the demands on chance for the origin of different versions of the breakthrough system (see Fig. 1) and hence the connections between these versions and different cosmological models of the universe.
Koonin clearly doesn't think this is how abiogenesis occured, nor does he claim that any of his assumed values are accurate. All he is postulating is that in a many worlds scenario spontaneous assembly could produce a number of functional replicating systems whose origination in a single universe would be vastly improbable.
You're advocating the weakening of the first line of defense against inferior science.
No, I'm suggesting that just because you think blind peer review is essential to the integrity of the process doesn't mean that it is.
In the absence of reviews from another journal for the same article there really isn't any way to settle what would or wouldn't have happened to it. Would it have got into Nature? Absolutely not. Would it have got into Theoretical Biology? Quite possibly.
You think that the reviews in Biology Direct are substantially different from anonymous reviews for other journals, but I'm not quite sure why.
I've had reviews back that I wouldn't consider any harsher than those, and I've had papers published even though one of the reviewers might have suggested it wasn't suitable for the journal.
Closed Peer Review is a black box and we really don't know what an article being published really means. All the reviewers could have said it was shit and the editor still decide to publish it. In a small field authors can often work out who a reviewer is, or at least they convince themselves that they do, because they are familiar with their work, interests and writing style ( that's if the review isn't already stuffed full of suggestions that they cite the reviewer's own research, which is not unheard of).
Don't you think things might have been clearer in the Meyer/Sternberg/PBSW affair if we could actually see what the reviewers had said about the paper?
I agree that the proliferation of many principally online journals over the last few years, especially in the biological sciences, means that there will be many more papers published and since the quality will vary more lower quality papers must be getting published. The question is what determines that evaluation of quality and does the open or closed nature of peer review make a difference.
A paper not being good enough for Nature or Cell isn't a new problem. Many papers go through a cycle of trying journals with successively lower impact factors until they hit one where they get published.
Most of these new journals don't have an open peer review process. That doesn't mean that more lower quality papers won't still be published in them. The journal's need to produce issues and there isn't an endless steady stream of top quality research.
TTFN,
WK
P.S. Maybe Peer review issues need their own thread, not that anyone seems to be saying anything much about the musculoskeletal system anyway.
Edited by Wounded King, : Removed grocers' apostrophe

This message is a reply to:
 Message 316 by Percy, posted 10-01-2010 12:06 PM Percy has replied

Replies to this message:
 Message 318 by Percy, posted 10-06-2010 9:08 AM Wounded King has replied

  
Wounded King
Member (Idle past 142 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
Message 320 of 527 (585163)
10-06-2010 10:27 AM
Reply to: Message 318 by Percy
10-06-2010 9:08 AM


Re: Peer review / topic drift
Hey,
Peer review is when an editor sends out anonymous copies of papers to other researchers in the same field to assess quality, validity and suitability. The feedback is addressed to the authors of the paper, not to the future readers.
Take out the word anonymous and essentially this is no different from what happens at Biology Direct, although very few journals use double blind peer review now. The reviewers make this assessment and if they don't think it suitable they refuse to review it, if they think it is pseudosicence then they notify the editor.
I haven't submitted a paper outside corporate in a while, but perhaps today the process is automated through websites.
It is, and what you tend to get back are often reviews not disimilar to those in Biology Direct, though I'll admit shorter than the first 2, and they tend to be directed to the editors rather than the authors or at least only indirectly to the authors.
Peer review is provided for the benefit of editors to help them in the review process, and for the authors of the papers so they can make changes/improvements.
Biology Direct's process does both those things.
They are short and pointed.
This is definitely variable.
They are private.
But that isn't a necessary defining characteristic of 'Peer review', that just happens to be how it is commonly done.
Are you actually receiving 3000 word anonymous peer reviews?.
I can't say I have word counted any recently, but I doubt I have had any quite that long. That said the length is the only distinction, I've certainly had reviews that were not just bullet point lists of issues but also discussions of the themes and conclusions of the paper. Also looking at other papers' reviews on Biology Direct the very long ones seem unusually long for that journal, compare the comments here for example.
We should obviously seek improvements, and the open journals represent experiments in this direction, but each thing we try must be assessed as to whether it is actually an improvement, and the evidence for open journals thus far seems to indicate an increase in quantity and a decrease in quality.
Do you mean open access, of which there are a growing number, or open review, of which there are very few? If you are talking about the review process I'd be interested in you finally providing some evidence for this decrease in quality and how you measured it.
I still find it hard to see what you find so objectionable about Koonin's paper? Is it worse than Maresca and Schwartz which got through more traditional peer review? When Schwartz turned up here you (Message 39) , interestingly, likened his hypothesis to that of Hameroff quoting Lawrence Krauss' response, "I think everything you say is nonsense. And maybe I'm being too polite."
If it is the calculations then you are making a fuss about nothing. No one except maybe creationists think the calculations are supposed to reflect the real world. I think Koonin makes a valid point about the IDist creationist faction when he notes ...
Koonin writes:
The possibility that the ID crowd interprets this paper as support for their cause is one of Bapteste's main concerns. Will they, actually? No doubt they will! However, the only way to prevent them from doing so is to stop publishing research on any hard problem in evolutionary biology and somehow declare these problems solved. The ID folks do no research themselves, so they apply all their considerable intellectual resources to turn published scientific work upside down and claim support for ID (it happened to several seemingly innocuous papers of mine, to my considerable amusement). I believe evolutionary biologists should not and actually can not worry about this, only about their own papers being correct and coherent.
Don't we see here time and again how creationists/IDists will constantly misunderstand and misinterpret any research to fit their preconceptions, all you have to do is look at Barbara's constant stream of ill informed wrongness or pretty much any other IDist creationist we have ever had here.
TTFN,
WK

This message is a reply to:
 Message 318 by Percy, posted 10-06-2010 9:08 AM Percy has seen this message but not replied

Replies to this message:
 Message 322 by barbara, posted 10-06-2010 12:03 PM Wounded King has replied

  
Wounded King
Member (Idle past 142 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
Message 323 of 527 (585183)
10-06-2010 12:22 PM
Reply to: Message 322 by barbara
10-06-2010 12:03 PM


Re: Peer review / topic drift
How interesting that Koonin wrote that creationists will misunderstand what he is actually stating in his findings.
And apparently how accurate.
I read his papers [...]
What all of them?
and most of them do support creationist thought process.
If by support you mean, are open to miinterpretation I am sure you are right, maybe we should start a Koonin specific thread and you can tell us about the research of this new accidental ID/creationist luminary.
He wanted his paper published and he knew that writing it the way he did would get the public's attention.
I doubt the public at large gave two hoots about it.
However still providing their conclusions even though they know they shouldn't do this.
Researchers shouldn't draw conclusions? Well I guess that is consistent since most IDists/creationists don't even seem to think being a researcher should actually entail genuine research in the first place.
Eventually all of these papers somehow get published as facts in scientific books to educate young people and the bullshit continues.
It certainly does Babs, every time that you post.
TTFN,
WK

This message is a reply to:
 Message 322 by barbara, posted 10-06-2010 12:03 PM barbara has not replied

  
Wounded King
Member (Idle past 142 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 521 of 527 (600359)
01-14-2011 5:58 AM
Reply to: Message 520 by Dr Adequate
01-13-2011 11:45 PM


Re: living transitional skeletons
I think the consensus is that sharks are descended from bony fish.
I think the term bony fish might be a bit confusing here. Do you mean teleostomi, the actual group known as bony fish? Or do you mean fish which had some bony structures like placoderms or agnathans?
If you are saying that chondricthyes, including sharks, evolved from teleosts then that is pretty contrary to what I understood to be the case.
TTFN,
WK

This message is a reply to:
 Message 520 by Dr Adequate, posted 01-13-2011 11:45 PM Dr Adequate has replied

Replies to this message:
 Message 524 by Dr Adequate, posted 01-14-2011 7:03 AM Wounded King has not replied

  
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