Evolving the Musculoskeletal System

I focused on the peer review process. Naturally I didn't mention the whole rest of the scientific process. If you want to misrepresent my understanding of it then posture away, I'll ignore it from here on.I stand by what I said about the process you're defending devaluing publication. What you're really asking is why I'm pointing out the flaws in an inferior process. Koonin's paper would have been very unlikely to receive any serious consideration by a reputable journal, and that appendix in particular would likely have received considerable critical attention. You're advocating the weakening of the first line of defense against inferior science.--Percy

Hi Percy,You just make a whole lot of assertion's here without anything to back them up. Well I would like to know what evidence you have that it is an inferior process. 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. 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 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. 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,WKP.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

Hi WK,We could go back and forth on this forever. You think my opinion is unwarranted by the facts available to me, and I disagree. I already told you what aspects of the process led me to call it inferior, and nothing you've said changes my mind.There was one thing you said that I found surprising: It almost feels like we're not talking about the same thing. 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.Based upon the feedback editors will either accept the paper, or request changes/improvements, or reject the paper. In the old days I would get back marked up photocopies of our paper where our author information had been blacked out. Later we would receive sanitized email feedback of a few paragraphs. I haven't submitted a paper outside corporate in a while, but perhaps today the process is automated through websites.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. They are short and pointed. They are private.You seem to be talking about something more like a book review or a movie review, which are after the fact and don't affect content or quality. In fact, those reviews of Koonin's paper (the first one was 3000 words) were longer and more detailed than most book and movie reviews (excluding magazines like the New Yorker). When you said that those reviews were not "substantially different from anonymous reivews for other journals," were you referring to the same type of peer review I am? Are you actually receiving 3000 word anonymous peer reviews?I'm not opposed to experimenting with the peer review process, but I think Koonin's paper is an excellent example of what can go wrong when it is weakened. The traditional peer review process has served us very well. 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.But as you say, this is inevitable anyway given the nature of the Internet. Of course, the members of any field know which are the good and bad journals, but everyone else not so much, and creationists not at all. As far as they're concerned, if it was published in a "peer reviewed" journal then it must be science.--Percy

Hi, Percy. While I favor the "traditional" peer review system, I'm kind of leaning towards WK's position on this.The Journal of Biogeography ("traditional" review system, impact factor > 3.5 over the last three years) published a Schwartz paper claiming that humans are more closely related to orangutans than chimpanzees. It was explicitly based on the assertion that molecular phylogenetics is less robust than morphological phylogenetics. Here is the paper.Incidentally, the journal published a disclaimer (actually called an "editorial") stating that the paper didn't really convince the reviewers, but that the editorial staff felt it was still worth putting out there for scientific scrutiny, at least in part because of the publicity it would probably receive.I think it would need a much more in-depth analysis than I think you've actually done to say whether Biology Direct's review process results in inferior science getting through.

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-Bluejay (a.k.a. Mantis, Thylacosmilus)Darwin loves you.

Hey, 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. 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. Biology Direct's process does both those things. This is definitely variable. But that isn't a necessary defining characteristic of 'Peer review', that just happens to be how it is commonly done. 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. 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 ... 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

If by "say" you mean "conclude," then I agree. As I said earlier, Koonin's cockamamie paper combined with the odd peer review process and the fact that he's the co-editor has all my alarm bells going off. I don't claim to have made an in-depth analysis, but I did see enough to form an opinion.--Percy

How interesting that Koonin wrote that creationists will misunderstand what he is actually stating in his findings. I read his papers and most of them do support creationist thought process. Since he already knew it when he wrote it perhaps he should have presented it using different words to explain it. I see this as manipulative on his part and it was deliberate. He wanted his paper published and he knew that writing it the way he did would get the public's attention. Presentation is better than content which translates to I will just bullshit a great story because after all nobody really understands or cares about the content.Information via the web is indicating many scientists do not share the same opinion or produce the same results on repeated studies. Often the journals indicate that the models used are not accurate because the data is no longer true or is incomplete yet to make a new model. However still providing their conclusions even though they know they shouldn't do this. Eventually all of these papers somehow get published as facts in scientific books to educate young people and the bullshit continues.

And apparently how accurate. What all of them? 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. I doubt the public at large gave two hoots about it. 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. It certainly does Babs, every time that you post.TTFN,WK

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I don't think you're stupid. I think you're ignorant. Ignorance is fixable; you just have to go and learn stuff.
  —Mr Jack

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Oh believe me he's definitely not ignorant. Edited by Flatland, : No reason given.

How does entropy work in evolution?

Living and reproducing is not 100% efficient work, thus if one does these things, it results in a net increase of entropy in the universe.

The same way it does it absolutely anything else. Do you mean how does the 2nd law of thermodynamics relate to evolution? In which case: it allows biological organisms to work at all.

Entropy increases with diversity and complexity.A completely uniform system has low entropy. A very complex and diverse system has higher entropy.

Organisms increase the entropy in a chemical system to produce the energy they need to live.

Actually, any work is not 100% efficient resulting in a net increase of entropy in the universe, right? I mean, entropy is not specific to living organisms.