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Is peer review a “sacred cow”?

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Ready “to be slaughtered”? Asks David Gorski at Science-based Medicine:

It seems to me that, at the very minimum, the era of asking scientists for suggestions for peer reviewers for their own manuscripts must end. The reasons why many (but by no means all) journals have done so for so many years are quite understandable but no longer defensible in the wake of these damaging and large scale incidents of self-peer review fraud. This practice must stop, even at the price of more work for already harried editors. One technological solution that might help would be a database of peer reviewers, each with his or her relevant field of expertise listed, as well as collaborators and those with whom they’ve published, so that editors can know not to send a manuscript to an author’s friend or collaborator for review. In the wake of these scandals, it might even be profitable for a company to develop such a database and sell access to publishers. Lacking a system like this, it will fall on the shoulders of editors to be more careful and to pick peer reviewers themselves, rather than using any recommendations by authors submitting manuscripts.

He provides an interesting summary of ways researchers defeat the system, also noting

Certainly, one problem is that, as much as we scientists want to do a good job at peer review, the fact remains that peer review is unpaid and, from an academic standpoint, doesn’t really contribute much to our career advancement. For instance, when going up for promotion, assistant professors do have to show evidence of scholarly activity, such as peer review, but peer review is of low value in that equation compared to other activities. More.

Hmmm. One wonders if there is an unofficial separate system of reward in that case, for desired peer reviews. We’ll call it “brownie points.” That might explain something.

Peer reviews are not, in any event, likely to be better than the peers, and Gorski’s summary does not fill one with confidence.

“Science-based” is a good thing, but conventional honesty and transparency are even better ones.

See also: If peer review is working, why all the retractions?

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Paul, they did publish at least one correction, to do with an error on graph axes. I can't find it now though, so maybe some-one went back and corrected the original article. Roy
paul sussman @5
It is a sign that it is working.
The post @1 (here in this thread) seems to show that something failed with the peer-review, doesn't it? Please, would you mind commenting on that? Can you answer the questions posted @1? Thanks. Dionisio
bornagain at 2, yes, I noticed that. Got 32 visits today as a result. Can you get the fellow to attack us more often? Anyone got any influence with him? - d. News
Obviously, peer review isn't perfect, and it can be abused, but it is still better than publishing in popular media (books, magazines, etc. ). There are all sorts of books that pretend to be about science, but publishers are only interested in one thing. Sales. Retractions and corrections are not a sign that the system is not working. It is a sign that it is working. I would be leary of any journal that does not have a history of publishing corrections and retractions. I have been reading through the articles in Bio-complexity and I have noticed that they have never published a correction or a retraction. And it appears that many of the articles are published by the editors and others listed as being responsible for the journal. The optics of this are obviously not good. paul sussman
jimmontg, "You would think something so stupendous as this would be at the forefront of the news except of course for what it points too, or maybe I should say Who?" You would think. I have no idea why so many supposedly smart people in science, from biology to cosmology, would 'suppress the truth'. Paul calls them fools for doing so:
Romans 1:18-22 For the wrath of God is revealed from heaven against all ungodliness and unrighteousness of men, who by their unrighteousness suppress the truth. For what can be known about God is plain to them, because God has shown it to them. For his invisible attributes, namely, his eternal power and divine nature, have been clearly perceived, ever since the creation of the world,[a] in the things that have been made. So they are without excuse. For although they knew God, they did not honor him as God or give thanks to him, but they became futile in their thinking, and their foolish hearts were darkened. Claiming to be wise, they became fools, https://www.biblegateway.com/passage/?search=Romans+1%3A18-22&version=ESV
To #2 BA I read and saw this same thing on another website that I just cannot remember. It showed the diagrams and data that you are talking about. I think it had something to do with "The Principle". You would think something so stupendous as this would be at the forefront of the news except of course for what it points too, or maybe I should say Who? I wished I could remember where I saw the reference to this. It had some other things about anomalies to some thoughts on the Big Bang. My memory just isn't what it used to be, especially if I have things that have to get done like now the 23rd of Dec. and 20+ people to help cook for. 10 lbs. mashed potatoes, at least 1 1/2 gallons of gravy and two green bean casseroles. That's just my part, so excuse me while I get to peeling. jimmontg
News, this is interesting. The first two sentences of your link read as such:
"I’ve frequently noted that one of the things most detested by quacks and promoters of pseudoscience is peer review. Creationists hate peer review."
He has the word Creationists hyper-linked. Clicking the link to Creationists, this is the article that pops up:
Breaking the Peer-Review Barrier - William Dembski - June 6, 2006 Excerpt: Look at the following abstract of a paper posted today at astro-ph:
Message in the Sky S. Hsu, A. Zee To appear in Mod.Phys.Lett.A http://xxx.lanl.gov/abs/physics/0510102 ABSTRACT: We argue that the cosmic microwave background (CMB) provides a stupendous opportunity for the Creator of our universe (assuming one exists) to have sent a message to its occupants, using known physics. Our work does not support the Intelligent Design movement in any way whatsoever, but asks, and attempts to answer, the entirely scientific question of what the medium and message might be IF there was actually a message. The medium for the message is unique. We elaborate on this observation, noting that it requires only careful adjustment of the fundamental Lagrangian, but no direct intervention in the subsequent evolution of the universe.
There was a small flurry of interest when the first submitted version of the paper was posted some months ago. You can download the paper and previous versions at the link above. Note especially how the statement about ID was inserted in the latest version. The abstract to version 1 reads:
ABSTRACT: We argue that the cosmic microwave background (CMB) provides a stupendous opportunity for the Creator of our universe (assuming one exists) to have sent a message to its occupants, using known physics. The medium for the message is unique. We elaborate on this observation, noting that it requires only careful adjustment of the fundamental Lagrangian, but no direct intervention in the subsequent evolution of the universe.
No doubt, the referee and possibly journal editor required that that statement be inserted before the paper was accepted for publication,,, https://uncommondesc.wpengine.com/intelligent-design/breaking-the-peer-review-barrier/
The interesting thing is is that since 2006 anomalies have been discovered in the cosmic microwave background (CMB) that empirically overturn the Copernican principle, which is the belief that the earth and humans have no privileged position in the universe.
Why is the solar system cosmically aligned? BY Dragan Huterer - 2007 The solar system seems to line up with the largest cosmic features. Is this mere coincidence or a signpost to deeper insights? Caption under figure on page 43: ODD ALIGNMENTS hide within the multipoles of the cosmic microwave background. In this combination of the quadrupole and octopole, a plane bisects the sphere between the largest warm and cool lobes. The ecliptic — the plane of Earth’s orbit projected onto the celestial sphere — is aligned parallel to the plane between the lobes. http://www-personal.umich.edu/~huterer/PRESS/CMB_Huterer.pdf Here is the actual graph of the alignment from the Huterer 2007 paper (worth a thousand words): http://i44.servimg.com/u/f44/16/14/18/96/axis_o10.jpg
Of note: The preceding article was written before the Planck data (with WMPA & COBE data), but the multipoles were, as the Planck video indicated, actually verified by Planck. Here is one of the papers which confirm Huterer's 2007 paper:
Large-scale alignments from WMAP and Planck – 2013 We revisit the alignments of the largest structures observed in the cosmic microwave background (CMB) using the seven and nine-year WMAP and first-year Planck data releases. The observed alignments — the quadrupole with the octopole and their joint alignment with the direction of our motion with respect to the CMB (the dipole direction) and the geometry of the Solar System (defined by the Ecliptic plane) — are generally in good agreement with results from the previous WMAP data releases.,,, both the WMAP and Planck data confirm the alignments of the largest observable CMB modes in the Universe. http://arxiv.org/abs/1311.4562
At the 13:55 minute mark of the following video, Max Tegmark, an atheist, finally admits, post Planck 2013, that the CMBR data does indeed line up with the earth and solar system
"Thoughtcrime: The Conspiracy to Stop The Principle" - video https://www.youtube.com/watch?feature=player_detailpage&v=0eVUSDy_rO0#t=832
Once again, what is curious about these 'anomalies', (that cannot be explained by the 'simple' inflation model of materialists), is that the earth lines up with these anomalies:
What Is Evil About The Axis Of Evil? - February 17, 2015 The Cosmic Microwave Background (CMB) Radiation contains small temperature fluctuations. When these temperature fluctuations are analyzed using image processing techniques (specifically spherical harmonics), they indicate a special direction in space, or, in a sense, an axis through the universe. This axis is correlated back to us, and causes many difficulties for the current big bang and standard cosmology theories. What has been discovered is shocking. Two scientists, Kate Land and João Magueijo, in a paper in 2005 describing the axis, dubbed it the “Axis of Evil” because of the damage it does to current theories, and (tongue in cheek) as a response to George Bush’ Axis of Evil speech regarding Iraq, Iran and, North Korea. (Youtube clip on site) In the above video, Max Tegmark describes in a simplified way how spherical harmonics analysis decomposes the small temperature fluctuations into more averaged and spatially arranged temperature components, known as multipoles. The “Axis of Evil” correlates to the earth’s ecliptic and equinoxes, and this represents a very unusual and unexpected special direction in space, a direct challenge to the Copernican Principle. http://www.theprinciplemovie.com/evil-axis-evil/
Moreover, the light from the CMB is found to be fine-tuned for intelligent life like humans to discover it:
The Fine-Tuning for Discoverability - Robin Collins - March 22, 2014 Excerpt: In every case that I was able to make calculations regarding whether the fundamental parameters of physics are optimized in this way, they appear to pass the test.,,, The most dramatic confirmation of the discoverability/livability optimality thesis (DLO) is the dependence of the Cosmic Microwave Background Radiation (CMB) on the baryon to photon ratio.,,, ...the intensity of CMB depends on the photon to baryon ratio, (??b), which is the ratio of the average number of photons per unit volume of space to the average number of baryons (protons plus neutrons) per unit volume. At present this ratio is approximately a billion to one (10^9) , but it could be anywhere from one to infinity; it traces back to the degree of asymmetry in matter and anti - matter right after the beginning of the universe – for approximately every billion particles of antimatter, there was a billion and one particles of matter.,,, The only livability effect this ratio has is on whether or not galaxies can form that have near - optimally livability zones. As long as this condition is met, the value of this ratio has no further effects on livability. Hence, the DLO predicts that within this range, the value of this ratio will be such as to maximize the intensity of the CMB as observed by typical observers. According to my calculations – which have been verified by three other physicists -- to within the margin of error of the experimentally determined parameters (~20%), the value of the photon to baryon ratio is such that it maximizes the CMB. This is shown in Figure 1 below. (pg. 13) It is easy to see that this prediction could have been disconfirmed. In fact, when I first made the calculations in the fall of 2011, I made a mistake and thought I had refuted this thesis since those calculations showed the intensity of the CMB maximizes at a value different than the photon - baryon ratio in our universe. So, not only does the DLO lead us to expect this ratio, but it provides an ultimate explanation for why it has this value,,, This is a case of a teleological thesis serving both a predictive and an ultimate explanatory role.,,, http://home.messiah.edu/~rcollins/Fine-tuning/Greer-Heard%20Forum%20paper%20draft%20for%20posting.pdf
Thus perhaps it is better to say that despite the prejudice of humans inherent in peer-review, peer-review, none-the-less, still works because it is, despite the inherent prejudice, still ultimately empirically driven by the evidence. as to this comment from the article Dr. Dembski referenced:
"cosmic microwave background (CMB) provides a stupendous opportunity for the Creator of our universe (assuming one exists) to have sent a message to its occupants"
And that message from the CMB is turning out to be that, contrary to popular belief, the earth and humans do indeed have some sort of significance that was planned since the beginning of time. Verse:
Genesis 1:1 In the beginning God created the heaven and the earth.
The paper referenced @1413 in the thread https://uncommondesc.wpengine.com/intelligent-design/mystery-at-the-heart-of-life/#comment-593218 seems to have an error in the conclusion. On the first eight pages the term "post-translational modifications (PTMs)" (both plural and singular) seems to appear around 10 times. The term "post-transcriptional modifications" doesn't seem to be mentioned even once. However, on the ninth page the "Conclusion" refers to "post-transcriptional modifications (PTMs)" instead. That seems like an error, doesn't it? If that's the case, then how did that error pass the review? How did it go unnoticed by the reviewers? Maybe that's not an error after all? Can someone read it and tell us whether that's an error or not? Thanks. BTW, note the article shows who reviewed the given paper and how long it took them to review it. Dionisio

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