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Author Topic:   Journal Watch: How Could They Print/Not Print That?
Omnivorous
Member (Idle past 1045 days)
Posts: 3808
From: Adirondackia
Joined: 07-21-2005


Message 1 of 18 (582452)
09-21-2010 12:45 PM


To paraphrase Art Linkletter, sometimes science journals print the darndest things.

With some regularity, we come across instances where creationist points of view are published in peer-reviewed journals despite the lack of data or analysis. We also hear complaints from creationists about their inability to persuade peer-reviewed journals to publish their papers. Often these cases are discussed tangentially in other threads, and we see neither the controversy fully unfolded nor its resolution.

I'd like this thread to track those cases as they arise, allowing us to ascertain what facts we can about the circumstances and then to discuss issues of peer review, bias, editorial judgment, etc. I think it would be particularly useful not only to learn about controversial cases but also to track them with updates, and perhaps sift out some common elements.

For our delectation, from the Virology Journal: "Influenza or not influenza: Analysis of a case of high fever that happened 2000 years ago in Biblical time".

Tara C. Smith, an assitant professor of etiology, provides a concise summary in her Aetiology blog:

quote:

Now, regular readers will know that I normally love this type of thing; digging back through history to look at Lincoln's smallpox; Cholera in Victorian London; potential causes of the Plague of Athens, the origin of syphilis, or whether Yersinia pestis really caused the Black Plague. I've even written a bit about the history of influenza. So analysis of a 2000-year old potential flu case? Bring it on.

But. For Christ's sake (really), *bring the evidence with you.* From the article's abstract:

The Bible describes the case of a woman with high fever cured by our Lord Jesus Christ. Based on the information provided by the gospels of Mark, Matthew and Luke, the diagnosis and the possible etiology of the febrile illness is discussed. Infectious diseases continue to be a threat to humanity, and influenza has been with us since the dawn of human history. If the postulation is indeed correct, the woman with fever in the Bible is among one of the very early description of human influenza disease.

Infectious diseases continue to be a threat to humanity, and influenza has been with us since the dawn of human history. We analysed a case of high fever that happened 2000 years ago in Biblical time and discussed possible etiologies.

OK, so they set up their premise. Fine, I'm on board with that, though it's obviously always a bit of a problem when using English translations of the Bible. Still, I'm all about checking out the descriptions, which include a high fever, being bed-ridden, and, oh yeah, that Jesus cured her, upon which time she "rose up and ministered unto them."

That's the extent of the information.

From this, the authors conclude that the fever must have been influenza. Their rationale? Well, they exclude bacterial septicemia because "the fever retreated instantaneously. This implies that the disease was probably not a severe acute bacterial infection (such as septicemia) or subacute endocarditis that would not resolved [sic] instantaneously."

Seriously. I'm not even sure what to do with this. From the wording of the abstract, it very much appears that the authors are Christians--so are they saying that Jesus could not have miraculously cured a bacterial infection, but he could have done so for flu? Or that the flu, on its own, resolved the instant Jesus stood over/touched the ill woman, without any divine intervention?


In the comment section at Prof. Smith's blog, Virology Journal's editor-in-chief responds:

quote:
As Editor-in-Chief of Virology Journal I wish to apologize for the publication of the article entitled ''Influenza or not influenza: Analysis of a case of high fever that happened 2000 years ago in Biblical time”, which clearly does not provide the type of robust supporting data required for a case report and does not meet the high standards expected of a peer-reviewed scientific journal. Virology Journal has always operated an exceptionally high standard of thorough peer review; this article has clearly not met these thresholds for balance and supporting data and as such, the article will be retracted. I should like to apologize for any confusion or concern that this article may have caused among our readership, or more widely.

Whilst only ever intended as an opinion piece and also a bit of relief from the ‘normal’ business of the journal, the speculations contained within this article clearly would be better expressed outside the confines of a peer-reviewed journal. Biomed Central does not support any views outlined in this article.

Posted by: Robert F. Garry, PhD


So was this a case of a casual "bit of relief" being taken too seriously by its detractors?

Should peer review (apparently it was recommended by 2 of 2 reviewers at this BioMed journal) have prevented publication?

Were the authors naively engaging in a bit of historical speculation (Did arsenic kill Napoleon?) and science guys are overreacting--or were they sneaking the creationist camel's nose into the scientific tent?

I'd say either Creation/Evolution in the News or Is It Science?

NB: I follow her blog, and you should, too.


Dost thou prate, rogue?
-Cassio

Real things always push back.
-William James


Replies to this message:
 Message 2 by Adminnemooseus, posted 09-21-2010 2:18 PM Omnivorous has responded
 Message 6 by Wounded King, posted 10-12-2010 10:38 AM Omnivorous has responded

    
Adminnemooseus
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Posts: 3879
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Message 2 of 18 (582476)
09-21-2010 2:18 PM
Reply to: Message 1 by Omnivorous
09-21-2010 12:45 PM


Let's focus on one article
I'd like this thread to track those cases as they arise, allowing us to ascertain what facts we can about the circumstances and then to discuss issues of peer review, bias, editorial judgment, etc. I think it would be particularly useful not only to learn about controversial cases but also to track them with updates, and perhaps sift out some common elements.

A big part of the "Proposed New Topic" (PNT) process is to have focus in the message 1. That at least gives us a starting point to try to have focus in the topic as a whole.

I'd like to discuss the one individual case first. Perhaps we can diversify the topic later, or start new topics for new articles. What you are proposing will result in a jumble of messages as new articles are introduced but older messages are still responded to.

Please modify your message 1, including having a specific relevant topic title. When done, please post a "changes done" type response to this message.

Adminnemooseus


New Members should start HERE to get an understanding of what makes great posts.

Report a problem etc. type topics:
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Admin writes:

It really helps moderators figure out if a topic is disintegrating because of general misbehavior versus someone in particular if the originally non-misbehaving members kept it that way. When everyone is prickly and argumentative and off-topic and personal then it's just too difficult to tell. We have neither infinite time to untie the Gordian knot, nor the wisdom of Solomon.

There used to be a comedian who presented his ideas for a better world, and one of them was to arm everyone on the highway with little rubber dart guns. Every time you see a driver doing something stupid, you fire a little dart at his car. When a state trooper sees someone driving down the highway with a bunch of darts all over his car he pulls him over for being an idiot.

Please make it easy to tell you apart from the idiots. Message 150


This message is a reply to:
 Message 1 by Omnivorous, posted 09-21-2010 12:45 PM Omnivorous has responded

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Omnivorous
Member (Idle past 1045 days)
Posts: 3808
From: Adirondackia
Joined: 07-21-2005


Message 3 of 18 (582480)
09-21-2010 2:33 PM
Reply to: Message 2 by Adminnemooseus
09-21-2010 2:18 PM


Thanks but no thanks.
Well, with all due respect, your proposed changes would eviscerate my intentions for the thread--focus is good, but not when it narrows so much we miss the larger view.

Nor do I see the single case in hand as being weighty enough to carry a thread on its own.

I appreciate the thoughtful sincerity of your response, but...never mind.

No harm, no foul: I enjoyed the process.


Dost thou prate, rogue?
-Cassio

Real things always push back.
-William James


This message is a reply to:
 Message 2 by Adminnemooseus, posted 09-21-2010 2:18 PM Adminnemooseus has acknowledged this reply

    
Admin
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Posts: 12579
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Joined: 06-14-2002
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Message 4 of 18 (585677)
10-09-2010 9:20 AM


Wounded King requested promotion of this thread in his Message 306, and Adminnemooseus seems to be otherwise occupied at present, so I'll promote this thread to Is It Science? and we'll see how it goes. I understand the concern about the potential to end up discussing any and all topics related to the creation/evolution controversy, and so I request that the participants keep the primary focus on issues regarding the publication process rather than the topics of the papers themselves.

I believe Wounded King wanted to include this paper by Eugene V. Koonin in the discussion: The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life. There was some discussion about it in the Evolving the Musculoskeletal System thread, probably the best place to begin is with my deprecating comments as Percy in Message 279 and read the message chain forward.


--Percy
EvC Forum Director

    
Admin
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Message 5 of 18 (585679)
10-09-2010 9:21 AM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Journal Watch: How Could They Print/Not Print That? thread in the Proposed New Topics forum.
    
Wounded King
Member (Idle past 2172 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 6 of 18 (586278)
10-12-2010 10:38 AM
Reply to: Message 1 by Omnivorous
09-21-2010 12:45 PM


I figured that before I start derailing your thread with my own examples I would address the one you give in the OP.

In terms of whether this was a "bit of relief" and solely an opinion piece, I can't see any reason why a reader should conclude this other than the article's daftness. As Tara Smith's comment pointsout, historical case studies are far from unheard of so I don't see why the editor felt that such a format should be treated as a joke.

Should peer review ... have prevented publication?

Frankly I'm surprised it ever got off the editor's desk. Having said that, a brief google on case studies of fictional characters brought up one for Anakin Skywalker which is equally short, and I would suggest daft, although arguably it has a more substantial body of evidence to discuss.

As to the authors intent; I don't think one has to look for a creationist agenda, as such, but they certainly seem to be coming to the case from a christian viewpoint, i.e. 'our lord Jesus Christ', and possibly a literalist one, although as I say case studies of fictional characters are not unknown.

*ABE*On the Retraction watch blog they have a comment from one of the authors who says that it was originally only supposed to be a piece in the debate section, which seems a bit better, but only a bit.*/ABE*

TTFN,

WK

Edited by Wounded King, : No reason given.


This message is a reply to:
 Message 1 by Omnivorous, posted 09-21-2010 12:45 PM Omnivorous has responded

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Omnivorous
Member (Idle past 1045 days)
Posts: 3808
From: Adirondackia
Joined: 07-21-2005


Message 7 of 18 (586286)
10-12-2010 10:55 AM
Reply to: Message 6 by Wounded King
10-12-2010 10:38 AM


Hi, WK: I don't think moving on immediately to another case will derail the thread at all. That is expressly what I want--opportunities to compare and contrast the merits of all perspectives on these controversies.

I chose the example in the OP precisely because it was so daft: as Tara Smith points out, its internal contradictions alone keep us from taking it seriously--the authors posit a miraculous cure, then attempt to diagnose the malady based on normal, non-miraculous clinical expectations.. I had hoped that even creationist critics of peer-reviewed journals could agree that this odd paper has no place in peer-reviewed journals, and we could move on to other examples they/we find less clear-cut.

OTOH, one hears, "What harm does it do?" to defend such material, citing entertainment value, stimulus of the imagination, etc. That seems fairly simple-minded to me, since displacing more rigorous pages is reason enough to avoid daffy fluff that fails on its own terms, and, to my mind, nothing stimulates the imagination like good science.

However, we seem to have no defenders for the paper, so perhaps my attempt to provoke discussion erred on the side of daftness.

Please do bring another case. I think we can enjoy a finer analysis with multiple cases of all sorts.

AbE: I realize the paper is not expressly creationist.

Edited by Omnivorous, : add


Dost thou prate, rogue?
-Cassio

Real things always push back.
-William James


This message is a reply to:
 Message 6 by Wounded King, posted 10-12-2010 10:38 AM Wounded King has not yet responded

    
Wounded King
Member (Idle past 2172 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 8 of 18 (586293)
10-12-2010 11:55 AM


How about a another pretty clear example: BIO-Complexity
I think another pretty clear example where we should almost all be able to agree that the trappings of peer review are being used as a creationist fig leaf is an article recently discussed on Panda's Thumb.

The Case Against a Darwinian Origin of Protein Folds. Douglas Axe. BIO-complexity, Vol 2010

Now we know Doug Axe gets published in the proper, real, grown up peer reviewed literature, but this doesn't seem to be one of those times. BIO-complexity seems to essentially be the Biologic istitutes in-house journal. Amongst its editors are Douglas Axe, Michael Behe, David Snoke, Richard Sternberg, Jonathan Wells, and William Dembski, a veritable who's who of ID luminaries.

Their Copy-editor is Ann Gauger, who some of you may remember as the Biologic institute researcher put in the embarassing position of essentially reporting having observed a novel beneficial mutation arising in her lab at the Wistar conference a few years ago.

As it currently stands the only 2 articles ever published in BIO-complexity are Axe's one and one with Ann Gauger as first author and another editorial board member Ralph Seelke as the last author.

To be honest Gauger's paper looks like it could easily have got published in a proper peer reviewed journal somewhere if the article was a bit less pushy and not so keen to make emphatic statements especially in the discussion, with no citation to back them up.

TTFN,

WK


Replies to this message:
 Message 9 by Omnivorous, posted 10-12-2010 12:40 PM Wounded King has not yet responded
 Message 10 by Omnivorous, posted 10-12-2010 2:11 PM Wounded King has not yet responded

    
Omnivorous
Member (Idle past 1045 days)
Posts: 3808
From: Adirondackia
Joined: 07-21-2005


Message 9 of 18 (586302)
10-12-2010 12:40 PM
Reply to: Message 8 by Wounded King
10-12-2010 11:55 AM


Re: How about a another pretty clear example: BIO-Complexity
I see that both papers are viewable as PDFs via your BIO-Complexity link; I'm wading through Axe's now.

The incestuous impersonation of peer-review you describe is striking; it is, as observed in some of the Panda's Thumb comments, akin to the Discovery Institute's tactic of obtaining campus appearance sponsorship from a religious student group, then trying to portray that as acceptance or even endorsement by that university's science faculty.

I do think they need to beef-up their copy-editing at BIO-Complexity; emphasis added to the amusing homophonic error in Axe's introduction:

quote:
INTRODUCTION
The elucidation of the genetic code in the late 1960s provided a
precise framework for understanding the effects of genetic mutations
on protein sequences. Because proteins perform most of the
molecular tasks needed for life, solving the code also opened the
possibility of understanding the connection between genotype and
phenotype on a scale that was not previously possible—the fine
scale of nucleotide bases rather than the course scale of whole
genes. Among other benefits, this promised unprecedented insight
into the inner workings of the evolutionary process at the molecular
level.

He seems to have wedded a false dilemma to incredulity, but I want to finish the paper before I make that "seems" an assertion.


Dost thou prate, rogue?
-Cassio

Real things always push back.
-William James


This message is a reply to:
 Message 8 by Wounded King, posted 10-12-2010 11:55 AM Wounded King has not yet responded

    
Omnivorous
Member (Idle past 1045 days)
Posts: 3808
From: Adirondackia
Joined: 07-21-2005


Message 10 of 18 (586317)
10-12-2010 2:11 PM
Reply to: Message 8 by Wounded King
10-12-2010 11:55 AM


Incredulity and big numbers
I've finished Axe's paper. While I can't pretend to understand everything he writes about protein folds (and I'll accept corrections of my misunderstandings humbly), a few things stood out that suggest to me that he is merely dressing up the incredulity of irreducible complexity with big numbers.

He depicts the (more than) literally astronomical number of possible protein folds, then argues that the difficulty of forming a de novo functional fold from that set is a search/sampling problem--finding a gemstone in a vast desert. He refers to (but does not cite) one estimate of the possible physical events in the universe since the Big Bang, notes only a fraction of those events could have pertained to protein folds, compares the two numbers, and concludes there is a vast probability disparity that is a problem for evolution.

He also makes this observation:

quote:
We can imagine a different world where, for example, the
planetary surface has rich deposits of abiotic amino acids, and
cells indiscriminately incorporate these amino acids into long
polypeptide chains, and these chains somehow benefit the cells
without performing complex functions. In that world the problem
we address here would not exist. But in our world things are strikingly
different. Here we see a planet with amino acids of strictly
biological origin, and we see cells going to extraordinary lengths
to manufacture, use, recycle, and scavenge all twenty of them.
We see elaborate error-checking mechanisms that minimize the
chances of confusing any one amino acid for any other during
protein synthesis, and (as already noted) we see that the products
of this tightly controlled process are long proteins. Lastly, we see
that these long proteins perform an impressive variety of functions
with equally impressive specificity and efficiency

So it seems to me that he presents familiar ID arguments of irreducible complexity and incredulity dressed up with misleading quantitative analogies.

First, he presents the odds of a particular successful protein fold mutation event as comparable to a search of the probability space of protein folds. This sounds awesome--until one considers how many microorganisms, for example, enjoy opportunities for mutation. So he tilts the scale impression by describing a singular search of a vast space, rather than a vast population searching a vast space.

He puts his thumb firmly on the scale again when he chooses for consideration protein folds functional in contemporaneous organisms, rather than postulating a simpler protein fold that could benefit a proto-organism, and thus provide grist for evolution's mill. Instead, he blithely describes a world with abiotic amino acids, then notes, "In our world things are strikingly different." That seems particularly disingenuous, since the planet we have does not exhibit the characteristics of the planet when life must first have appeared.

So...I don't want to get bogged down in the specifics of his paper, but it seems to me that a solid editorial process and rigorous peer review would at a minimum have excised some of his rhetorical sleights of hand. Perhaps that is why, despite the paper's six month online lifespan at BIO-Complexity, there are only three comments, all with little to no substance.

The DI wants the appearance of peer review; unfortunately for them, the appearance is not persuasive, given your outline above--and by settling for appearances, this paper, at least, fails to benefit from the close critiques peer review would have provided.

Edited by Omnivorous, : clarity


Dost thou prate, rogue?
-Cassio

Real things always push back.
-William James


This message is a reply to:
 Message 8 by Wounded King, posted 10-12-2010 11:55 AM Wounded King has not yet responded

Replies to this message:
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caffeine
Member
Posts: 1600
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.4


Message 11 of 18 (586412)
10-13-2010 6:25 AM
Reply to: Message 10 by Omnivorous
10-12-2010 2:11 PM


Re: Incredulity and big numbers
But in our world things are strikingly different. Here we see a planet with amino acids of strictly biological origin

This bit's simply not true. There are amino acids on meteorites. Unless the author's claiming to know something we don't about extraterrestrial life, I don't think you can call that a strictly biological origin.


This message is a reply to:
 Message 10 by Omnivorous, posted 10-12-2010 2:11 PM Omnivorous has responded

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Omnivorous
Member (Idle past 1045 days)
Posts: 3808
From: Adirondackia
Joined: 07-21-2005


Message 12 of 18 (586662)
10-14-2010 11:31 AM
Reply to: Message 11 by caffeine
10-13-2010 6:25 AM


Amino acids in Murchison Meterorite
caffeine writes:

Axe writes:

But in our world things are strikingly different. Here we see a planet with amino acids of strictly biological origin


This bit's simply not true. There are amino acids on meteorites. Unless the author's claiming to know something we don't about extraterrestrial life, I don't think you can call that a strictly biological origin.

That didn't occur to me--you're right.

From Wiki, regarding the Murchison Meterorite (emphasis added):

quote:
The meteorite belongs to the CM group of carbonaceous chondrites (see meteorite classification). Like most CM chondrites, Murchison is petrologic type 2, which means that it experienced extensive alteration by water-rich fluids on its parent body[2] before falling to Earth. CM chondrites, together with the CI group, are rich in carbon and are among the most chemically primitive meteorites in our collections. Like other CM chondrites, Murchison contains abundant CAIs. Over 100 amino acids (some of the basic components of life) have been identified in the meteorite.

Perhaps some authentic peer review would have raised that objection prior to publication.


Dost thou prate, rogue?
-Cassio

Real things always push back.
-William James


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 Message 11 by caffeine, posted 10-13-2010 6:25 AM caffeine has not yet responded

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nwr
Member
Posts: 5585
From: Geneva, Illinois
Joined: 08-08-2005


Message 13 of 18 (586703)
10-14-2010 12:41 PM
Reply to: Message 12 by Omnivorous
10-14-2010 11:31 AM


Re: Amino acids in Murchison Meterorite
Omnivorous writes:
Perhaps some authentic peer review would have raised that objection prior to publication.

As I read it, the text that you quoted does not assert that the amino acids are of biological origin. It only asserts that some of them are useful for biology.
This message is a reply to:
 Message 12 by Omnivorous, posted 10-14-2010 11:31 AM Omnivorous has responded

Replies to this message:
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Omnivorous
Member (Idle past 1045 days)
Posts: 3808
From: Adirondackia
Joined: 07-21-2005


Message 14 of 18 (586730)
10-14-2010 2:29 PM
Reply to: Message 13 by nwr
10-14-2010 12:41 PM


Re: Amino acids in Murchison Meterorite
Again, with emphasis added:

Axe writes:

But in our world things are strikingly different. Here we see a planet with amino acids of strictly biological origin...

The quote seems clear to me.


Dost thou prate, rogue?
-Cassio

Real things always push back.
-William James


This message is a reply to:
 Message 13 by nwr, posted 10-14-2010 12:41 PM nwr has responded

Replies to this message:
 Message 15 by nwr, posted 10-14-2010 3:04 PM Omnivorous has responded

    
nwr
Member
Posts: 5585
From: Geneva, Illinois
Joined: 08-08-2005


Message 15 of 18 (586737)
10-14-2010 3:04 PM
Reply to: Message 14 by Omnivorous
10-14-2010 2:29 PM


Re: Amino acids in Murchison Meterorite
Omnivorous writes:
The quote seems clear to me.

Okay. But I am not seeing anything wrong with that.

As stated, it does not exclude that we also see amino acids of non-biological origin.

I am not arguing for the Axe paper. I am just questioning why that particular assertion about amino acids is seen as a problem.


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 Message 14 by Omnivorous, posted 10-14-2010 2:29 PM Omnivorous has responded

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