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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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February 3, 2012

How the Andrulis Paper Got Published

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Posted by Derek

The editor of the journal Life has published an attempt at detailing how the notorious Andrulis paper managed to make its way into print. See how convincing you find it. In the course of explaining that it can be hard to find reviewers for interdisciplinary topics, and how the journal tries to find reputable people in each field (and carefully checks author suggestions for reviewers), we have this:

Life is a new journal that deals with new and sometime difficult interdisciplinary matters. Consequently, the journal will occasionally be presented with submitted articles that are controversial and/or outside conventional scientific views. Some papers recently accepted for publication in Life have attracted significant attention. Moreover, members of the Editorial Board have objected to these papers; some have resigned, and others have questioned the scientific validity of the contributions. . .

. . .In the case of the Dr. Andrulis’s long paper, the two reviewers were both faculty members of reputable universities different than the author’s and both went to considerable trouble presenting lengthy review reports. Dr. Andrulis revised his manuscript as requested, and the paper was subsequently published.

Really? Is that how it really went? I know what I would have said if they'd sent the paper to me: that it was a perfect example of what happens when an active, learned mind begins to slip loose from its moorings, and that while the paper appeared to have no scientific merit at all, it was quite useful as a diagnostic sign of oncoming psychosis.

If you only read the Life editor's remarks without reading any of the original paper, you might find them reasonable. But that's because you haven't been exposed to a theory that purports to explain the abiotic origins of life, the underlying principles of biochemistry, the formation of the solar system, the expansion of the universe, global weather patterns, the structure of cellular membranes, the distributions of comets and asteroids, the origins of riboviruses, the protein folding problem, the nature of biological aging, and the unification of quantum mechanics with general relativity. I have not made any of that up, it's all in the paper, and I would very much like to see a reviewer who could let all that go past. "Publish with revisions", sure.

Comments (23) + TrackBacks (0) | Category: The Scientific Literature


COMMENTS

1. RM on February 3, 2012 3:37 PM writes...

I'm guessing the editor conveniently ignored the dozen plus potential reviewers which took one look at the paper and replied "Please do not contact me again". Anyone with much sense would have said "I'm not going to review this dreck" - and "I'm not going to review" doesn't technically count as a negative review.

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2. PharmaHeretic on February 3, 2012 3:53 PM writes...

Publishing is a BUSINESS! As long as they can show growth in the business revenue, profit or reach- it is all good.

Do you really think that people who run business nowadays care about the long term? Have a look at the pharma and biotech sector.. It is all about the short term and MBAese doublethink.

If anything, I am surprised that journals are not publishing more papers like this.

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3. LeeH on February 3, 2012 4:00 PM writes...

I suspect that the reviewers were impressed by the detail of the paper (as bizarre as it was) and let it by, rather than admit that they didn't understand the content and could not make the intellectual leap that it was really a set of unintelligible rants.

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4. weirdo on February 3, 2012 4:06 PM writes...

Imagine that you have agreed to be a reviewer for a new journal. Let's call it "Everything". You may be a little suspect of a journal with such a lofty title, but you're willing to give a shot.

A few weeks later, you get a 150-page tome that is complete and utter dreck. Do you think:

a) Not worth my time. I'll send it back.
b) I'll skim it, then write a few lines pointing out key errors in logic.
c) You say to yourself, "Self, what editor worthy of the name would send me a piece of drivel like this, when he should have sent it back to the author with big red "X's" all over it. I know what I'll do -- I'll turn in a reasonable-sounding review and see if the editor even reads it. If he publishes the paper, that will (fortunately) be the end of this obviously doomed journal, and I will have done the scientific world a real service."

I'd like to believe "c".

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5. Tony on February 3, 2012 4:08 PM writes...

My guess? This is publicity. All sorts of bloggers going nuts about this is going to draw attention to the journal in question. Yeah, it's negative publicity, but in the mainstream press this paper was not actually questioned. Fast forward a little bit to when some company starts selling dietary supplements, they can refer back to this 'paper' when all the hubbub has subsided. They will get followers that are just as crazy as the author defending them to the death.

I think this all goes to plan.

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6. DrSnowboard on February 3, 2012 5:00 PM writes...

So, the editor is saying they stepped in to 'guest edit'a special issue. Sadly they had no competence in the field of the 'special issue' so they relied on the 'peer review process'.
So an editor is just a secretary now? An administrative position with no 'view' on content, no responsibility for content.

Bollocks. Goodbye editor, goodbye useless journal.
I hope the article author gets the help he needs.

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7. Emily Willingham on February 3, 2012 5:12 PM writes...

I asked the editor (by email) when the paper was published what the review process had been, and he said that the paper had been sent to more than two reviewers but that only two responses had been received, both rating the paper "accept with minor revisions." If that information is accurate, the journal didn't receive other, thumbs-down reviews.

The editor on this "special issue" also happens to be the journal publisher, and he has a roster of several other journals. His dog in this hunt is business, obviously.

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8. RKN on February 3, 2012 9:17 PM writes...

A few weeks later, you get a 150-page tome that is complete and utter dreck. Do you think:

I might have thought I was being used as a positive control for the review process.

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9. Secondaire on February 3, 2012 11:38 PM writes...

To me, this reads as editorial mumbo-jumbo that translates (roughly) to "we got caught with our pants down, and we really don't quite know how to fix this rubbish."

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10. joel on February 4, 2012 2:04 AM writes...

This sheer scope of this paper reminds me of Stephen Wolfram's "A New Kind of Science". At least Wolfram wasn't so tawdry and made it into a book.

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11. Special Guest Lecturer on February 4, 2012 10:43 AM writes...

This example is one of many reasons why I think the reviews should be published alongside the paper. Still anonymous, but there for the world to see.

The reason I believe in this policy is that it would protect authors from political tricks of their competitors suggesting unnecessary and onerous additional experiments. However, it would also allow readers to evaluate how well the peer review process worked for individual articles.

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12. dearieme on February 4, 2012 11:58 AM writes...

"I may have completely missed the point, and this chap may be the next Newton, BUT....": that's how I started one review - why couldn't the reviewers here?

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13. Nick on February 4, 2012 7:46 PM writes...

I wonder whether this was the first time that this paper was submitted for publication anywhere or whether it has been doing the rounds for a few submit/review/reject cycles. If the latter, the reviews would make interesting reading in comparison to the BS spouted by the Life editor.

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14. newnickname on February 5, 2012 6:49 PM writes...

I think that AJ Birch told the story about RB Woodward: RBW said he doesn't referee mss. Birch said, ~'But don't you owe it to the community to referee a few papers every now and then? After all, they referee your papers.' RBW said, ~'My papers don't need refereeing.'

And, of course, there are the stories that RBW would return mss without revision regardless of the referee comments and tell the editors to publish as is. And they did.

(RE: Previous "Future of Pharma" topic. I will post this Q there. Even with google, I can't figure out what a Kayson(?) Event is. What is it? Please reply to the correct topic.)

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15. wwjd on February 6, 2012 10:28 AM writes...

Do you mean Kaizen event?

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16. Morten G on February 9, 2012 9:59 AM writes...

Kaizen event is the complete subversion of the Kaizen philosophy.

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17. nettle on February 13, 2012 7:54 AM writes...

"I know what I would have said if they'd sent the paper to me: that it was a perfect example of what happens when an active, learned mind begins to slip loose from its moorings, and that while the paper appeared to have no scientific merit at all, it was quite useful as a diagnostic sign of oncoming psychosis."

I suspect you would come to that conclusion because you are a psychiatrist and not a scientist willing to struggle through a radically new interpretation of reality?

Speaking as a scientist, I can say present science (and medicine for that matter) is chock full of omissions and wrong theory. Psychiatry is way over medicating.

I have spent years in discussions with Erik over this paper and voluminous additional unpublished material. Erik is fully sane. He has corrected and modified his paper multiple times. I know because he has shared multiple versions with me.

So are people who don't want to do the hard mental labor to understand his paper. It's a tough slog, just as learning, say, Mandarin is. Far easier to dismiss it. Far more fun to mock it.

Also, for your consideration: http://milesmathis.com/erik.pdf

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18. nettle on February 18, 2012 10:16 AM writes...

I would like to supplement my previous post with some lengthy defenses of Erik's paper.

I can see quite clearly that the RNA world hypothesis says nothing about the flow of genetic information in an extant cell (central dogma) and the central dogma says nothing about the origin and evolution of RNA. The point Erik was trying to make is that current models/theories/hypotheses/ideas are ad hoc and thus should be considered provisional at best and wrong at worst. Could you point out the illogic there?

As for how theory treats those three problems (translation apparatus, genetic code, and biometabolic pathways), I would call your attention to where these problems are treated:

- p. 43 Origin of the genetic code

Erik’s core model shows that systems organize in units of threes, creating a system that has high potential energy but less exergy than the evolutionarily prior system. The tri-quantal system (as he calls it) is the tri-nucleotide, with each component of the system having a relative amount of energy (see section 2.4.5, pp. 13-14), “(i) a high energy (exergic), unstable, excited form; (ii) an intermediate energy, quasi-stable, transition form; and (iii) a low energy, stable, ground form.” My read of this is that the first nucleotide is the most stable, the second is the quasi-stable, and the third position of the codon is the least stable. His model echoes what I know about the wobble hypothesis and the variability of the genetic code. Is there a problem with the interpretation that I am missing?

Erik has proposed that the code evolved autocatalytically, from the metabolism of the orthophosphate bonds between the 2nd and/or 3rd nucleotides. Perhaps the reason why I don’t find Erik’s proposal so outlandish is that it is fully consistent with mainstream scientific ideas: both the Nobelist Eigen and complexity theorist Kauffmann argue that the origin of RNA involved autocatalytic systems. I assume you are familiar with their work.

- pp. 45-48 Specificity of genetic code; origin of translation apparatus.

Three RNA classes (mRNA, tRNA, rRNA) are required for the formation of a polypeptide. Erik models these RNAs as being the tri-quantal state that drives the emergence of and exists in a quarternary complex with one or more amino acid(s). Again, points for Erik, as this is, in fact, what one observes in existing cells (in fact, to the best of my knowledge, RNA scientists have shown that the peptide bond can form sans accessory ribosomal proteins; more points). The cycling of one RNA (the rRNA) leaves a ternary complex of the amino acid (linked to the tRNA, Erik calls it aa-tRNA) and the mRNA. And, just as the rRNA can cycle in and out of the quarternary complex, Erik models the mRNA cycling in and out that previously mentioned ternary complex. Both cycling phenomena are depicted accurately by the gyre and the latter of the two reveals a co-adaptational relationship between the aa-tRNA and the mRNA.

My only problem in understanding is how the genetic information of RNA is transferred to the link between the amino acids that make up the polypeptide chain. Erik points out that the formation of the amide bond is, first, a consequence of loss of mRNA and rRNA relationships with the aa-tRNA. (I think he means after the tRNA passes from the A site to the P site in the ribosome.) Next, the nitrogen link imports information from the tRNA into the amide bond as is subsequently cycled out, too. (I think he means after the tRNA passes from the P site to the E site in the ribosome.) He relies on an axiom (the tenth one) to take this position. Seeing as this axiom applies to all systems in his theory, and finding no experimental evidence to refute it, I cannot dismiss it outright as wrong.

- pp. 30-60 Biometabolic pathways

Other than page 35, Erik does not use the term “biometabolic pathways” (because he did raise it up front, points against Erik). Perhaps the reason for this oversight is that every single pathway in the cell is a biometabolic pathway? In this regard, these 30 cited pages contain a large amount of discussion of many distinct aspects of cellular metabolism. If there’s one particular example you wanna go over, lemme know.

Permalink to Comment

19. nettle on February 18, 2012 10:22 AM writes...

Contrast a NTP and a NDP. One NXP can’t be NTP and NDP at the same time.

The deposition of the orthophosphate puts NXP into a high energy state.
The eviction of the orthophosphate put NXP into a low energy state.

So, just as the earth cycles around the sun with an aphelion and a perihelion, so does the NXP, a particle, oscillate around the orthophophate which it absorbs and ejects — with high energy states (e.g. ATP) and low energy state (e.g. ADP).

Thus, through the oscillation of these states we have a wave (or if you prefer, cycle) — the gyre.

The gyre maps the space-time path of the individual particle as it oscillates between the two states.

The quantum captures the entire phenomenon — i.e. the quantum is a shorthand notation for compressing the biological (or any) process — both the wave and the particle. Thus, the quantum is just a way of representing the two states and you know that a process that has already been described in the literature (NTP NDP+P), but you don’t know which state the NXP is in until you observe it.

This arrangement is exactly like Schroedingers’ cat. We don’t know if its dead or alive until we observe it.

As a wave, the NXP has a time period (wavelength) for the cycle, an amplitude (set by the high and low energy states), and it has a frequency (as wavelength and frequency are directly related).

As a particle, the NXP necessarily is moving through space and time, has a rotation (as does every molecule), and vibrates and stretches (just as every molecule).

By the way, the standard method for measuring the stretching and vibrating of bonds is IR (infrared spectrometers).

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20. n on February 19, 2012 7:24 AM writes...

@ 17 nettle

Um?

That article you link to is a rebuttal of a rebuttal of Andrulis, in which the author dissects criticism of Andrulis without having read the original paper or ideas or anything. It also has wonderful lines like

"I am just going to assume [the guy dissing Andrulis] is with some government agency until he proves he isn't. This is a good bet, since most of what you read under major mastheads—on the internet and off—is written now by government agencies or at their behest."

And your 'explanation' of Andrulis' ideas doesn't make any sense, at least to me. In biological and chemical systems, things sometimes happen in threes. Sure. What can we predict from this hypothesis? Is it universal? A lot of things I see in biological and chemical systems happen in pairs, or quaternary etc structures with many components, like proteins. Is there anything about the hypothesis which is more than observing a pattern which is sometimes repeated, and then deriving a whole lot of mysticism from it?

Permalink to Comment

21. nettle on February 19, 2012 11:42 AM writes...

@n
"That article you link to is a rebuttal of a rebuttal of Andrulis, in which the author dissects criticism of Andrulis without having read the original paper or ideas or anything"
You totally miss the point which is that Erik has the right to publish without being persecuted.

It makes complete sense. You just don't understand it. Too bad

If you can't draw /any/ meaning from the mathis article, which I agree has that insipid line, then you clear don't stand a chance of grasping an inkling of Erik's paper.

@all (except n, because there is /no way/ he/she will understand)
For further elucidation and defense of the paper see my extensive and numerous comments on the following two sites:

http://retractionwatch.wordpress.com/2012/02/03/editor-who-published-andrulis-paper-tries-to-explain-how-it-happened/

http://retractionwatch.wordpress.com/2012/01/28/case-western-explains-why-it-withdrew-press-release-about-andrulis-origin-of-life-paper/

CWRU is being cowardly.

Permalink to Comment

22. Getheren on June 18, 2013 10:36 AM writes...

Paging Dr. Sokal to the front desk ... Dr. Sokal, please.

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23. MaryKaye on August 30, 2013 10:15 PM writes...

I once reviewed a biomedical paper whose cover letter from the editor said, "I'm sorry to ask you to review this, but I hope a formal review will make the author leave me alone."

The paper was not incoherent like this one, but it was amateurish to an incredible degree (citations to "my sister the registered nurse says") and started right off with two very basic mistakes in biological facts that undercut its entire argument. It did give my household a cherished turn of phrase, though, so I'm not sorry I read it....

I was also collared by a relative to "review" an essay by a friend of theirs, which turned out to argue that the (untruth) that birth defects are inherited only from the male parent is due to God cherishing each egg but not being able to keep up with all the sperm. Not apparently meant as a joke.

It's amazing the extent to which people can function in day to day life with wildly strange inner worlds.

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