Yesterday, Ivan wrote on his Tumblr about Case Western’s Erik D. Andrulis‘ paper, “Theory of the Origin, Evolution, and Nature of Life:”

The paper is 105 pages, which includes a whopping 800 references. It depends heavily on the gyre:

In the theory proposed herein, I use the heterodox yet simple gyre—a spiral, vortex, whorl, or similar circular pattern—as a core model for understanding life. Because many elements of the gyre model (gyromodel) are alien, I introduce neologisms and important terms in bold italics to identify them; a theoretical lexicon is presented in Table 1. The central idea of this theory is that all physical reality, stretching from the so-called inanimate into the animate realm and from micro- to meso- to macrocosmic scales, can be interpreted and modeled as manifestations of a single geometric entity, the gyre.

Andrulis concludes:

…this catholic theory provides an innovative and elegant solution to the origin, evolution, and nature of life in the cosmos. I humbly proffer my theory as a viable system for knowing life.

Our humble author also includes paragraphs like this, which led some on Twitter to wonder if the paper was for real:

The philosopher Bachelard claimed that scientific history is replete with unconsciously constructed or immanent “epistemological obstacles,” that are eventually broken through and shed during “epistemological rupture [796].” I conclude that my theoretical work elicits a Bachelardian rupture of intradisciplinary noöspheres and interdisciplinary boundaries. Kuhn proposed a related concept of “paradigm shift” to explain the process surrounding worldview conversion during a scientific revolution [797]. Whether the advent of this theory elicits a Kuhnian gestalt switch is debatable, though such an iconoclastic event has been foretold [798-800].

On Thursday, Case Western had put out a press release about the study. That release is still available on ScienceDaily and other sites, but the medical school removed it from their own site. Today, Liz Lear, senior director, School of Medicine Marketing and Communications, tells us:

The School of Medicine’s public affairs office promotes all faculty research as possible. We have been evaluating our processes regarding media outreach and elected to remove the release from our website while we assess our policies surrounding promotional communications.

We’ll continue to update this story as we find out more. In the meantime, you can read PZ Myers’ take, in which he suggests that “the comparison to jabberwocky” is inevitable, and John Timmer’s, in which he wonders “How the craziest f#@!ing “theory of everything” got published and promoted.”

The retraction notice for “Multiple HLA class I and II associations in classical Hodgkin lymphoma and EBV status defined subgroups,” dated January 20 and signed by all of the authors, clearly explains what went wrong, taking pains to note that there was no misconduct involved:

The authors wish to retract the 10 November 2011 article cited above, prepublished on 14 September 2011, because they miscalculated some of the HLA allele frequencies due to missing information on split alleles (mainly in controls). Individuals with missing split allele information were erroneously left out of the analyses, which caused some (3/11) of the reported significant associations to be incorrect. The authors noticed the errors themselves and directly contacted the editors of Blood. It was an honest mistake, not fraud or scientific misconduct. The authors sincerely apologize to the readers, reviewers and editors of Blood for making this unfortunate mistake.

Corresponding author Anke van den Berg told us she had nothing to add:

I think that all relevant information is already mentioned in the retraction and I have no further comments. Our and the journal’s goal was to correct the scientific record.

We asked Blood editor Cynthia Dunbar how the errors came the group’s attention:

Dr. van den Berg contacted us, I believe her group internally discovered the issue. Another investigator also brought the issue to our attention in a letter to the editor submitted a few days later, having read the paper and working the data in comparison with some of his own, realized the control allele frequencies had to be incorrect, but he told me he had not contacted Dr. van den Berg himself.

Hat tip: Clare Francis

Here’s the notice for the paper, which has been cited 23 times, according to Thomson Scientific’s Web of Knowledge:

Retraction for “Structural basis for nucleotide exchange on Gαi subunits and receptor coupling specificity,” by Christopher A. Johnston and David P. Siderovski, which appeared in issue 6, February 6, 2007, of Proc Natl Acad Sci USA (104:2001–2006; first published January 30, 2007; 10.1073/pnas.0608599104).

The authors wish to note the following: “In our paper, a cocrystal structure at 2.2 Å resolution was described of the heterotrimeric G-protein alpha subunit Gαi1 bound to two peptides: one from an artificial sequence that promotes nucleotide exchange (KB-752) and a second peptide (D2N) from the third intracellular loop of the D2 dopamine receptor (PDB ID code 2HLB). Further examination of the unbiased electron density map has revealed that, while electron density exists for the KB-752 peptide, there is a lack of clear and continuous electron density for the D2N receptor peptide in the complex. Because the structural model represents a major conclusion of the paper but is unsupported by the experimental electron density map, we wish to retract the paper. Both authors deeply regret this mistake and sincerely apologize.”

The reason for the retraction is essentially the same as the one for the Structure paper. We’ve contacted Siderovski for comment, and will update with anything we hear back.

Siderovski has collaborated with the late Maria Diverse-Pierluissi, four of whose papers were retracted after her death. Siderovski and Diverse-Pierluissi published two papers together, neither of which has been retracted — although a former postdoc in Diverse-Pierluissi’s lab suggests there may be issues with one of them. And Mount Sinai, where Diverse-Pierluissi worked, told us several months ago that they considered their investigation closed.

In other words, we have no reason to think the retractions are related. But this seems to be the first case of two groups linked by disparate retractions.

Update, 2 p.m. Eastern, 1/26/12: It turns out we missed a correction by the same group that was released the same day in PNAS — and for basically the same reason as the retraction:

Correction for “Regulators of G-protein Signaling accelerate GPCR signaling kinetics and govern sensitivity solely by accelerating GTPase activity,” by Nevin A. Lambert, Christopher A. Johnston, Steven D. Cappell, Sudhakiranmayi Kuravi, Adam J. Kimple, Francis S. Willard, andDavid P. Siderovski, which appeared in issue 15, April 13, 2010, of Proc Natl Acad Sci USA (107:7066–7071; first published March 29, 2010; 10.1073/pnas.0912934107).

The authors note that Fig. 1 appeared incorrectly. They also wish to note the following: “Upon further evaluation of the unbiased electron density maps for the structural models of Gαi1(G202A)·GDP (PDB id 2PZ2) and Gαi1(G202A)·GDP·AlF4–(PDB id 2PZ3), there is a lack of clear and continuous density to support an entirely ordered switch II region or to support the presence of aluminum tetrafluoride in the latter structure. We have therefore obsoleted the x-ray structure model PDB 2PZ3 from the Protein Data Bank. We have replaced PDB 2PZ2 with PDB 3UMS in the Protein Data Bank to reflect the more accurate refinement of the Gαi1(G202A)·GDP structural model.”

The corrected figure and its corresponding legend appear below. This error does not affect the conclusions of the article.

Hat tips: Clare Francis, Vladimir Svetlov

Das, via UConn

Dipak Das, the UConn red wine researcher charged by his institution with rampant misconduct that will likely lead to dozens of retractions, is evidently a 99%-er — when it comes to accuracy, that is.

According to a statement purportedly from his lawyer refuting those charges, Das claims, among other things, that the output from his lab was nearly perfect. He also has a lot to say about a 60,000-page report that the statement says he may not have actually downloaded.

We might note a lot more things about the letter, which we received from Bill Sardi, president of Longevinex, a resveratrol company which has worked with Das. Sardi has been sending Das defenses since the story broke; we posted some of them and Derek Lowe has posted parts of another. But here’s the letter, in its entirety:

Note: this 9-point document was obtained from legal counsel for Dipak Das, PhD, a researcher at the University of Connecticut recently accused of scientific fraud.

Discovery of an online document involving allegations against a University of Connecticut Health Center researcher accused of scientific fraud reveals a long-standing internal battle between the accused researcher and an administrative physician at the institution that may have resulted in false allegations being generated.  That document reveals the following:

1. Dr. Dipak Das, PhD, the accused, alleges all of the original documents involving 42 years of research which includes images of tests known as western blots, were confiscated by a representative of the university and were destroyed.  These original raw western blot images, which would serve to completely exonerate Dr. Das, are no longer available for comparison with altered images that were later published in scientific journals.  This same antagonist within the university proceeded to write hundreds of letters to scientific journals and funding sources, says Dr. Das, making false allegations that “I made up all the western blot tests.”

2. Dr. Das further alleges, once the original images were destroyed and could not be used for comparison in his defense, the university chose to employ software that can detect alterations to graphic images, software that has a high rate of false-positives and is not considered reliable unless original images are available for comparison purposes.  Dr. Das says: “no one will use this software on the published paper unless originals are NOT available.”

3.  Dr. Das counter attacks the University of Connecticut’s 60,000 page damning report which accuses him of altering images in order to fraudulently gain research grant money.  Dr. Das claims he is an eminent scientist who was pre-funded by the National Institutes of Health and did not have to publish to gain grant money.

4. Dr. Das indicates, in this available online document, that he never personally performed any of these western blot tests that are now in question and that the person who performed most of these tests is retired and surprisingly not on the list of researchers accused of submitting fraudulent data to scientific journals.

5.  Dr. Das then says he proceeded to examine the work of others in his laboratory and found their work to be “99% correct.”  Dr. Das said he is considered an expert in reviewing research papers and had been requested to review western blot tests for various scientific journals.

6. Contrary to what the University of Connecticut report contends, Dr. Das denies he was the only person who had keys to his office and that many other students and post-doctorates had access to his computer to enter results of experiments they conducted.

7. Dr. Das categorically denies, as the university pejoratively alleges, that he “de-funded” a student because she did not produce the test results he demanded.  Dr. Das claims he only took her off of his budget because she was working exclusively for another researcher.

8. The 60,000-page report describing the alleged scientific misconduct by Dr. Das, while only recently released to the public to put him on trial in the court of public opinion, was produced sometime in 2010, but it is unclear whether Dr. Das ever had an opportunity to even view it in its totality because he could not download it onto his computer because of its large size.

9. Dr. Das claims the allegations against him and his East-Indian colleagues began with a change in the administration at the university and for unknown reasons only focuses on East-Indian researchers when researchers of other ethnic origins performed most of the tests now in question.

Because of the seriousness of the charges and the fact they involve federally funded research studies, and the possibility that tissue samples as well as test data may have been intentionally destroyed by the university, it appears federal investigators need to intervene as quickly as possible.

In fact, the Office of Research Integrity, which investigates alleged misconduct by federal grant recipients, was the one that tipped off UConn to the case.

The letter appears to be from Scott Tips, a “health freedom” lawyer in California and president of the National Health Federation. The NHF calls itself

an international nonprofit, consumer-education, health-freedom organization working to protect individuals’ rights to choose to consume healthy food, take supplements, and use alternative therapies without government restrictions.

Das, meanwhile, has apparently been lecturing in Kolkata, India.

Shortly after publication, Kazmirski,  director of the National Center for Photovoltaics at the National Renewable Energy Laboratory, in Golden, Colo., received an email from one of the listed co-authors of the article complaining that he and another co-author had not consented to submit the work. Kazmirski contacted the lead author, Afshin Mazandarani, who agreed to withdraw the paper.

The result was the following notice, which appeared in October (we only recently saw it):

WITHDRAWN: Investigating the need of nuclear power plants for sustainable energy in Iran
Renewable and Sustainable Energy Reviews, Volume 15, Issue 8, October 2011, Pages 3575-3587
A. Mazandarani

This article has been retracted at the request of the author as it contains significant scientific errors. The paper was also submitted without the consent of the co-authors. The lead author apologizes sincerely for the technical oversight and to the coauthors for submitting without consultation.

As a consequence, pages 3575–3587 originally occupied by the retracted article are missing from the printed issue. The publisher apologizes for any inconvenience this may cause.

In addition to Mazandarani are three other authors, T.M.I., Mahlia , W.T., Chong , M., Moghavvemi, all at the University of Malaya. We’re guessing — although we couldn’t confirm this — that Chong did not lodge the complaint, because his website lists the article, whereas Mahlia’s and Moghavvemi’s do not.

Kazmersky told us that in cases of authorship disputes, his journal’s policy has been to allow the paper to be resubmitted — provided, of course, the problem can be straightened out. He said that in the past year or so, he has dealt with “four or five” articles that have involved authorship issues.

I as the editor will always write the [main] author and say, How do you respond to this?

We wondered whether Mazandarani’s colleagues didn’t pull away from the article given its controversial nature. Although we couldn’t find the full paper, we did manage to dig up the abstract, which makes the politically charged claim that Iran not only should have a nuclear power complex, it is the country’s “assured right”:

Over the decades, the consumption of all types of energy such as electricity increased rapidly in Iran. Therefore, the government decided to redevelop its nuclear program to meet the rising electricity demand and decrease consumption of fossil fuels. In this paper, the effect of this policy in four major aspects of energy sustainability in the country, including energy price, environmental issues, energy demand and energy security have been verified. To investigate the relative cost of electricity generated in each alternative generator, the simple levelized electricity cost was selected as a method. The results show that electricity cost in fossil fuel… Highlights: • Using nuclear energy including its fuel cycle is Iran’s assured right. • Electricity cost in fossil fuel power plants presumably will be cheaper than nuclear. • Constructing more nuclear power plants will not cause the energy sustainability in Iran. • The main threats for Iran’s energy security are economic dependency on crude oil export. • Most important action is reforming inefficient oil and gas consumption in all sectors.

Kazmerski said that while Mazandarani (who did not reply to a request for comment) was cooperative and agreed to resubmit the paper, he has not heard anything from the researcher in months. Still, he liked the article and would be glad to republish it.

I found the paper quite interesting. The authors wrote it from a sustainable energy point of view, and  we don’t get a lot of articles about nuclear power.

Indeed, the journal does not have a section editor for nuclear matters.

My argument is that the nuclear and the renewable people should be a hell of a lot more friendly. We both have problems and we both have benefits.

The retraction notice is quite clear about why the paper is being withdrawn:

The following article from Journal of Neurochemistry, “Functional nerve growth factor and trkA autocrine/paracrine circuits in adult rat cortex are revealed by episodic ethanol exposure and withdrawal” by Bruns M. and Miller MW., published online on 22 December 2006, Volume 100, Issue 5, 2007, pages 1155–1168 (now available through http://www.onlinelibrary.wiley.com) has been retracted by the Chief Editors. This action follows the advice from the President of SUNY Upstate after an investigation into allegations of research misconduct by Dr. Michael Miller. The preponderance of evidence reviewed in that investigation suggested that Figures 2 to 6 in this publication have been falsified. Dr. Bruns was not the subject of any investigation.

The paper has been cited five times, according to Thomson Scientific’s Web of Knowledge.

Michael W. Miller, whose hiring was the subject of a 2000 Upstate press release,  is no longer employed at Upstate, and we do not know his whereabouts. We understand that the case has been referred to the Office of Research Integrity (ORI), which investigates allegations of fraud by federally funded scientists. According to the 2000 release:

Miller brings to SUNY Upstate more than $3 million in research grants, much of it dedicated to the study of the effect of alcohol on brain cells, fetal alcohol syndrome and alcohol neurotoxicity. His grant support comes from the National Cancer Institute, National Institute of Alcoholism and Alcohol Abuse and the Department of Veterans Affairs. His research interests include, the cerebral cortex, developmental neurobiology, growth factors, neuronal death, neuronal plasticity and neurotoxicology.

Miller’s co-author, Marla Bruns, whom the notice makes clear was not the subject of the investigation, is now a neurology resident at Ohio State. We’ve tried to reach her as well as Upstate, and will update with anything we hear back. [Update, 1:30 p.m. Eastern, 1/25/12: Bruns returned our call to say she had no comment on the case.]

In an unrelated case, the ORI recently found that a former SUNY Upstate grad student had manipulated Western blots.

Hat tip: Greg Pattyn

This being the JBC, the retraction notice for “Human T-cell Leukemia Virus Type I Tax Down-regulates the Expression of Phosphatidylinositol 3,4,5-Trisphosphate Inositol Phosphatases via the NF-κB Pathway” is the very definition of opaque:

This article has been withdrawn by the authors.

The paper has been cited 13 times, according to Thomson Scientific’s Web of Knowledge.

The corresponding author of the paper, Takashi Tsuji, appears to be a fairly prominent researcher. Last year, he and his colleagues published a study in PLoS ONE in which they showed how a tooth could be grown from stem cells. The paper garnered significant media attention. He also studies hair regeneration.

We’ve contacted Tsuji, and the JBC, for more information, and will update with anything we find out.

Hat tip: Clare Francis

Here’s the notice, which also appears in this month’s print edition:

Withdrawn: Dong X, Shi W, Zeng Q, Xie L. Roles of Adherence and Matrix Metalloproteinases in Growth Patterns of Fungal Pathogens in Cornea. Current Eye Research 2005; 30(8):613–620

doi:10.1080/02713680590968196

Withdrawn: Ma L, Xie L, Dong X, Shi W. Role of extracellular phospholipase B of Canddida albicans as a virulent factor in experimental keratomycosis. Current Eye Research 2009; 34(9):761–768

doi:10.1080/02713680903056391

Withdrawn: Min X, Zhou Q, Dong X, Wang Y, Xie L. Expression Profile and Regulation of Telomerase Reverse Transcriptase on Oxygen-Induced Retinal Neovascularization. Current Eye Research 2011; 36(2):135–142

doi:10.3109/02713683.2010.525679

The above articles duplicate previously published work and are hereby retracted in both the print and online editions of Current Eye Research. These articles appeared earlier in Chinese-language journals (referenced below). As far as can be determined, no permission was sought for the translation and re-publication of the articles. The English-language versions do not cite or refer to the prior publications, and are therefore redundant to scientific literature. The articles submitted in English to Current Eye Research were peer-reviewed and published in good faith.

Roles of Adherence and Matrix Metalloproteinases in Growth Patterns of Fungal Pathogens in Cornea in by Xiaoguang Dong, Weiyun Shi, Qingyan Zeng and Lixin Xie of the Shandong Eye Institute, Qingdao People’s Republic of China, was previously published by Dong, X., Shi,W., Zeng, Q., and Xie, L. (2004) in the Chinese Journal of Ophthalmology, Volume 40, pages: 774–776.

Role of extracellular phospholipase B of Canddida albicans as a virulent factor in experimental keratomycosis by Lin Ma, Lixin Xie, Xiaoguang Dong and Weiyun Shi of The State Key Lab Cultivation Base, Shandong Provincial Key Lab of Ophthalmology and Shandong Eye Institute, Qingdao, China was previously published with the same authors as Virulence of extracellular phospholipase B of Candida albicans in rabbit experimental keratomycosis in the Chinese Journal of Ophthalmology, Volume 44, pages: 237-43.

Expression Profile and Regulation of Telomerase Reverse Transcriptase on Oxygen-Induced Retinal Neovascularization by Xiaojie Min, Qingjun Zhou, Xiaoguang Dong, Yiqiang Wang, Lixin Xie of the State Key Lab Cultivation Base, Shandong Provincial Key Lab of Ophthalmology, Shandong Eye Institute, Qingdao, China (Xiaojie Min now works at the Department of Ophthalmology, Fourth Affiliated Hospital, China Medical University, Shenyang, China) was previously published as: Min X, Zhou Q, Liu T, Yin H, Dong X, Xie L. Expression of mouse telomerase reverse transcription in a mouse model of oxygen-induced retinopathy. Chinese Journal of Ophthalmology 2009;45:199–205, 2009; and: Min X, Dong X, Zhou Q, Liu T, Yin H, Xie L. TERT-siRNA inhibits oxygen-induced retinal neovascularization in mice. Chinese Journal of Ophthalmology 2009;45:1111–1117.

The journal’s policy in this respect is clear: Current Eye Research considers all manuscripts on the strict condition that they have been submitted only to Current Eye Research, that they neither contain material that has been published already, nor are they under consideration for publication or in press elsewhere.

Current Eye Research published these articles in good faith, and on the basis of legal warranties made by the corresponding authors regarding the originality of their work.

The Publishers

This kind of situation has come up before, for example in a similar case involving the American Journal of Psychiatry. There, the journal simply issued an Expression of Concern. As we noted then:

Our understanding is that such duplications are only acceptable if a journal editor knows the material has been published elsewhere in another language, and gives the authors permission to publish a translation. That doesn’t seem to have been the case here.

Hat tip: “Ressci Integrity”

Somehow, we’re not surprised to learn that Saccomanni may not have been totally above board in other ways, too.

According to Robert Lindsay, editor of Osteoporosis International, whose journal has retracted one of Saccomanni’s plagiarized manuscripts, the researcher’s stated affiliation on several recent papers — Gabriele D’ Annunzio University Chieti — had long ago severed ties with him:

We wrote to the Dean of Faculty of Medicine at the University “G. d’Annunzio” of Chieti in response to the report sent to him about Saccomanni. Saccomanni provided this institution as his affiliation for many of his plagiarised submissions, although not the OI submission. According to the Dean, Saccomanni has not been at the University for “many” years, although he does not provide details. He claims they are going to take legal procedures to caution Saccomanni against the use of affiliation in future.

via Wikimedia

Today, without us having planned it, has become the day of retracted papers that found a new home.

This morning, we posted an item about a chimp “culture” paper that was retracted from Biology Letters after its authors found some errors, and then published, with corrections, in the Journal of Human Evolution. This afternoon, we bring you the news of a PLoS ONE paper on longevity genes that is the corrected version of a Science paper retracted last year:

After online publication of our report “Genetic Signatures of Exceptional Longevity in Humans” (1) we discovered that technical errors in the Illumina 610 array and an inadequate quality control protocol introduced false positive single nucleotide polymorphisms (SNPs) in our findings. An independent laboratory subsequently performed stringent quality control measures, ambiguous SNPs were then removed, and resultant genotype data were validated using an independent platform. We then reanalyzed the reduced data set using the same methodology as in the published paper. We feel the main scientific findings remain supported by the available data: (i) A model consisting of multiple specific SNPs accurately differentiates between centenarians and controls; (ii) genetic profiles cluster into specific signatures; and (iii) signatures are associated with ages of onset of specific age-related diseases and subjects with the oldest ages. However, the specific details of the new analysis change substantially from those originally published online to the point of becoming a new report. Therefore, we retract the original manuscript and will pursue alternative publication of the new findings.

Science, in an accompanying statement at the time, emphasized

that there was no misconduct by Sebastiani and colleagues. The researchers worked exhaustively to correct the errors in the original paper and we regret that the outcome of the extensive revision and re-review process was not more favorable.

The new paper, by Boston University’s Thomas Perls, Paola Sebastiani, and colleagues, “Genetic Signatures of Exceptional Longevity in Humans,” concludes that

90% of centenarians can be grouped into clusters characterized by different ‘‘genetic signatures’’ of varying predictive values for exceptional longevity.

The Sebastiani-Perls group has published two papers since the Science retraction; today’s is the third. One, Perls told Retraction Watch, “Health Span Approximates Life Span Among Many Supercentenarians: Compression of Morbidity at the Approximate Limit of Life Span,” published in the Journals of Gerontology Series A, indicated

…that people who live to 110+ years on average compress the time they experience illness into about the last 5% of their lives. This supports the compression of morbidity hypothesis.. that is, that as a member of a species approaches the limit of life span, it necessarily has to compress the time they are sick towards the very end of their life. Along these lines we found the supercentenarians to be quite homogeneous and this is consistent with our finding in the genetic signatures paper that there is a strong genetic component to achieving these ages.

In the other, “Whole genome sequences of a male and female supercentenarian, ages greater than 114 years,” published in Frontiers in Genetics of Aging,

…the whole genome sequencing for two people over the age of 114 years, we found functional variants for a number of the genes that are part of the model that predicts exceptional longevity in the paper coming out this afternoon.

Unlike the paper we covered this morning, today’s new study does not cite the now-retracted paper that preceded it. We asked whether the authors had considered doing so:

…it frankly did not occur to me to do so (nor did any reviewer or editor suggest it). Afterall, it seems to me that it was Science’s intention to erase the paper we submitted to them from the scientific record as if it never existed so that we could publish it elsewhere… thus, what would be the purpose of citing the retraction? I do know that the current editor’s goal was to obtain as much of an unbiased review as possible, having the current paper reviewed for its current merit, independent of any history.

Fair enough, and that logic makes sense. There’s no official obligation to cite a paper you’ve retracted. At the same time, we’d argue that it was precisely because the previous paper had issues that reviewers and readers would want to know about it. Showing a particular thread of research as it progresses is, after all, consistent with the self-correcting nature of science.

Update, 11:15 p.m. Eastern, 1/18/12: The PLoS ONE editors wrote a blog post about the paper. It concludes:

While we recognize that aspects of this study will attract attention owing to the history and the strong claims made in the paper, the handling editor, Greg Gibson, made the decision that publication is warranted, balancing the extensive peer review and the spirit of PLoS ONE to allow important new results and approaches to be available to the scientific community so long as scientific standards have been met.  We trust that publication will facilitate full evaluation of the study.